2024-04-24 02:11
ftp://ftp.de.debian.org/debian/pool/main/c/clustalw/clustalw_2.1+lgpl.orig.tar.gz
cppcheck-options: --library=posix --library=gnu  --check-library --inconclusive --enable=style,information --inline-suppr --disable=missingInclude --suppress=unmatchedSuppression --template=daca2 --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning -D__GNUC__ --platform=unix64 -j2
platform: Linux-6.6.15-amd64-x86_64-with-glibc2.37
python: 3.11.8
client-version: 1.3.53
compiler: g++ (Debian 13.2.0-13) 13.2.0
cppcheck: head 2.14.0
head-info: 7dab204 (2024-04-23 22:20:29 +0200)
count: 1378 1378
elapsed-time: 10.5 10.3
head-timing-info:

old-timing-info:

head results:
clustalw-2.1/src/Help.h:31:12: style:inconclusive: Technically the member function 'Help::GetSection' can be const. [functionConst]
clustalw-2.1/src/Help.cpp:818:14: note: Technically the member function 'Help::GetSection' can be const.
clustalw-2.1/src/Help.h:31:12: note: Technically the member function 'Help::GetSection' can be const.
clustalw-2.1/src/Help.h:33:12: style:inconclusive: Technically the member function 'Help::GetSectionTitle' can be const. [functionConst]
clustalw-2.1/src/Help.cpp:833:14: note: Technically the member function 'Help::GetSectionTitle' can be const.
clustalw-2.1/src/Help.h:33:12: note: Technically the member function 'Help::GetSectionTitle' can be const.
clustalw-2.1/src/Help.cpp:818:32: performance: Function parameter 'marker' should be passed by const reference. [passedByValue]
clustalw-2.1/src/Help.cpp:833:37: performance: Function parameter 'marker' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/SquareMat.h:88:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/SymMatrix.h:49:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/SymMatrix.h:94:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/SymMatrix.h:154:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/SymMatrix.h:253:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:125:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:376:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:631:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:676:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:807:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:932:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:1012:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:1048:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:1688:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:1747:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Array2D.h:110:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:249:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:361:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:433:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:602:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:730:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:907:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:919:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:1485:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:1694:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:1784:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:1798:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:1829:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Alignment.cpp:2028:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/Clustal.cpp:877:5: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
clustalw-2.1/src/general/SymMatrix.h:31:9: warning: Member variable 'SymMatrix::sizeElements' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/general/SymMatrix.h:31:9: warning: Member variable 'SymMatrix::index' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/general/SymMatrix.h:31:9: warning: Member variable 'SymMatrix::sizeSubElements' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/general/SymMatrix.h:32:9: warning: Member variable 'SymMatrix::index' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/general/SymMatrix.h:32:9: warning: Member variable 'SymMatrix::sizeSubElements' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/alignment/Alignment.h:168:9: style: The class 'NameIterator' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
clustalw-2.1/src/Clustal.cpp:51:5: performance: Variable 'helpFileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/SquareMat.h:34:6: style:inconclusive: Technically the member function 'clustalw::SquareMat::GetAt' can be const. [functionConst]
clustalw-2.1/src/general/SquareMat.h:64:8: style:inconclusive: Technically the member function 'clustalw::SquareMat::getSize' can be const. [functionConst]
clustalw-2.1/src/general/SquareMat.h:82:9: style:inconclusive: Technically the member function 'clustalw::SquareMat::printArray' can be const. [functionConst]
clustalw-2.1/src/general/SymMatrix.h:100:21: performance:inconclusive: Technically the member function 'clustalw::SymMatrix::setAllArrayToVal' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/SymMatrix.h:108:20: style:inconclusive: Technically the member function 'clustalw::SymMatrix::getSize' can be const. [functionConst]
clustalw-2.1/src/general/SymMatrix.h:143:14: performance:inconclusive: Technically the member function 'clustalw::SymMatrix::printArray' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/SymMatrix.h:166:20: performance:inconclusive: Technically the member function 'clustalw::SymMatrix::getIndex' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.h:52:30: performance:inconclusive: Technically the member function 'clustalw::Utility::MIN' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.h:53:30: performance:inconclusive: Technically the member function 'clustalw::Utility::MAX' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/UserParameters.h:47:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getInteractive' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:49:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getGui' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:51:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getGapOpen' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:53:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getGapExtend' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:55:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getPWGapOpen' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:57:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getPWGapExtend' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:59:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getAAGapOpen' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:61:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getAAGapExtend' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:63:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getAAPWGapOpen' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:65:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getAAPWGapExtend' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:67:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getMaxAA' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:69:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getGapPos1' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:71:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getGapPos2' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:73:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getProfileNum' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:75:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getMenuFlag' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:77:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDNAFlag' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:79:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDistanceTree' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:81:16: style:inconclusive: Technically the member function 'clustalw::UserParameters::getSeqName' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:83:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDNAGapOpen' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:85:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDNAGapExtend' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:87:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getProteinGapOpen' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:89:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getProteinGapExtend' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:91:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getGapDist' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:93:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputOrder' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:96:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDivergenceCutoff' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:100:16: style:inconclusive: Technically the member function 'clustalw::UserParameters::getHydResidues' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:102:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getNoWeights' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:104:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getUseNegMatrix' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:107:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getNoHydPenalties' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:110:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getNoVarPenalties' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:112:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getNoPrefPenalties' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:115:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getUseEndGaps' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:118:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getEndGapPenalties' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:120:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getResetAlignmentsNew' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:122:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getResetAlignmentsAll' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:125:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputStructPenalties' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:127:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getStructPenalties1' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:129:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getStructPenalties2' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:131:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getUseSS1' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:134:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getUseSS2' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:137:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getHelixPenalty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:139:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getStrandPenalty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:141:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getLoopPenalty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:143:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getHelixEndMinus' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:145:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getHelixEndPlus' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:147:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getStrandEndMinus' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:149:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getStrandEndPlus' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:151:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getHelixEndPenalty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:153:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getStrandEndPenalty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:155:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getUseAmbiguities' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:157:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDNAPWGapOpenPenalty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:159:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDNAPWGapExtendPenalty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:161:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getProteinPWGapOpenPenalty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:163:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getProteinPWGapExtendPenalty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:166:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getQuickPairAlign' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:169:15: style:inconclusive: Technically the member function 'clustalw::UserParameters::getTransitionWeight' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:171:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDNAKtup' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:173:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDNAWindowGap' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:175:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDNASignif' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:177:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDNAWindow' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:179:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getAAKtup' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:181:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getAAWindowGap' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:183:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getAASignif' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:185:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getAAWindow' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:187:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getPercent' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:189:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getTossGaps' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:192:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getKimura' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:195:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getBootNumTrials' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:197:22: style:inconclusive: Technically the member function 'clustalw::UserParameters::getBootRanSeed' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:199:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDebug' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:201:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getExplicitDNAFlag' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:203:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getLowercase' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:206:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getClSeqNumbers' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:209:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getSeqRange' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:212:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputClustal' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:215:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputGCG' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:218:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputPhylip' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:221:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputNbrf' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:224:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputGde' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:227:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputNexus' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:230:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputFasta' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:233:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getShowAlign' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:236:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getSaveParameters' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:239:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputTreeClustal' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:242:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputTreePhylip' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:245:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputTreeDistances' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:248:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputTreeNexus' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:251:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutputPim' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:253:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getBootstrapFormat' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:256:16: style:inconclusive: Technically the member function 'clustalw::UserParameters::getProfile1Name' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:258:16: style:inconclusive: Technically the member function 'clustalw::UserParameters::getProfile2Name' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:260:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getEmpty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:262:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getProfile1Empty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:264:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getProfile2Empty' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:266:16: style:inconclusive: Technically the member function 'clustalw::UserParameters::getOutfileName' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:268:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getUseTreeFile' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:270:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getNewTreeFile' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:272:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getUseTree1File' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:274:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getUseTree2File' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:276:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getNewTree1File' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:278:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getNewTree2File' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:280:16: style:inconclusive: Technically the member function 'clustalw::UserParameters::getAminoAcidCodes' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:281:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getAminoAcidCode' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:283:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getKtup' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:285:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getWindow' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:287:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getWindowGap' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:289:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getSignif' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:291:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getRangeFrom' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:292:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getRangeTo' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:295:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getRangeFromToSet' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:311:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getNumIterations' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:313:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDoRemoveFirstIteration' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:317:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getClusterAlgorithm' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:320:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getDisplayInfo' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:321:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getHelpFlag' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:323:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getFullHelpFlag' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:326:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getMaxAllowedSeqLength' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.h:328:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::ResetGapsIsEnabled' can be const. [functionConst]
clustalw-2.1/src/alignment/Sequence.h:42:23: style:inconclusive: Technically the member function 'clustalw::Sequence::getIdentifier' can be const. [functionConst]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:67:13: style:inconclusive: Technically the member function 'clustalw::SubMatrix::getQTAAHistMatNum' can be const. [functionConst]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:68:13: style:inconclusive: Technically the member function 'clustalw::SubMatrix::getQTDNAHistMatNum' can be const. [functionConst]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:73:13: style:inconclusive: Technically the member function 'clustalw::SubMatrix::getQTsegmentDNAMatNum' can be const. [functionConst]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:75:13: style:inconclusive: Technically the member function 'clustalw::SubMatrix::getQTsegmentAAMatNum' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.h:93:28: style:inconclusive: Technically the member function 'clustalw::Alignment::getSequence' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.h:111:13: style:inconclusive: Technically the member function 'clustalw::Alignment::getMaxAlnLength' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.h:144:13: style:inconclusive: Technically the member function 'clustalw::Alignment::getProfile1NumSeqs' can be const. [functionConst]
clustalw-2.1/src/fileInput/FileParser.h:46:13: style:inconclusive: Technically the member function 'clustalw::FileParser::getParseExitCode' can be const. [functionConst]
clustalw-2.1/src/Clustal.h:37:14: performance:inconclusive: Technically the member function 'clustalw::Clustal::getHelp' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/Clustal.cpp:913:15: note: Technically the member function 'clustalw::Clustal::getHelp' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/Clustal.h:37:14: note: Technically the member function 'clustalw::Clustal::getHelp' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/Clustal.h:51:14: performance:inconclusive: Technically the member function 'clustalw::Clustal::QTremoveShortSegments' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/Clustal.cpp:1502:15: note: Technically the member function 'clustalw::Clustal::QTremoveShortSegments' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/Clustal.h:51:14: note: Technically the member function 'clustalw::Clustal::QTremoveShortSegments' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/Clustal.h:60:14: performance:inconclusive: Technically the member function 'clustalw::Clustal::initInterface' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/Clustal.cpp:1175:15: note: Technically the member function 'clustalw::Clustal::initInterface' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/Clustal.h:60:14: note: Technically the member function 'clustalw::Clustal::initInterface' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/Clustal.h:61:14: performance:inconclusive: Technically the member function 'clustalw::Clustal::calcGapPenaltyMask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/Clustal.cpp:1186:15: note: Technically the member function 'clustalw::Clustal::calcGapPenaltyMask' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/Clustal.h:61:14: note: Technically the member function 'clustalw::Clustal::calcGapPenaltyMask' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/ProfileBase.h:26:25: style:inconclusive: Technically the member function 'clustalw::ProfileBase::getProfilePtr' can be const. [functionConst]
clustalw-2.1/src/tree/AlignmentSteps.h:37:37: style:inconclusive: Technically the member function 'clustalw::AlignmentSteps::getSteps' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/LowScoreSegProfile.h:25:25: style:inconclusive: Technically the member function 'clustalw::LowScoreSegProfile::getProfilePtr' can be const. [functionConst]
clustalw-2.1/src/general/Stats.h:46:12: style:inconclusive: Technically the member function 'clustalw::Stats::getStatsFile' can be const. [functionConst]
clustalw-2.1/src/general/Stats.h:55:10: style:inconclusive: Technically the member function 'clustalw::Stats::isEnabled' can be const. [functionConst]
clustalw-2.1/src/general/ClustalWResources.h:39:17: style:inconclusive: Technically the member function 'clustalw::ClustalWResources::getDefaultPath' can be const. [functionConst]
clustalw-2.1/src/general/ClustalWResources.h:40:17: style:inconclusive: Technically the member function 'clustalw::ClustalWResources::getInstallPath' can be const. [functionConst]
clustalw-2.1/src/general/ClustalWResources.h:41:17: style:inconclusive: Technically the member function 'clustalw::ClustalWResources::getExecutablePath' can be const. [functionConst]
clustalw-2.1/src/general/ClustalWResources.h:42:17: style:inconclusive: Technically the member function 'clustalw::ClustalWResources::getHomePath' can be const. [functionConst]
clustalw-2.1/src/general/Array2D.h:33:8: style:inconclusive: Technically the member function 'Array2D < int >::getRowSize' can be const. [functionConst]
clustalw-2.1/src/general/Array2D.h:38:8: style:inconclusive: Technically the member function 'Array2D < int >::getColSize' can be const. [functionConst]
clustalw-2.1/src/general/Array2D.h:47:6: style:inconclusive: Technically the member function 'Array2D < int >::GetAt' can be const. [functionConst]
clustalw-2.1/src/general/Array2D.h:104:9: style:inconclusive: Technically the member function 'Array2D < int >::printArray' can be const. [functionConst]
clustalw-2.1/src/general/SymMatrix.h:44:17: warning: Class 'SymMatrix' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
clustalw-2.1/src/general/SymMatrix.h:44:17: warning: Class 'SymMatrix' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
clustalw-2.1/src/general/SquareMat.h:19:4: style: Class 'SquareMat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/general/SymMatrix.h:32:9: style: Class 'SymMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/general/UserParameters.h:33:9: style: Class 'UserParameters' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/fileInput/InFileStream.h:26:5: style: Class 'InFileStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/fileInput/ClustalFileParser.h:19:9: style: Class 'ClustalFileParser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/fileInput/PearsonFileParser.h:24:9: style: Class 'PearsonFileParser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/fileInput/PIRFileParser.h:19:9: style: Class 'PIRFileParser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/fileInput/GDEFileParser.h:19:9: style: Class 'GDEFileParser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/fileInput/MSFFileParser.h:19:9: style: Class 'MSFFileParser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/fileInput/RSFFileParser.h:19:9: style: Class 'RSFFileParser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/fileInput/EMBLFileParser.h:19:9: style: Class 'EMBLFileParser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/general/DebugLog.h:29:9: style: Class 'DebugLog' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/fileInput/ClustalFileParser.h:20:10: style: The destructor '~ClustalFileParser' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:35:18: note: Virtual destructor in base class
clustalw-2.1/src/fileInput/ClustalFileParser.h:20:10: note: Destructor in derived class
clustalw-2.1/src/fileInput/ClustalFileParser.h:21:26: style: The function 'getSeq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:37:26: note: Virtual function in base class
clustalw-2.1/src/fileInput/ClustalFileParser.h:21:26: note: Function in derived class
clustalw-2.1/src/fileInput/ClustalFileParser.h:22:34: style: The function 'getSeqRange' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:36:34: note: Virtual function in base class
clustalw-2.1/src/fileInput/ClustalFileParser.h:22:34: note: Function in derived class
clustalw-2.1/src/fileInput/ClustalFileParser.h:23:21: style: The function 'countSeqs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:38:21: note: Virtual function in base class
clustalw-2.1/src/fileInput/ClustalFileParser.h:23:21: note: Function in derived class
clustalw-2.1/src/fileInput/ClustalFileParser.h:24:22: style: The function 'getSecStructure' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:39:22: note: Virtual function in base class
clustalw-2.1/src/fileInput/ClustalFileParser.h:24:22: note: Function in derived class
clustalw-2.1/src/fileInput/PearsonFileParser.h:25:34: style: The function 'getSeqRange' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:36:34: note: Virtual function in base class
clustalw-2.1/src/fileInput/PearsonFileParser.h:25:34: note: Function in derived class
clustalw-2.1/src/fileInput/PearsonFileParser.h:26:26: style: The function 'getSeq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:37:26: note: Virtual function in base class
clustalw-2.1/src/fileInput/PearsonFileParser.h:26:26: note: Function in derived class
clustalw-2.1/src/fileInput/PearsonFileParser.h:27:21: style: The function 'countSeqs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:38:21: note: Virtual function in base class
clustalw-2.1/src/fileInput/PearsonFileParser.h:27:21: note: Function in derived class
clustalw-2.1/src/fileInput/PearsonFileParser.h:28:22: style: The function 'getSecStructure' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:39:22: note: Virtual function in base class
clustalw-2.1/src/fileInput/PearsonFileParser.h:28:22: note: Function in derived class
clustalw-2.1/src/fileInput/PIRFileParser.h:20:26: style: The function 'getSeq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:37:26: note: Virtual function in base class
clustalw-2.1/src/fileInput/PIRFileParser.h:20:26: note: Function in derived class
clustalw-2.1/src/fileInput/PIRFileParser.h:21:34: style: The function 'getSeqRange' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:36:34: note: Virtual function in base class
clustalw-2.1/src/fileInput/PIRFileParser.h:21:34: note: Function in derived class
clustalw-2.1/src/fileInput/PIRFileParser.h:22:21: style: The function 'countSeqs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:38:21: note: Virtual function in base class
clustalw-2.1/src/fileInput/PIRFileParser.h:22:21: note: Function in derived class
clustalw-2.1/src/fileInput/PIRFileParser.h:23:22: style: The function 'getSecStructure' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:39:22: note: Virtual function in base class
clustalw-2.1/src/fileInput/PIRFileParser.h:23:22: note: Function in derived class
clustalw-2.1/src/fileInput/GDEFileParser.h:20:10: style: The destructor '~GDEFileParser' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:35:18: note: Virtual destructor in base class
clustalw-2.1/src/fileInput/GDEFileParser.h:20:10: note: Destructor in derived class
clustalw-2.1/src/fileInput/GDEFileParser.h:21:34: style: The function 'getSeqRange' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:36:34: note: Virtual function in base class
clustalw-2.1/src/fileInput/GDEFileParser.h:21:34: note: Function in derived class
clustalw-2.1/src/fileInput/GDEFileParser.h:22:26: style: The function 'getSeq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:37:26: note: Virtual function in base class
clustalw-2.1/src/fileInput/GDEFileParser.h:22:26: note: Function in derived class
clustalw-2.1/src/fileInput/GDEFileParser.h:23:21: style: The function 'countSeqs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:38:21: note: Virtual function in base class
clustalw-2.1/src/fileInput/GDEFileParser.h:23:21: note: Function in derived class
clustalw-2.1/src/fileInput/GDEFileParser.h:24:22: style: The function 'getSecStructure' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:39:22: note: Virtual function in base class
clustalw-2.1/src/fileInput/GDEFileParser.h:24:22: note: Function in derived class
clustalw-2.1/src/fileInput/MSFFileParser.h:20:26: style: The function 'getSeq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:37:26: note: Virtual function in base class
clustalw-2.1/src/fileInput/MSFFileParser.h:20:26: note: Function in derived class
clustalw-2.1/src/fileInput/MSFFileParser.h:21:34: style: The function 'getSeqRange' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:36:34: note: Virtual function in base class
clustalw-2.1/src/fileInput/MSFFileParser.h:21:34: note: Function in derived class
clustalw-2.1/src/fileInput/MSFFileParser.h:22:21: style: The function 'countSeqs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:38:21: note: Virtual function in base class
clustalw-2.1/src/fileInput/MSFFileParser.h:22:21: note: Function in derived class
clustalw-2.1/src/fileInput/MSFFileParser.h:23:22: style: The function 'getSecStructure' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:39:22: note: Virtual function in base class
clustalw-2.1/src/fileInput/MSFFileParser.h:23:22: note: Function in derived class
clustalw-2.1/src/fileInput/RSFFileParser.h:20:34: style: The function 'getSeqRange' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:36:34: note: Virtual function in base class
clustalw-2.1/src/fileInput/RSFFileParser.h:20:34: note: Function in derived class
clustalw-2.1/src/fileInput/RSFFileParser.h:21:26: style: The function 'getSeq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:37:26: note: Virtual function in base class
clustalw-2.1/src/fileInput/RSFFileParser.h:21:26: note: Function in derived class
clustalw-2.1/src/fileInput/RSFFileParser.h:22:21: style: The function 'countSeqs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:38:21: note: Virtual function in base class
clustalw-2.1/src/fileInput/RSFFileParser.h:22:21: note: Function in derived class
clustalw-2.1/src/fileInput/RSFFileParser.h:23:22: style: The function 'getSecStructure' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:39:22: note: Virtual function in base class
clustalw-2.1/src/fileInput/RSFFileParser.h:23:22: note: Function in derived class
clustalw-2.1/src/fileInput/EMBLFileParser.h:20:10: style: The destructor '~EMBLFileParser' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:35:18: note: Virtual destructor in base class
clustalw-2.1/src/fileInput/EMBLFileParser.h:20:10: note: Destructor in derived class
clustalw-2.1/src/fileInput/EMBLFileParser.h:21:26: style: The function 'getSeq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:37:26: note: Virtual function in base class
clustalw-2.1/src/fileInput/EMBLFileParser.h:21:26: note: Function in derived class
clustalw-2.1/src/fileInput/EMBLFileParser.h:22:34: style: The function 'getSeqRange' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:36:34: note: Virtual function in base class
clustalw-2.1/src/fileInput/EMBLFileParser.h:22:34: note: Function in derived class
clustalw-2.1/src/fileInput/EMBLFileParser.h:23:21: style: The function 'countSeqs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:38:21: note: Virtual function in base class
clustalw-2.1/src/fileInput/EMBLFileParser.h:23:21: note: Function in derived class
clustalw-2.1/src/fileInput/EMBLFileParser.h:24:22: style: The function 'getSecStructure' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/fileInput/FileParser.h:39:22: note: Virtual function in base class
clustalw-2.1/src/fileInput/EMBLFileParser.h:24:22: note: Function in derived class
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:19:11: style: The destructor '~FullPairwiseAlign' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/pairwise/PairwiseAlignBase.h:18:12: note: Virtual destructor in base class
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:19:11: note: Destructor in derived class
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:21:22: style: The function 'pairwiseAlign' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/pairwise/PairwiseAlignBase.h:20:22: note: Virtual function in base class
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:21:22: note: Function in derived class
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:19:11: style: The destructor '~FastPairwiseAlign' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/pairwise/PairwiseAlignBase.h:18:12: note: Virtual destructor in base class
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:19:11: note: Destructor in derived class
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:21:22: style: The function 'pairwiseAlign' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/pairwise/PairwiseAlignBase.h:20:22: note: Virtual function in base class
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:21:22: note: Function in derived class
clustalw-2.1/src/general/UserParameters.h:81:16: performance: Function 'getSeqName()' should return member 'seqName' by const reference. [returnByReference]
clustalw-2.1/src/general/UserParameters.h:100:16: performance: Function 'getHydResidues()' should return member 'hydResidues' by const reference. [returnByReference]
clustalw-2.1/src/general/UserParameters.h:256:16: performance: Function 'getProfile1Name()' should return member 'profile1Name' by const reference. [returnByReference]
clustalw-2.1/src/general/UserParameters.h:258:16: performance: Function 'getProfile2Name()' should return member 'profile2Name' by const reference. [returnByReference]
clustalw-2.1/src/general/UserParameters.h:266:16: performance: Function 'getOutfileName()' should return member 'outfileName' by const reference. [returnByReference]
clustalw-2.1/src/general/UserParameters.h:280:16: performance: Function 'getAminoAcidCodes()' should return member 'aminoAcidCodes' by const reference. [returnByReference]
clustalw-2.1/src/general/Stats.h:46:12: performance: Function 'getStatsFile()' should return member 'logfilename' by const reference. [returnByReference]
clustalw-2.1/src/general/ClustalWResources.h:39:17: performance: Function 'getDefaultPath()' should return member 'defaultPath' by const reference. [returnByReference]
clustalw-2.1/src/general/ClustalWResources.h:40:17: performance: Function 'getInstallPath()' should return member 'installPath' by const reference. [returnByReference]
clustalw-2.1/src/general/ClustalWResources.h:41:17: performance: Function 'getExecutablePath()' should return member 'executablePath' by const reference. [returnByReference]
clustalw-2.1/src/general/ClustalWResources.h:42:17: performance: Function 'getHomePath()' should return member 'homePath' by const reference. [returnByReference]
clustalw-2.1/src/general/SymMatrix.h:51:17: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
clustalw-2.1/src/general/SymMatrix.h:96:17: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
clustalw-2.1/src/general/SymMatrix.h:254:21: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
clustalw-2.1/src/Clustal.cpp:787:17: error: Memory leak: phylipName [memleak]
clustalw-2.1/src/Clustal.cpp:878:1: error: Memory leak: phylipName [memleak]
clustalw-2.1/src/alignment/Alignment.h:88:13: style:inconclusive: Technically the member function 'clustalw::Alignment::countGaps' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:539:16: note: Technically the member function 'clustalw::Alignment::countGaps' can be const.
clustalw-2.1/src/alignment/Alignment.h:88:13: note: Technically the member function 'clustalw::Alignment::countGaps' can be const.
clustalw-2.1/src/alignment/Alignment.h:91:15: style:inconclusive: Technically the member function 'clustalw::Alignment::countid' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:692:18: note: Technically the member function 'clustalw::Alignment::countid' can be const.
clustalw-2.1/src/alignment/Alignment.h:91:15: note: Technically the member function 'clustalw::Alignment::countid' can be const.
clustalw-2.1/src/alignment/Alignment.h:107:16: style:inconclusive: Technically the member function 'clustalw::Alignment::getSecStructName1' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:971:19: note: Technically the member function 'clustalw::Alignment::getSecStructName1' can be const.
clustalw-2.1/src/alignment/Alignment.h:107:16: note: Technically the member function 'clustalw::Alignment::getSecStructName1' can be const.
clustalw-2.1/src/alignment/Alignment.h:108:16: style:inconclusive: Technically the member function 'clustalw::Alignment::getSecStructName2' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:976:19: note: Technically the member function 'clustalw::Alignment::getSecStructName2' can be const.
clustalw-2.1/src/alignment/Alignment.h:108:16: note: Technically the member function 'clustalw::Alignment::getSecStructName2' can be const.
clustalw-2.1/src/alignment/Alignment.h:110:13: style:inconclusive: Technically the member function 'clustalw::Alignment::getMaxNames' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:966:16: note: Technically the member function 'clustalw::Alignment::getMaxNames' can be const.
clustalw-2.1/src/alignment/Alignment.h:110:13: note: Technically the member function 'clustalw::Alignment::getMaxNames' can be const.
clustalw-2.1/src/alignment/Alignment.h:113:13: style:inconclusive: Technically the member function 'clustalw::Alignment::getLengthLongestSequence' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:932:16: note: Technically the member function 'clustalw::Alignment::getLengthLongestSequence' can be const.
clustalw-2.1/src/alignment/Alignment.h:113:13: note: Technically the member function 'clustalw::Alignment::getLengthLongestSequence' can be const.
clustalw-2.1/src/alignment/Alignment.h:114:13: style:inconclusive: Technically the member function 'clustalw::Alignment::getLengthLongestSequence' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:949:16: note: Technically the member function 'clustalw::Alignment::getLengthLongestSequence' can be const.
clustalw-2.1/src/alignment/Alignment.h:114:13: note: Technically the member function 'clustalw::Alignment::getLengthLongestSequence' can be const.
clustalw-2.1/src/alignment/Alignment.h:116:13: style:inconclusive: Technically the member function 'clustalw::Alignment::getSecStructMask1Element' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:1002:16: note: Technically the member function 'clustalw::Alignment::getSecStructMask1Element' can be const.
clustalw-2.1/src/alignment/Alignment.h:116:13: note: Technically the member function 'clustalw::Alignment::getSecStructMask1Element' can be const.
clustalw-2.1/src/alignment/Alignment.h:117:13: style:inconclusive: Technically the member function 'clustalw::Alignment::getSecStructMask2Element' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:1014:16: note: Technically the member function 'clustalw::Alignment::getSecStructMask2Element' can be const.
clustalw-2.1/src/alignment/Alignment.h:117:13: note: Technically the member function 'clustalw::Alignment::getSecStructMask2Element' can be const.
clustalw-2.1/src/alignment/Alignment.h:118:13: style:inconclusive: Technically the member function 'clustalw::Alignment::getGapPenaltyMask1Element' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:1026:16: note: Technically the member function 'clustalw::Alignment::getGapPenaltyMask1Element' can be const.
clustalw-2.1/src/alignment/Alignment.h:118:13: note: Technically the member function 'clustalw::Alignment::getGapPenaltyMask1Element' can be const.
clustalw-2.1/src/alignment/Alignment.h:119:13: style:inconclusive: Technically the member function 'clustalw::Alignment::getGapPenaltyMask2Element' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:1038:16: note: Technically the member function 'clustalw::Alignment::getGapPenaltyMask2Element' can be const.
clustalw-2.1/src/alignment/Alignment.h:119:13: note: Technically the member function 'clustalw::Alignment::getGapPenaltyMask2Element' can be const.
clustalw-2.1/src/alignment/Alignment.h:120:13: style:inconclusive: Technically the member function 'clustalw::Alignment::getOutputIndex' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:1090:16: note: Technically the member function 'clustalw::Alignment::getOutputIndex' can be const.
clustalw-2.1/src/alignment/Alignment.h:120:13: note: Technically the member function 'clustalw::Alignment::getOutputIndex' can be const.
clustalw-2.1/src/alignment/Alignment.h:123:16: style:inconclusive: Technically the member function 'clustalw::Alignment::getName' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:1050:19: note: Technically the member function 'clustalw::Alignment::getName' can be const.
clustalw-2.1/src/alignment/Alignment.h:123:16: note: Technically the member function 'clustalw::Alignment::getName' can be const.
clustalw-2.1/src/alignment/Alignment.h:124:16: style:inconclusive: Technically the member function 'clustalw::Alignment::getTitle' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:1078:19: note: Technically the member function 'clustalw::Alignment::getTitle' can be const.
clustalw-2.1/src/alignment/Alignment.h:124:16: note: Technically the member function 'clustalw::Alignment::getTitle' can be const.
clustalw-2.1/src/alignment/Alignment.h:135:13: style:inconclusive: Technically the member function 'clustalw::Alignment::searchForString' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:1356:16: note: Technically the member function 'clustalw::Alignment::searchForString' can be const.
clustalw-2.1/src/alignment/Alignment.h:135:13: note: Technically the member function 'clustalw::Alignment::searchForString' can be const.
clustalw-2.1/src/alignment/Alignment.h:152:23: style:inconclusive: Technically the member function 'clustalw::Alignment::getUniqueId' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:1066:26: note: Technically the member function 'clustalw::Alignment::getUniqueId' can be const.
clustalw-2.1/src/alignment/Alignment.h:152:23: note: Technically the member function 'clustalw::Alignment::getUniqueId' can be const.
clustalw-2.1/src/alignment/Alignment.h:155:14: performance:inconclusive: Technically the member function 'clustalw::Alignment::debugPrintSeqArray' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/alignment/Alignment.cpp:1766:17: note: Technically the member function 'clustalw::Alignment::debugPrintSeqArray' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/Alignment.h:155:14: note: Technically the member function 'clustalw::Alignment::debugPrintSeqArray' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/Alignment.h:184:14: performance:inconclusive: Technically the member function 'clustalw::Alignment::swap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/alignment/Alignment.cpp:1347:17: note: Technically the member function 'clustalw::Alignment::swap' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/Alignment.h:184:14: note: Technically the member function 'clustalw::Alignment::swap' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/Alignment.h:176:22: style:inconclusive: Technically the member function 'clustalw::Alignment::NameIterator::end' can be const. [functionConst]
clustalw-2.1/src/alignment/Alignment.cpp:383:31: note: Technically the member function 'clustalw::Alignment::NameIterator::end' can be const.
clustalw-2.1/src/alignment/Alignment.h:176:22: note: Technically the member function 'clustalw::Alignment::NameIterator::end' can be const.
clustalw-2.1/src/alignment/Alignment.h:107:16: performance: Function 'getSecStructName1()' should return member 'secStructName1' by const reference. [returnByReference]
clustalw-2.1/src/alignment/Alignment.h:108:16: performance: Function 'getSecStructName2()' should return member 'secStructName2' by const reference. [returnByReference]
clustalw-2.1/src/Clustal.cpp:462:16: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/Clustal.cpp:462:19: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/Clustal.cpp:462:22: style: The scope of the variable 'dscore' can be reduced. [variableScope]
clustalw-2.1/src/Clustal.cpp:1356:11: style: The scope of the variable 'sum' can be reduced. [variableScope]
clustalw-2.1/src/Clustal.cpp:1356:16: style: The scope of the variable 'prevSum' can be reduced. [variableScope]
clustalw-2.1/src/Clustal.cpp:1504:15: style: The scope of the variable 'start' can be reduced. [variableScope]
clustalw-2.1/src/Clustal.cpp:1559:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/Clustal.cpp:1559:12: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/Clustal.cpp:1561:11: style: The scope of the variable 'dscore' can be reduced. [variableScope]
clustalw-2.1/src/Clustal.cpp:1568:10: style: The scope of the variable 'treeName' can be reduced. [variableScope]
clustalw-2.1/src/Clustal.cpp:1152:40: style:inconclusive: Function 'phylogeneticTree' argument 1 names different: declaration 'phylip_name' definition 'phylipName'. [funcArgNamesDifferent]
clustalw-2.1/src/Clustal.h:45:39: note: Function 'phylogeneticTree' argument 1 names different: declaration 'phylip_name' definition 'phylipName'.
clustalw-2.1/src/Clustal.cpp:1152:40: note: Function 'phylogeneticTree' argument 1 names different: declaration 'phylip_name' definition 'phylipName'.
clustalw-2.1/src/Clustal.cpp:1152:60: style:inconclusive: Function 'phylogeneticTree' argument 2 names different: declaration 'clustal_name' definition 'clustalName'. [funcArgNamesDifferent]
clustalw-2.1/src/Clustal.h:45:60: note: Function 'phylogeneticTree' argument 2 names different: declaration 'clustal_name' definition 'clustalName'.
clustalw-2.1/src/Clustal.cpp:1152:60: note: Function 'phylogeneticTree' argument 2 names different: declaration 'clustal_name' definition 'clustalName'.
clustalw-2.1/src/Clustal.cpp:1152:81: style:inconclusive: Function 'phylogeneticTree' argument 3 names different: declaration 'dist_name' definition 'distName'. [funcArgNamesDifferent]
clustalw-2.1/src/Clustal.h:45:82: note: Function 'phylogeneticTree' argument 3 names different: declaration 'dist_name' definition 'distName'.
clustalw-2.1/src/Clustal.cpp:1152:81: note: Function 'phylogeneticTree' argument 3 names different: declaration 'dist_name' definition 'distName'.
clustalw-2.1/src/Clustal.cpp:1153:40: style:inconclusive: Function 'phylogeneticTree' argument 4 names different: declaration 'nexus_name' definition 'nexusName'. [funcArgNamesDifferent]
clustalw-2.1/src/Clustal.h:46:39: note: Function 'phylogeneticTree' argument 4 names different: declaration 'nexus_name' definition 'nexusName'.
clustalw-2.1/src/Clustal.cpp:1153:40: note: Function 'phylogeneticTree' argument 4 names different: declaration 'nexus_name' definition 'nexusName'.
clustalw-2.1/src/Clustal.cpp:1165:37: style:inconclusive: Function 'bootstrapTree' argument 1 names different: declaration 'phylip_name' definition 'phylipName'. [funcArgNamesDifferent]
clustalw-2.1/src/Clustal.h:47:36: note: Function 'bootstrapTree' argument 1 names different: declaration 'phylip_name' definition 'phylipName'.
clustalw-2.1/src/Clustal.cpp:1165:37: note: Function 'bootstrapTree' argument 1 names different: declaration 'phylip_name' definition 'phylipName'.
clustalw-2.1/src/Clustal.cpp:1165:57: style:inconclusive: Function 'bootstrapTree' argument 2 names different: declaration 'clustal_name' definition 'clustalName'. [funcArgNamesDifferent]
clustalw-2.1/src/Clustal.h:47:57: note: Function 'bootstrapTree' argument 2 names different: declaration 'clustal_name' definition 'clustalName'.
clustalw-2.1/src/Clustal.cpp:1165:57: note: Function 'bootstrapTree' argument 2 names different: declaration 'clustal_name' definition 'clustalName'.
clustalw-2.1/src/Clustal.cpp:1165:78: style:inconclusive: Function 'bootstrapTree' argument 3 names different: declaration 'nexus_name' definition 'nexusName'. [funcArgNamesDifferent]
clustalw-2.1/src/Clustal.h:47:79: note: Function 'bootstrapTree' argument 3 names different: declaration 'nexus_name' definition 'nexusName'.
clustalw-2.1/src/Clustal.cpp:1165:78: note: Function 'bootstrapTree' argument 3 names different: declaration 'nexus_name' definition 'nexusName'.
clustalw-2.1/src/general/Stats.h:40:30: performance: Function parameter 'f' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/ClustalWResources.h:45:44: performance: Function parameter 'file' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/ClustalWResources.h:46:54: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue]
clustalw-2.1/src/Clustal.cpp:913:30: performance: Function parameter 'helpPointer' should be passed by const reference. [passedByValue]
clustalw-2.1/src/Clustal.cpp:991:35: performance: Function parameter 'profile1Name' should be passed by const reference. [passedByValue]
clustalw-2.1/src/Clustal.cpp:1029:35: performance: Function parameter 'profile2Name' should be passed by const reference. [passedByValue]
clustalw-2.1/src/Clustal.cpp:1153:58: performance: Function parameter 'pimName' should be passed by const reference. [passedByValue]
clustalw-2.1/src/Clustal.cpp:1618:58: performance: Function parameter 'fileNames' should be passed by const reference. [passedByValue]
clustalw-2.1/src/Clustal.cpp:1623:57: performance: Function parameter 'fileNames' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/SymMatrix.h:47:30: style: Variable 'e' can be declared as reference to const [constVariableReference]
clustalw-2.1/src/general/SymMatrix.h:92:30: style: Variable 'e' can be declared as reference to const [constVariableReference]
clustalw-2.1/src/general/SymMatrix.h:251:34: style: Variable 'e' can be declared as reference to const [constVariableReference]
clustalw-2.1/src/Clustal.cpp:1152:40: style: Parameter 'phylipName' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/Clustal.cpp:1152:60: style: Parameter 'clustalName' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/Clustal.cpp:1152:81: style: Parameter 'distName' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/Clustal.cpp:1153:40: style: Parameter 'nexusName' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/Clustal.cpp:1165:37: style: Parameter 'phylipName' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/Clustal.cpp:1165:57: style: Parameter 'clustalName' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/Clustal.cpp:1165:78: style: Parameter 'nexusName' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/Clustal.cpp:1720:13: style: Variable 'ptrToMsg' can be declared as pointer to const [constVariablePointer]
clustalw-2.1/src/Clustal.cpp:1780:13: style: Variable 'ptrToMsg' can be declared as pointer to const [constVariablePointer]
clustalw-2.1/src/general/SymMatrix.h:143:33: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/general/SquareMat.h:26:18: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/Clustal.cpp:353:17: style: Variable '_length' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/Clustal.cpp:523:17: style: Variable '_length' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/Clustal.cpp:877:16: style: Variable 'phylipName' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/Clustal.cpp:1759:32: style: Variable 'phylipName' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/general/Array2D.h:28:18: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/Alignment.cpp:541:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:542:9: style: The scope of the variable 'q' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:542:12: style: The scope of the variable 'r' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:617:18: style: The scope of the variable 'sl' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:694:9: style: The scope of the variable 'c1' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:694:13: style: The scope of the variable 'c2' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:1131:11: style: The scope of the variable 'median' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:1131:19: style: The scope of the variable 'mean' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:1371:9: style: The scope of the variable 'code' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:1462:9: style: The scope of the variable 'numGaps' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:1536:9: style: The scope of the variable 'numGaps' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:1729:21: style: The scope of the variable 'vecToAdd' can be reduced. [variableScope]
clustalw-2.1/src/alignment/Alignment.cpp:539:30: style:inconclusive: Function 'countGaps' argument 1 names different: declaration 's1' definition 'seq1'. [funcArgNamesDifferent]
clustalw-2.1/src/alignment/Alignment.h:88:27: note: Function 'countGaps' argument 1 names different: declaration 's1' definition 'seq1'.
clustalw-2.1/src/alignment/Alignment.cpp:539:30: note: Function 'countGaps' argument 1 names different: declaration 's1' definition 'seq1'.
clustalw-2.1/src/alignment/Alignment.cpp:539:40: style:inconclusive: Function 'countGaps' argument 2 names different: declaration 's2' definition 'seq2'. [funcArgNamesDifferent]
clustalw-2.1/src/alignment/Alignment.h:88:35: note: Function 'countGaps' argument 2 names different: declaration 's2' definition 'seq2'.
clustalw-2.1/src/alignment/Alignment.cpp:539:40: note: Function 'countGaps' argument 2 names different: declaration 's2' definition 'seq2'.
clustalw-2.1/src/alignment/Alignment.cpp:539:50: style:inconclusive: Function 'countGaps' argument 3 names different: declaration 'l' definition 'len'. [funcArgNamesDifferent]
clustalw-2.1/src/alignment/Alignment.h:88:43: note: Function 'countGaps' argument 3 names different: declaration 'l' definition 'len'.
clustalw-2.1/src/alignment/Alignment.cpp:539:50: note: Function 'countGaps' argument 3 names different: declaration 'l' definition 'len'.
clustalw-2.1/src/alignment/Alignment.cpp:1308:21: style: Local variable 's' shadows outer variable [shadowVariable]
clustalw-2.1/src/alignment/Alignment.cpp:1125:15: note: Shadowed declaration
clustalw-2.1/src/alignment/Alignment.cpp:1308:21: note: Shadow variable
clustalw-2.1/src/alignment/Alignment.cpp:1425:9: style: Local variable 'gapPos1' shadows outer variable [shadowVariable]
clustalw-2.1/src/alignment/Alignment.h:207:13: note: Shadowed declaration
clustalw-2.1/src/alignment/Alignment.cpp:1425:9: note: Shadow variable
clustalw-2.1/src/alignment/Alignment.cpp:1426:9: style: Local variable 'gapPos2' shadows outer variable [shadowVariable]
clustalw-2.1/src/alignment/Alignment.h:207:22: note: Shadowed declaration
clustalw-2.1/src/alignment/Alignment.cpp:1426:9: note: Shadow variable
clustalw-2.1/src/alignment/Alignment.cpp:1467:9: style: Local variable 'gapPos1' shadows outer variable [shadowVariable]
clustalw-2.1/src/alignment/Alignment.h:207:13: note: Shadowed declaration
clustalw-2.1/src/alignment/Alignment.cpp:1467:9: note: Shadow variable
clustalw-2.1/src/alignment/Alignment.cpp:1468:9: style: Local variable 'gapPos2' shadows outer variable [shadowVariable]
clustalw-2.1/src/alignment/Alignment.h:207:22: note: Shadowed declaration
clustalw-2.1/src/alignment/Alignment.cpp:1468:9: note: Shadow variable
clustalw-2.1/src/alignment/Alignment.cpp:1533:9: style: Local variable 'gapPos1' shadows outer variable [shadowVariable]
clustalw-2.1/src/alignment/Alignment.h:207:13: note: Shadowed declaration
clustalw-2.1/src/alignment/Alignment.cpp:1533:9: note: Shadow variable
clustalw-2.1/src/alignment/Alignment.cpp:1534:9: style: Local variable 'gapPos2' shadows outer variable [shadowVariable]
clustalw-2.1/src/alignment/Alignment.h:207:22: note: Shadowed declaration
clustalw-2.1/src/alignment/Alignment.cpp:1534:9: note: Shadow variable
clustalw-2.1/src/alignment/Alignment.cpp:873:42: performance: Function parameter 'nameToAdd' should be passed by const reference. [passedByValue]
clustalw-2.1/src/alignment/Alignment.cpp:878:42: performance: Function parameter 'nameToAdd' should be passed by const reference. [passedByValue]
clustalw-2.1/src/alignment/Alignment.cpp:1356:75: performance: Function parameter 'search' should be passed by const reference. [passedByValue]
clustalw-2.1/src/alignment/Alignment.cpp:207:45: style: Parameter 'outputIndexToAdd' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/alignment/Alignment.cpp:853:49: style: Parameter 'secStructMaskToAdd' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/alignment/Alignment.cpp:858:49: style: Parameter 'secStructMaskToAdd' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/alignment/Alignment.cpp:863:50: style: Parameter 'gapPenaltyMaskToAdd' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/alignment/Alignment.cpp:868:50: style: Parameter 'gapPenaltyMaskToAdd' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/alignment/Alignment.cpp:1420:57: style: Parameter 'selected' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/alignment/Alignment.cpp:1460:64: style: Parameter 'selected' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/alignment/Alignment.cpp:1605:76: style: Parameter 'selected' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/alignment/Alignment.cpp:1251:20: style: Variable 'median' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/Alignment.cpp:1255:20: style: Variable 'median' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/Alignment.cpp:1259:20: style: Variable 'median' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/Alignment.cpp:1424:29: style: Variable 'lengthOfSelectedSeq' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/Alignment.cpp:1462:17: style: Variable 'numGaps' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/Alignment.cpp:1536:17: style: Variable 'numGaps' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/Alignment.cpp:1715:24: style: Variable 'posToAddTo' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/Alignment.cpp:1881:21: style: Unused variable: vecToAdd [unusedVariable]
clustalw-2.1/src/alignment/Alignment.cpp:240:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:362:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:400:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:402:77: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:838:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:841:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:1727:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:1741:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:1774:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:1780:33: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:1804:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:1811:33: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:1835:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:1842:33: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:1879:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/Alignment.cpp:1897:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:65:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:109:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:516:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:545:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:592:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:778:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_SCALE_FACTOR [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:962:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1098:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1305:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1556:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1743:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2215:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2310:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2386:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2452:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:18:17: warning: Member variable 'ObjectiveScore::matrix' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:18:17: warning: Member variable 'ObjectiveScore::weightScale' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/alignment/ObjectiveScore.h:33:15: style:inconclusive: Technically the member function 'clustalw::ObjectiveScore::scoreLetters' can be const. [functionConst]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:111:23: note: Technically the member function 'clustalw::ObjectiveScore::scoreLetters' can be const.
clustalw-2.1/src/alignment/ObjectiveScore.h:33:15: note: Technically the member function 'clustalw::ObjectiveScore::scoreLetters' can be const.
clustalw-2.1/src/alignment/ObjectiveScore.h:34:15: style:inconclusive: Technically the member function 'clustalw::ObjectiveScore::scoreGaps' can be const. [functionConst]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:170:23: note: Technically the member function 'clustalw::ObjectiveScore::scoreGaps' can be const.
clustalw-2.1/src/alignment/ObjectiveScore.h:34:15: note: Technically the member function 'clustalw::ObjectiveScore::scoreGaps' can be const.
clustalw-2.1/src/alignment/ObjectiveScore.h:35:14: performance:inconclusive: Technically the member function 'clustalw::ObjectiveScore::calcNormalisedSeqWeights' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:263:22: note: Technically the member function 'clustalw::ObjectiveScore::calcNormalisedSeqWeights' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/ObjectiveScore.h:35:14: note: Technically the member function 'clustalw::ObjectiveScore::calcNormalisedSeqWeights' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/ObjectiveScore.cpp:60:11: style: The scope of the variable 'w1' can be reduced. [variableScope]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:156:9: style: The scope of the variable 'scoreMatch' can be reduced. [variableScope]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:60:18: style: Variable 'w2' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:61:18: style: Variable 'weight' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:63:26: style: Variable 'pwScoreLetters' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:63:43: style: Variable 'pwScoreGaps' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:63:56: style: Variable 'pwScore' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/ObjectiveScore.cpp:156:20: style: Variable 'scoreMatch' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/alignment/Sequence.cpp:100:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Sequence.cpp:110:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Sequence.cpp:135:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/Sequence.h:47:14: style: Unused private function: 'Sequence::checkIntegrity' [unusedPrivateFunction]
clustalw-2.1/src/alignment/Sequence.cpp:54:5: performance: Variable '_encodedSequence' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/alignment/Sequence.cpp:55:5: performance: Variable '_name' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/alignment/Sequence.cpp:56:5: performance: Variable '_title' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/alignment/Sequence.h:38:14: style:inconclusive: Technically the member function 'clustalw::Sequence::isEmpty' can be const. [functionConst]
clustalw-2.1/src/alignment/Sequence.cpp:171:16: note: Technically the member function 'clustalw::Sequence::isEmpty' can be const.
clustalw-2.1/src/alignment/Sequence.h:38:14: note: Technically the member function 'clustalw::Sequence::isEmpty' can be const.
clustalw-2.1/src/alignment/Sequence.h:39:21: style:inconclusive: Technically the member function 'clustalw::Sequence::getName' can be const. [functionConst]
clustalw-2.1/src/alignment/Sequence.cpp:153:23: note: Technically the member function 'clustalw::Sequence::getName' can be const.
clustalw-2.1/src/alignment/Sequence.h:39:21: note: Technically the member function 'clustalw::Sequence::getName' can be const.
clustalw-2.1/src/alignment/Sequence.h:40:21: style:inconclusive: Technically the member function 'clustalw::Sequence::getTitle' can be const. [functionConst]
clustalw-2.1/src/alignment/Sequence.cpp:162:23: note: Technically the member function 'clustalw::Sequence::getTitle' can be const.
clustalw-2.1/src/alignment/Sequence.h:40:21: note: Technically the member function 'clustalw::Sequence::getTitle' can be const.
clustalw-2.1/src/alignment/Sequence.h:47:14: style:inconclusive: Technically the member function 'clustalw::Sequence::checkIntegrity' can be const. [functionConst]
clustalw-2.1/src/alignment/Sequence.cpp:130:16: note: Technically the member function 'clustalw::Sequence::checkIntegrity' can be const.
clustalw-2.1/src/alignment/Sequence.h:47:14: note: Technically the member function 'clustalw::Sequence::checkIntegrity' can be const.
clustalw-2.1/src/alignment/Sequence.h:48:14: performance:inconclusive: Technically the member function 'clustalw::Sequence::copyStringIntoVector' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/alignment/Sequence.cpp:89:16: note: Technically the member function 'clustalw::Sequence::copyStringIntoVector' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/Sequence.h:48:14: note: Technically the member function 'clustalw::Sequence::copyStringIntoVector' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/Sequence.h:39:21: performance: Function 'getName()' should return member '_name' by const reference. [returnByReference]
clustalw-2.1/src/alignment/Sequence.h:40:21: performance: Function 'getTitle()' should return member '_title' by const reference. [returnByReference]
clustalw-2.1/src/alignment/Sequence.cpp:24:41: style: Parameter 'name' can be declared as reference to const [constParameterReference]
clustalw-2.1/src/alignment/Sequence.cpp:24:55: style: Parameter 'title' can be declared as reference to const [constParameterReference]
clustalw-2.1/src/alignment/Sequence.cpp:33:51: style: Parameter 'name' can be declared as reference to const [constParameterReference]
clustalw-2.1/src/alignment/Sequence.cpp:33:70: style: Parameter 'title' can be declared as reference to const [constParameterReference]
clustalw-2.1/src/alignment/Sequence.cpp:51:68: style: Parameter 'name' can be declared as reference to const [constParameterReference]
clustalw-2.1/src/alignment/Sequence.cpp:51:87: style: Parameter 'title' can be declared as reference to const [constParameterReference]
clustalw-2.1/src/alignment/Sequence.cpp:51:38: style: Parameter 'encodedSequence' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/alignment/Sequence.cpp:219:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:79:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:228:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:272:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:26:5: performance: Variable 'fileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/fileInput/ClustalFileParser.h:32:14: performance:inconclusive: Technically the member function 'clustalw::ClustalFileParser::clustalBlankline' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:591:25: note: Technically the member function 'clustalw::ClustalFileParser::clustalBlankline' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/ClustalFileParser.h:32:14: note: Technically the member function 'clustalw::ClustalFileParser::clustalBlankline' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:99:17: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:318:17: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:374:17: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:516:17: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:540:17: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:67:12: style: The scope of the variable 'characterSeq' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:68:12: style: The scope of the variable 'name' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:69:12: style: The scope of the variable 'title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:71:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:71:12: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:72:19: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:73:12: style: The scope of the variable 'blank' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:180:10: style: The scope of the variable 'line' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:181:9: style: The scope of the variable '_nseqs' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:265:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:265:12: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:265:15: style: The scope of the variable 'len' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:265:20: style: The scope of the variable 'ix' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:265:24: style: The scope of the variable 'struct_index' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:266:10: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:37:71: style:inconclusive: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'. [funcArgNamesDifferent]
clustalw-2.1/src/fileInput/ClustalFileParser.h:22:64: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:37:71: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:24:45: performance: Function parameter 'filePath' should be passed by const reference. [passedByValue]
clustalw-2.1/src/fileInput/ClustalFileParser.cpp:591:48: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/alignment/AlignmentOutput.h:52:14: performance:inconclusive: Technically the member function 'clustalw::AlignmentOutput::printSecStructMask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2123:23: note: Technically the member function 'clustalw::AlignmentOutput::printSecStructMask' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:52:14: note: Technically the member function 'clustalw::AlignmentOutput::printSecStructMask' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:64:16: performance:inconclusive: Technically the member function 'clustalw::AlignmentOutput::nameonly' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2364:25: note: Technically the member function 'clustalw::AlignmentOutput::nameonly' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:64:16: note: Technically the member function 'clustalw::AlignmentOutput::nameonly' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:66:14: performance:inconclusive: Technically the member function 'clustalw::AlignmentOutput::findRangeValues' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2226:23: note: Technically the member function 'clustalw::AlignmentOutput::findRangeValues' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:66:14: note: Technically the member function 'clustalw::AlignmentOutput::findRangeValues' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:68:14: performance:inconclusive: Technically the member function 'clustalw::AlignmentOutput::openExplicitFile' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:512:23: note: Technically the member function 'clustalw::AlignmentOutput::openExplicitFile' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:68:14: note: Technically the member function 'clustalw::AlignmentOutput::openExplicitFile' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:69:16: performance:inconclusive: Technically the member function 'clustalw::AlignmentOutput::openOutputFile' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:535:25: note: Technically the member function 'clustalw::AlignmentOutput::openOutputFile' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:69:16: note: Technically the member function 'clustalw::AlignmentOutput::openOutputFile' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:71:13: performance:inconclusive: Technically the member function 'clustalw::AlignmentOutput::SeqGCGCheckSum' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2393:22: note: Technically the member function 'clustalw::AlignmentOutput::SeqGCGCheckSum' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:71:13: note: Technically the member function 'clustalw::AlignmentOutput::SeqGCGCheckSum' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/alignment/AlignmentOutput.h:72:14: style:inconclusive: Technically the member function 'clustalw::AlignmentOutput::showAlign' can be const. [functionConst]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2409:23: note: Technically the member function 'clustalw::AlignmentOutput::showAlign' can be const.
clustalw-2.1/src/alignment/AlignmentOutput.h:72:14: note: Technically the member function 'clustalw::AlignmentOutput::showAlign' can be const.
clustalw-2.1/src/alignment/AlignmentOutput.cpp:673:5: style: Exception should be caught by reference. [catchExceptionByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:868:5: style: Exception should be caught by reference. [catchExceptionByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1027:5: style: Exception should be caught by reference. [catchExceptionByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1156:5: style: Exception should be caught by reference. [catchExceptionByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1445:5: style: Exception should be caught by reference. [catchExceptionByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1560:5: style: Exception should be caught by reference. [catchExceptionByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2095:5: style: Exception should be caught by reference. [catchExceptionByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2102:5: style: Exception should be caught by reference. [catchExceptionByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2351:5: style: Exception should be caught by reference. [catchExceptionByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2261:14: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:636:17: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:640:17: note: Found duplicate branches for 'if' and 'else'.
clustalw-2.1/src/alignment/AlignmentOutput.cpp:636:17: note: Found duplicate branches for 'if' and 'else'.
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:85:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:232:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:261:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:448:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:484:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:582:10: style: The scope of the variable 'residue' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:583:9: style: The scope of the variable 'val' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:584:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:584:12: style: The scope of the variable 'ii' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:585:9: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:585:12: style: The scope of the variable 'slen' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:586:9: style: The scope of the variable 'lineLength' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:694:10: style: The scope of the variable 'residue' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:695:9: style: The scope of the variable 'val' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:696:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:696:12: style: The scope of the variable 'ii' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:696:16: style: The scope of the variable 'chunks' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:696:24: style: The scope of the variable 'block' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:697:9: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:697:12: style: The scope of the variable 'k' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:697:15: style: The scope of the variable 'pos1' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:697:21: style: The scope of the variable 'pos2' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:698:10: style: The scope of the variable 'grandChecksum' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:749:13: style: The scope of the variable '_index' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:771:15: style: The scope of the variable '_seqWeight' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:894:19: style: The scope of the variable 'pos1' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:894:25: style: The scope of the variable 'pos2' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:896:14: style: The scope of the variable 'warn' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1053:19: style: The scope of the variable 'pos1' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1053:25: style: The scope of the variable 'pos2' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1181:9: style: The scope of the variable 'length' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1189:16: style: The scope of the variable 'slen' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1462:10: style: The scope of the variable 'residue' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1463:9: style: The scope of the variable 'val' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1464:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1464:12: style: The scope of the variable 'ii' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1465:9: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1465:12: style: The scope of the variable 'slen' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1466:9: style: The scope of the variable 'lineLength' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1598:13: style: The scope of the variable 'pos' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1598:18: style: The scope of the variable 'ptr' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2126:12: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2227:37: style:inconclusive: Function 'findRangeValues' argument 4 names different: declaration 'lastRes' definition 'len'. [funcArgNamesDifferent]
clustalw-2.1/src/alignment/AlignmentOutput.h:66:85: note: Function 'findRangeValues' argument 4 names different: declaration 'lastRes' definition 'len'.
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2227:37: note: Function 'findRangeValues' argument 4 names different: declaration 'lastRes' definition 'len'.
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2393:51: style:inconclusive: Function 'SeqGCGCheckSum' argument 1 names different: declaration 'sequence' definition 'seq'. [funcArgNamesDifferent]
clustalw-2.1/src/alignment/AlignmentOutput.h:71:42: note: Function 'SeqGCGCheckSum' argument 1 names different: declaration 'sequence' definition 'seq'.
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2393:51: note: Function 'SeqGCGCheckSum' argument 1 names different: declaration 'sequence' definition 'seq'.
clustalw-2.1/src/alignment/AlignmentOutput.cpp:245:63: performance: Function parameter 'fileNames' should be passed by const reference. [passedByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:326:50: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:512:76: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:535:76: performance: Function parameter 'prompt' should be passed by const reference. [passedByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:536:47: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:536:60: performance: Function parameter 'fileExtension' should be passed by const reference. [passedByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:2364:41: performance: Function parameter 's' should be passed by const reference. [passedByValue]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1708:34: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1796:34: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
clustalw-2.1/src/alignment/AlignmentOutput.cpp:1927:31: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:26:5: performance: Variable 'fileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/fileInput/EMBLFileParser.h:32:14: performance:inconclusive: Technically the member function 'clustalw::EMBLFileParser::getSwissFeature' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:407:22: note: Technically the member function 'clustalw::EMBLFileParser::getSwissFeature' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/EMBLFileParser.h:32:14: note: Technically the member function 'clustalw::EMBLFileParser::getSwissFeature' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/EMBLFileParser.h:33:14: performance:inconclusive: Technically the member function 'clustalw::EMBLFileParser::getSwissMask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:457:22: note: Technically the member function 'clustalw::EMBLFileParser::getSwissMask' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/EMBLFileParser.h:33:14: note: Technically the member function 'clustalw::EMBLFileParser::getSwissMask' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:304:21: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:414:13: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:67:10: style: The scope of the variable '_sname' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:69:12: style: The scope of the variable 'characterSeq' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:70:12: style: The scope of the variable 'name' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:71:12: style: The scope of the variable 'title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:74:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:76:10: style: The scope of the variable 'gotSeq' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:77:19: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:78:9: style: The scope of the variable '_currentSeqNum' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:79:12: style: The scope of the variable 'blank' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:203:9: style: The scope of the variable 'numSeqs' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:249:10: style: The scope of the variable '_title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:252:10: style: The scope of the variable '_sname' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:253:10: style: The scope of the variable '_feature' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:254:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:409:10: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:409:13: style: The scope of the variable 's' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:409:16: style: The scope of the variable 'feature' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:410:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:459:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:42:68: style:inconclusive: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'. [funcArgNamesDifferent]
clustalw-2.1/src/fileInput/EMBLFileParser.h:22:64: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:42:68: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:24:39: performance: Function parameter 'filePath' should be passed by const reference. [passedByValue]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:407:44: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:457:41: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/fileInput/EMBLFileParser.cpp:251:10: style: Variable '_lin2' is not assigned a value. [unassignedVariable]
clustalw-2.1/src/fileInput/FileParser.cpp:66:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/FileParser.cpp:55:9: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
clustalw-2.1/src/fileInput/FileParser.cpp:24:13: warning: Member variable 'FileParser::chartab' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/fileInput/FileParser.cpp:24:13: warning: Member variable 'FileParser::_fileIn' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/fileInput/FileParser.h:43:14: performance:inconclusive: Technically the member function 'clustalw::FileParser::getDelimiter' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/fileInput/FileParser.cpp:60:18: note: Technically the member function 'clustalw::FileParser::getDelimiter' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/FileParser.h:43:14: note: Technically the member function 'clustalw::FileParser::getDelimiter' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/FileParser.h:49:14: performance:inconclusive: Technically the member function 'clustalw::FileParser::freeFileResources' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/fileInput/FileParser.cpp:49:18: note: Technically the member function 'clustalw::FileParser::freeFileResources' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/FileParser.h:49:14: note: Technically the member function 'clustalw::FileParser::freeFileResources' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/FileParser.cpp:38:19: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/FileParser.cpp:60:38: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
clustalw-2.1/src/fileInput/FileParser.cpp:55:17: style: Variable 'filePtr' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/fileInput/FileReader.cpp:76:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/FileReader.cpp:176:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/FileReader.cpp:355:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/FileReader.cpp:463:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:80:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:209:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:238:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/FileReader.h:45:14: performance:inconclusive: Technically the member function 'clustalw::FileReader::noEmptySequence' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/fileInput/FileReader.cpp:50:18: note: Technically the member function 'clustalw::FileReader::noEmptySequence' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/FileReader.h:45:14: note: Technically the member function 'clustalw::FileReader::noEmptySequence' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/FileReader.cpp:37:5: warning: Class 'FileReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
clustalw-2.1/src/fileInput/FileReader.cpp:37:5: warning: Class 'FileReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
clustalw-2.1/src/fileInput/FileReader.cpp:555:5: style: Exception should be caught by reference. [catchExceptionByValue]
clustalw-2.1/src/fileInput/FileReader.cpp:119:10: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
clustalw-2.1/src/fileInput/FileReader.cpp:127:5: note: Found duplicate branches for 'if' and 'else'.
clustalw-2.1/src/fileInput/FileReader.cpp:119:10: note: Found duplicate branches for 'if' and 'else'.
clustalw-2.1/src/fileInput/FileReader.cpp:50:51: style:inconclusive: Function 'noEmptySequence' argument 1 names different: declaration 'seqRangeVector' definition 'seqVector'. [funcArgNamesDifferent]
clustalw-2.1/src/fileInput/FileReader.h:45:47: note: Function 'noEmptySequence' argument 1 names different: declaration 'seqRangeVector' definition 'seqVector'.
clustalw-2.1/src/fileInput/FileReader.cpp:50:51: note: Function 'noEmptySequence' argument 1 names different: declaration 'seqRangeVector' definition 'seqVector'.
clustalw-2.1/src/fileInput/FileReader.cpp:53:57: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:27:5: performance: Variable 'fileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:64:10: style: The scope of the variable '_sname' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:65:12: style: The scope of the variable 'characterSeq' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:66:12: style: The scope of the variable 'name' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:67:12: style: The scope of the variable 'title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:68:12: style: The scope of the variable 'blank' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:72:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:73:19: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:74:9: style: The scope of the variable '_currentSeqNum' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:179:9: style: The scope of the variable '_nseqs' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:227:10: style: The scope of the variable '_title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:230:10: style: The scope of the variable '_sname' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:231:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:231:12: style: The scope of the variable 'len' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:232:19: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:40:67: style:inconclusive: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'. [funcArgNamesDifferent]
clustalw-2.1/src/fileInput/GDEFileParser.h:21:64: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/GDEFileParser.cpp:40:67: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/GDEFileParser.cpp:25:37: performance: Function parameter 'filePath' should be passed by const reference. [passedByValue]
clustalw-2.1/src/fileInput/GDEFileParser.cpp:229:10: style: Variable '_lin2' is not assigned a value. [unassignedVariable]
clustalw-2.1/src/fileInput/InFileStream.cpp:60:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/InFileStream.cpp:103:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:75:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:232:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:78:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:278:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:28:5: performance: Variable 'fileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:27:5: performance: Variable 'fileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:62:10: style: The scope of the variable '_sname' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:63:10: style: The scope of the variable '_title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:64:12: style: The scope of the variable 'characterSeq' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:65:12: style: The scope of the variable 'name' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:66:12: style: The scope of the variable 'title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:67:12: style: The scope of the variable 'blank' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:70:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:71:19: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:72:9: style: The scope of the variable '_currentSeqNum' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:173:29: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:175:9: style: The scope of the variable 'numSeqs' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:175:18: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:176:10: style: The scope of the variable 'seqOk' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PIRFileParser.cpp:35:67: style:inconclusive: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'. [funcArgNamesDifferent]
clustalw-2.1/src/fileInput/PIRFileParser.h:21:64: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/PIRFileParser.cpp:35:67: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/PIRFileParser.cpp:25:37: performance: Function parameter 'filePath' should be passed by const reference. [passedByValue]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:61:10: style: The scope of the variable '_sname' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:62:12: style: The scope of the variable 'characterSeq' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:63:12: style: The scope of the variable 'name' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:64:12: style: The scope of the variable 'title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:65:12: style: The scope of the variable 'blank' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:68:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:68:12: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:68:15: style: The scope of the variable 'k' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:69:19: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:186:10: style: The scope of the variable '_line' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:187:9: style: The scope of the variable '_numSeqs' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/MSFFileParser.cpp:34:67: style:inconclusive: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'. [funcArgNamesDifferent]
clustalw-2.1/src/fileInput/MSFFileParser.h:21:64: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/MSFFileParser.cpp:34:67: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/MSFFileParser.cpp:26:37: performance: Function parameter 'filePath' should be passed by const reference. [passedByValue]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:76:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:214:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:401:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:72:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:195:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:262:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:421:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:38:5: performance: Variable 'fileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:54:12: style: The scope of the variable 'characterSeq' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:56:12: style: The scope of the variable 'title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:58:12: style: The scope of the variable 'greater' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:60:22: style: The scope of the variable 'seqRangeVector' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:66:9: style: The scope of the variable 'nSeqsRead' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:67:19: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:68:10: style: The scope of the variable 'delim' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:69:9: style: The scope of the variable '_currentSeqNum' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:205:12: style: The scope of the variable 'characterSeq' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:207:12: style: The scope of the variable 'title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:208:12: style: The scope of the variable 'blank' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:209:12: style: The scope of the variable 'greater' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:216:19: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:217:10: style: The scope of the variable 'delim' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:218:9: style: The scope of the variable '_currentSeqNum' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:391:9: style: The scope of the variable '_nseqs' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:392:12: style: The scope of the variable 'line2' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:393:10: style: The scope of the variable 'delim' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:52:50: style:inconclusive: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'nSeqsToRead'. [funcArgNamesDifferent]
clustalw-2.1/src/fileInput/PearsonFileParser.h:25:64: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'nSeqsToRead'.
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:52:50: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'nSeqsToRead'.
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:79:16: style: Local variable 'line' shadows outer variable [shadowVariable]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:62:12: note: Shadowed declaration
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:79:16: note: Shadow variable
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:237:16: style: Local variable 'line' shadows outer variable [shadowVariable]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:212:12: note: Shadowed declaration
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:237:16: note: Shadow variable
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:36:45: performance: Function parameter 'filePath' should be passed by const reference. [passedByValue]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:104:22: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:260:16: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:145:21: warning: Either the condition 'iterator1!=line.end()' is redundant or there is possible dereference of an invalid iterator: iterator1. [derefInvalidIteratorRedundantCheck]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:118:33: note: Assuming that condition 'iterator1!=line.end()' is not redundant
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:145:21: note: Dereference of an invalid iterator
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:330:15: warning: Either the condition 'iterator1!=seqLine.end()' is redundant or there is possible dereference of an invalid iterator: iterator1. [derefInvalidIteratorRedundantCheck]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:314:27: note: Assuming that condition 'iterator1!=seqLine.end()' is not redundant
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:330:15: note: Dereference of an invalid iterator
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:57:12: style: Variable 'blank' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:62:12: style: Unused variable: line [unusedVariable]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:212:12: style: Unused variable: line [unusedVariable]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:143:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/fileInput/PearsonFileParser.cpp:328:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:27:5: performance: Variable 'fileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/fileInput/RSFFileParser.h:31:14: performance:inconclusive: Technically the member function 'clustalw::RSFFileParser::getRSFFeature' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:379:21: note: Technically the member function 'clustalw::RSFFileParser::getRSFFeature' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/RSFFileParser.h:31:14: note: Technically the member function 'clustalw::RSFFileParser::getRSFFeature' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/RSFFileParser.h:32:14: performance:inconclusive: Technically the member function 'clustalw::RSFFileParser::keyword' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:433:21: note: Technically the member function 'clustalw::RSFFileParser::keyword' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/RSFFileParser.h:32:14: note: Technically the member function 'clustalw::RSFFileParser::keyword' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/fileInput/RSFFileParser.cpp:387:13: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:57:10: style: The scope of the variable '_sname' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:58:12: style: The scope of the variable 'characterSeq' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:59:12: style: The scope of the variable 'name' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:60:12: style: The scope of the variable 'title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:61:12: style: The scope of the variable 'blank' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:64:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:65:19: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:66:9: style: The scope of the variable '_currentSeqNum' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:188:9: style: The scope of the variable 'numSeqs' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:249:10: style: The scope of the variable '_title' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:252:10: style: The scope of the variable '_sname' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:253:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:381:10: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:381:13: style: The scope of the variable 's' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:382:10: style: The scope of the variable 'str1' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:382:29: style: The scope of the variable 'str2' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:382:48: style: The scope of the variable 'feature' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:383:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:31:67: style:inconclusive: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'. [funcArgNamesDifferent]
clustalw-2.1/src/fileInput/RSFFileParser.h:20:64: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/RSFFileParser.cpp:31:67: note: Function 'getSeqRange' argument 2 names different: declaration 'num' definition 'no'.
clustalw-2.1/src/fileInput/RSFFileParser.cpp:25:37: performance: Function parameter 'filePath' should be passed by const reference. [passedByValue]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:379:41: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:433:35: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/fileInput/RSFFileParser.cpp:251:10: style: Variable '_lin2' is not assigned a value. [unassignedVariable]
clustalw-2.1/src/general/DebugLog.cpp:25:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/DebugLog.cpp:24:5: warning: Class 'DebugLog' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
clustalw-2.1/src/general/DebugLog.cpp:24:5: warning: Class 'DebugLog' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
clustalw-2.1/src/general/DebugLog.cpp:44:35: performance: Function parameter 'msg' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/InvalidCombination.cpp:25:18: style:inconclusive: Technically the member function 'clustalw::InvalidCombination::whatHappened' can be const. [functionConst]
clustalw-2.1/src/general/ClustalWResources.cpp:61:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DIRDELIM [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/ClustalWResources.cpp:105:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DIRDELIM [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/ClustalWResources.cpp:106:10: error: Array 'delim[1]' accessed at index 1, which is out of bounds. [arrayIndexOutOfBounds]
clustalw-2.1/src/general/ClustalWResources.cpp:33:5: performance: Variable 'defaultPath' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/ClustalWResources.cpp:36:5: performance: Variable 'executablePath' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/ClustalWResources.cpp:39:5: performance: Variable 'installPath' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/ClustalWResources.h:57:17: performance:inconclusive: Technically the member function 'clustalw::ClustalWResources::dirname' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/ClustalWResources.cpp:54:27: note: Technically the member function 'clustalw::ClustalWResources::dirname' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/ClustalWResources.h:57:17: note: Technically the member function 'clustalw::ClustalWResources::dirname' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/ClustalWResources.cpp:49:52: style:inconclusive: Function 'setPathToExecutable' argument 1 names different: declaration 'pathToFiles' definition 'path'. [funcArgNamesDifferent]
clustalw-2.1/src/general/ClustalWResources.h:36:42: note: Function 'setPathToExecutable' argument 1 names different: declaration 'pathToFiles' definition 'path'.
clustalw-2.1/src/general/ClustalWResources.cpp:49:52: note: Function 'setPathToExecutable' argument 1 names different: declaration 'pathToFiles' definition 'path'.
clustalw-2.1/src/general/ClustalWResources.cpp:49:52: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/ClustalWResources.cpp:54:42: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/ClustalWResources.cpp:84:49: performance: Function parameter 'file' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/ClustalWResources.cpp:126:59: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/OutputFile.cpp:45:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable trunc [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/OutputFile.cpp:78:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/OutputFile.h:20:14: style:inconclusive: Technically the member function 'clustalw::OutputFile::isOpen' can be const. [functionConst]
clustalw-2.1/src/general/OutputFile.cpp:58:18: note: Technically the member function 'clustalw::OutputFile::isOpen' can be const.
clustalw-2.1/src/general/OutputFile.h:20:14: note: Technically the member function 'clustalw::OutputFile::isOpen' can be const.
clustalw-2.1/src/general/OutputFile.h:24:21: performance:inconclusive: Technically the member function 'clustalw::OutputFile::getOutputFileName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/OutputFile.cpp:68:25: note: Technically the member function 'clustalw::OutputFile::getOutputFileName' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/OutputFile.h:24:21: note: Technically the member function 'clustalw::OutputFile::getOutputFileName' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/OutputFile.cpp:39:27: style: Condition 'fileName->empty()' is always true [knownConditionTrueFalse]
clustalw-2.1/src/general/OutputFile.cpp:35:24: note: Assuming that condition 'fileName->empty()' is not redundant
clustalw-2.1/src/general/OutputFile.cpp:39:27: note: Condition 'fileName->empty()' is always true
clustalw-2.1/src/general/OutputFile.cpp:32:68: performance: Function parameter 'msg' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/OutputFile.cpp:33:41: performance: Function parameter 'ext' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/OutputFile.cpp:33:64: performance: Function parameter 'fileType' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/OutputFile.cpp:68:61: performance: Function parameter 'prompt' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/OutputFile.cpp:68:81: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/OutputFile.cpp:69:61: performance: Function parameter 'fileExtension' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/Stats.cpp:239:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Stats.cpp:277:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Stats.cpp:339:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Stats.cpp:270:13: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
clustalw-2.1/src/general/Stats.cpp:281:80: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled]
clustalw-2.1/src/general/Stats.h:95:11: performance:inconclusive: Technically the member function 'clustalw::Stats::pairwiseIdentity' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Stats.cpp:86:8: note: Technically the member function 'clustalw::Stats::pairwiseIdentity' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Stats.h:95:11: note: Technically the member function 'clustalw::Stats::pairwiseIdentity' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Stats.cpp:272:12: style: Unused variable: hash [unusedVariable]
clustalw-2.1/src/general/Utility.cpp:116:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:157:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:181:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:219:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:330:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DIRDELIM [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:362:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:387:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:412:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:427:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:442:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:457:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:474:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.cpp:490:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/UserParameters.cpp:42:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLUSTALW_VERSION [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/UserParameters.cpp:314:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/general/Utility.h:27:15: performance:inconclusive: Technically the member function 'clustalw::Utility::rTrim' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:51:17: note: Technically the member function 'clustalw::Utility::rTrim' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:27:15: note: Technically the member function 'clustalw::Utility::rTrim' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:28:14: performance:inconclusive: Technically the member function 'clustalw::Utility::rTrim' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:36:15: note: Technically the member function 'clustalw::Utility::rTrim' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:28:14: note: Technically the member function 'clustalw::Utility::rTrim' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:29:15: performance:inconclusive: Technically the member function 'clustalw::Utility::blankToUnderscore' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:72:17: note: Technically the member function 'clustalw::Utility::blankToUnderscore' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:29:15: note: Technically the member function 'clustalw::Utility::blankToUnderscore' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:30:16: performance:inconclusive: Technically the member function 'clustalw::Utility::blankToUnderscore' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:93:17: note: Technically the member function 'clustalw::Utility::blankToUnderscore' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:30:16: note: Technically the member function 'clustalw::Utility::blankToUnderscore' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:31:14: performance:inconclusive: Technically the member function 'clustalw::Utility::getStr' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:155:15: note: Technically the member function 'clustalw::Utility::getStr' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:31:14: note: Technically the member function 'clustalw::Utility::getStr' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:33:16: performance:inconclusive: Technically the member function 'clustalw::Utility::getReal' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:173:17: note: Technically the member function 'clustalw::Utility::getReal' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:33:16: note: Technically the member function 'clustalw::Utility::getReal' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:34:13: performance:inconclusive: Technically the member function 'clustalw::Utility::getInt' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:212:14: note: Technically the member function 'clustalw::Utility::getInt' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:34:13: note: Technically the member function 'clustalw::Utility::getInt' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:35:23: performance:inconclusive: Technically the member function 'clustalw::Utility::getUniqueSequenceIdentifier' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:513:24: note: Technically the member function 'clustalw::Utility::getUniqueSequenceIdentifier' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:35:23: note: Technically the member function 'clustalw::Utility::getUniqueSequenceIdentifier' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:36:14: performance:inconclusive: Technically the member function 'clustalw::Utility::lineType' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:248:15: note: Technically the member function 'clustalw::Utility::lineType' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:36:14: note: Technically the member function 'clustalw::Utility::lineType' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:38:14: performance:inconclusive: Technically the member function 'clustalw::Utility::blankLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:265:15: note: Technically the member function 'clustalw::Utility::blankLine' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:38:14: note: Technically the member function 'clustalw::Utility::blankLine' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:39:14: performance:inconclusive: Technically the member function 'clustalw::Utility::blankLineNumericLabel' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:291:15: note: Technically the member function 'clustalw::Utility::blankLineNumericLabel' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:39:14: note: Technically the member function 'clustalw::Utility::blankLineNumericLabel' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:41:14: performance:inconclusive: Technically the member function 'clustalw::Utility::getPath' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:322:15: note: Technically the member function 'clustalw::Utility::getPath' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:41:14: note: Technically the member function 'clustalw::Utility::getPath' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:57:14: performance:inconclusive: Technically the member function 'clustalw::Utility::isNumeric' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:140:15: note: Technically the member function 'clustalw::Utility::isNumeric' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:57:14: note: Technically the member function 'clustalw::Utility::isNumeric' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:58:16: performance:inconclusive: Technically the member function 'clustalw::Utility::average' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:526:17: note: Technically the member function 'clustalw::Utility::average' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:58:16: note: Technically the member function 'clustalw::Utility::average' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:60:16: performance:inconclusive: Technically the member function 'clustalw::Utility::median' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/Utility.cpp:553:17: note: Technically the member function 'clustalw::Utility::median' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.h:60:16: note: Technically the member function 'clustalw::Utility::median' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/Utility.cpp:175:9: style: The scope of the variable 'status' can be reduced. [variableScope]
clustalw-2.1/src/general/Utility.cpp:214:14: style: The scope of the variable 'status' can be reduced. [variableScope]
clustalw-2.1/src/general/Utility.cpp:486:13: style: The scope of the variable 'ap' can be reduced. [variableScope]
clustalw-2.1/src/general/Utility.cpp:114:32: performance: Function parameter 'instr' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/Utility.cpp:155:29: performance: Function parameter 'instr' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/Utility.cpp:322:30: performance: Function parameter 'str' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/Utility.cpp:526:46: style: Parameter 'v' can be declared as reference to const [constParameterReference]
clustalw-2.1/src/general/Utility.cpp:248:30: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/general/Utility.cpp:265:31: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/general/Utility.cpp:291:43: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/general/Utility.cpp:347:17: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
clustalw-2.1/src/general/Utility.cpp:535:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
clustalw-2.1/src/general/Utility.cpp:549:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
clustalw-2.1/src/general/Utility.cpp:253:7: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/general/Utility.cpp:255:7: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/general/Utility.cpp:534:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/general/UserParameters.cpp:42:5: performance: Variable 'revisionLevel' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/UserParameters.cpp:46:5: performance: Variable 'seqName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/UserParameters.cpp:55:5: performance: Variable 'hydResidues' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/UserParameters.cpp:120:5: performance: Variable 'profile1Name' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/UserParameters.cpp:121:5: performance: Variable 'profile2Name' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/UserParameters.cpp:125:5: performance: Variable 'outfileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/UserParameters.cpp:133:5: performance: Variable 'aminoAcidCodes' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/general/UserParameters.h:35:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::createParameterOutput' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.cpp:295:22: note: Technically the member function 'clustalw::UserParameters::createParameterOutput' can be const.
clustalw-2.1/src/general/UserParameters.h:35:14: note: Technically the member function 'clustalw::UserParameters::createParameterOutput' can be const.
clustalw-2.1/src/general/UserParameters.h:36:13: performance:inconclusive: Technically the member function 'clustalw::UserParameters::resIndex' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/general/UserParameters.cpp:473:21: note: Technically the member function 'clustalw::UserParameters::resIndex' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/UserParameters.h:36:13: note: Technically the member function 'clustalw::UserParameters::resIndex' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/general/UserParameters.h:45:16: style:inconclusive: Technically the member function 'clustalw::UserParameters::getRevisionLevel' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.cpp:568:24: note: Technically the member function 'clustalw::UserParameters::getRevisionLevel' can be const.
clustalw-2.1/src/general/UserParameters.h:45:16: note: Technically the member function 'clustalw::UserParameters::getRevisionLevel' can be const.
clustalw-2.1/src/general/UserParameters.h:297:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getQTScorePlotScale' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.cpp:1292:21: note: Technically the member function 'clustalw::UserParameters::getQTScorePlotScale' can be const.
clustalw-2.1/src/general/UserParameters.h:297:13: note: Technically the member function 'clustalw::UserParameters::getQTScorePlotScale' can be const.
clustalw-2.1/src/general/UserParameters.h:299:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getQTResExceptionCutOff' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.cpp:1302:21: note: Technically the member function 'clustalw::UserParameters::getQTResExceptionCutOff' can be const.
clustalw-2.1/src/general/UserParameters.h:299:13: note: Technically the member function 'clustalw::UserParameters::getQTResExceptionCutOff' can be const.
clustalw-2.1/src/general/UserParameters.h:301:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::getQTseqWeightCalculated' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.cpp:1312:22: note: Technically the member function 'clustalw::UserParameters::getQTseqWeightCalculated' can be const.
clustalw-2.1/src/general/UserParameters.h:301:14: note: Technically the member function 'clustalw::UserParameters::getQTseqWeightCalculated' can be const.
clustalw-2.1/src/general/UserParameters.h:303:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getQTminLenLowScoreSegment' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.cpp:1322:21: note: Technically the member function 'clustalw::UserParameters::getQTminLenLowScoreSegment' can be const.
clustalw-2.1/src/general/UserParameters.h:303:13: note: Technically the member function 'clustalw::UserParameters::getQTminLenLowScoreSegment' can be const.
clustalw-2.1/src/general/UserParameters.h:305:13: style:inconclusive: Technically the member function 'clustalw::UserParameters::getQTlowScoreDNAMarkingScale' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.cpp:1332:21: note: Technically the member function 'clustalw::UserParameters::getQTlowScoreDNAMarkingScale' can be const.
clustalw-2.1/src/general/UserParameters.h:305:13: note: Technically the member function 'clustalw::UserParameters::getQTlowScoreDNAMarkingScale' can be const.
clustalw-2.1/src/general/UserParameters.h:314:14: style:inconclusive: Technically the member function 'clustalw::UserParameters::IterationIsEnabled' can be const. [functionConst]
clustalw-2.1/src/general/UserParameters.cpp:1342:22: note: Technically the member function 'clustalw::UserParameters::IterationIsEnabled' can be const.
clustalw-2.1/src/general/UserParameters.h:314:14: note: Technically the member function 'clustalw::UserParameters::IterationIsEnabled' can be const.
clustalw-2.1/src/general/UserParameters.h:45:16: performance: Function 'getRevisionLevel()' should return member 'revisionLevel' by const reference. [returnByReference]
clustalw-2.1/src/general/VectorOutOfRange.cpp:28:31: error: Returning pointer to local variable 'outputMessage' that will be invalid when returning. [returnDanglingLifetime]
clustalw-2.1/src/general/VectorOutOfRange.cpp:28:31: note: Pointer to container is created here.
clustalw-2.1/src/general/VectorOutOfRange.cpp:27:17: note: Variable created here.
clustalw-2.1/src/general/VectorOutOfRange.cpp:28:31: note: Returning pointer to local variable 'outputMessage' that will be invalid when returning.
clustalw-2.1/src/general/VectorOutOfRange.cpp:37:31: error: Returning pointer to local variable 'outputMessage' that will be invalid when returning. [returnDanglingLifetime]
clustalw-2.1/src/general/VectorOutOfRange.cpp:37:31: note: Pointer to container is created here.
clustalw-2.1/src/general/VectorOutOfRange.cpp:36:17: note: Variable created here.
clustalw-2.1/src/general/VectorOutOfRange.cpp:37:31: note: Returning pointer to local variable 'outputMessage' that will be invalid when returning.
clustalw-2.1/src/general/VectorOutOfRange.cpp:28:5: error: Dangerous usage of c_str(). The value returned by c_str() is invalid after this call. [stlcstr]
clustalw-2.1/src/general/VectorOutOfRange.cpp:37:5: error: Dangerous usage of c_str(). The value returned by c_str() is invalid after this call. [stlcstr]
clustalw-2.1/src/general/UserParameters.cpp:299:12: style: The scope of the variable 'message' can be reduced. [variableScope]
clustalw-2.1/src/general/UserParameters.cpp:706:10: style: The scope of the variable 'hydResidue' can be reduced. [variableScope]
clustalw-2.1/src/general/UserParameters.cpp:473:37: performance: Function parameter 't' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/UserParameters.cpp:573:46: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/UserParameters.cpp:651:40: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/UserParameters.cpp:703:44: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/UserParameters.cpp:1190:45: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/UserParameters.cpp:1195:45: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/UserParameters.cpp:1215:44: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/UserParameters.cpp:1255:47: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
clustalw-2.1/src/interface/InteractiveMenu.cpp:43:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:92:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:147:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:259:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:362:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:490:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:537:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:633:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:688:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:792:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:944:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:1045:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:1127:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:1192:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:1198:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:1240:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/CommandLineParser.cpp:131:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/CommandLineParser.cpp:358:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/CommandLineParser.cpp:1093:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/CommandLineParser.cpp:1407:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/CommandLineParser.cpp:2740:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/CommandLineParser.cpp:2777:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/CommandLineParser.cpp:2785:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable default_commandsep [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/CommandLineParser.cpp:2793:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable default_commandsep [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:29:18: warning: Member variable 'InteractiveMenu::choice' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/interface/InteractiveMenu.cpp:33:9: warning: Class 'InteractiveMenu' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
clustalw-2.1/src/interface/InteractiveMenu.cpp:33:9: warning: Class 'InteractiveMenu' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
clustalw-2.1/src/interface/InteractiveMenu.cpp:1111:12: style: The scope of the variable 'option' can be reduced. [variableScope]
clustalw-2.1/src/interface/InteractiveMenu.cpp:1113:9: style: The scope of the variable 'matn' can be reduced. [variableScope]
clustalw-2.1/src/interface/InteractiveMenu.cpp:1197:29: style: Variable 'currentAlgorithm' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/interface/InteractiveMenu.cpp:1239:29: style: Variable 'currentIteration' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/interface/CommandLineParser.h:65:14: style: Unused private function: 'CommandLineParser::printCmdLineData' [unusedPrivateFunction]
clustalw-2.1/src/interface/CommandLineParser.h:63:13: performance:inconclusive: Technically the member function 'clustalw::CommandLineParser::findMatch' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/interface/CommandLineParser.cpp:2696:24: note: Technically the member function 'clustalw::CommandLineParser::findMatch' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/interface/CommandLineParser.h:63:13: note: Technically the member function 'clustalw::CommandLineParser::findMatch' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/interface/CommandLineParser.h:64:21: performance:inconclusive: Technically the member function 'clustalw::CommandLineParser::getCmdLineDataStruct' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/interface/CommandLineParser.cpp:2731:32: note: Technically the member function 'clustalw::CommandLineParser::getCmdLineDataStruct' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/interface/CommandLineParser.h:64:21: note: Technically the member function 'clustalw::CommandLineParser::getCmdLineDataStruct' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/interface/CommandLineParser.h:65:14: performance:inconclusive: Technically the member function 'clustalw::CommandLineParser::printCmdLineData' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/interface/CommandLineParser.cpp:2738:25: note: Technically the member function 'clustalw::CommandLineParser::printCmdLineData' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/interface/CommandLineParser.h:65:14: note: Technically the member function 'clustalw::CommandLineParser::printCmdLineData' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/interface/CommandLineParser.h:66:16: performance:inconclusive: Technically the member function 'clustalw::CommandLineParser::ConvertStringToLower' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/interface/CommandLineParser.cpp:2763:27: note: Technically the member function 'clustalw::CommandLineParser::ConvertStringToLower' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/interface/CommandLineParser.h:66:16: note: Technically the member function 'clustalw::CommandLineParser::ConvertStringToLower' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/interface/CommandLineParser.h:67:14: performance:inconclusive: Technically the member function 'clustalw::CommandLineParser::exitWithErrorMsg' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/interface/CommandLineParser.cpp:2775:26: note: Technically the member function 'clustalw::CommandLineParser::exitWithErrorMsg' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/interface/CommandLineParser.h:67:14: note: Technically the member function 'clustalw::CommandLineParser::exitWithErrorMsg' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/interface/CommandLineParser.cpp:109:9: warning: Class 'CommandLineParser' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
clustalw-2.1/src/interface/CommandLineParser.cpp:109:9: warning: Class 'CommandLineParser' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
clustalw-2.1/src/interface/CommandLineParser.cpp:1231:40: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
clustalw-2.1/src/interface/CommandLineParser.cpp:1230:83: note: outer condition: (*paramArg)[i]!=""
clustalw-2.1/src/interface/CommandLineParser.cpp:1231:40: note: identical inner condition: (*paramArg)[i]!=""
clustalw-2.1/src/interface/CommandLineParser.cpp:2153:17: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/interface/CommandLineParser.cpp:347:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/interface/CommandLineParser.cpp:347:12: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/interface/CommandLineParser.cpp:569:16: style: The scope of the variable 'msg' can be reduced. [variableScope]
clustalw-2.1/src/interface/CommandLineParser.cpp:1078:9: style: The scope of the variable 'len' can be reduced. [variableScope]
clustalw-2.1/src/interface/CommandLineParser.cpp:2699:9: style: The scope of the variable 'count' can be reduced. [variableScope]
clustalw-2.1/src/interface/CommandLineParser.cpp:620:44: style: Checking if unsigned expression '(*paramArg)[setInfile].length()' is less than zero. [unsignedLessThanZero]
clustalw-2.1/src/interface/CommandLineParser.cpp:665:46: style: Checking if unsigned expression '(*paramArg)[setProfile1].length()' is less than zero. [unsignedLessThanZero]
clustalw-2.1/src/interface/CommandLineParser.cpp:675:46: style: Checking if unsigned expression '(*paramArg)[setProfile2].length()' is less than zero. [unsignedLessThanZero]
clustalw-2.1/src/interface/CommandLineParser.cpp:2696:41: performance: Function parameter 'probe' should be passed by const reference. [passedByValue]
clustalw-2.1/src/interface/CommandLineParser.cpp:2775:50: performance: Function parameter 'msg' should be passed by const reference. [passedByValue]
clustalw-2.1/src/interface/CommandLineParser.cpp:2781:55: performance: Function parameter 'option' should be passed by const reference. [passedByValue]
clustalw-2.1/src/interface/CommandLineParser.cpp:2781:70: performance: Function parameter 'expectedType' should be passed by const reference. [passedByValue]
clustalw-2.1/src/interface/CommandLineParser.cpp:2790:59: performance: Function parameter 'option' should be passed by const reference. [passedByValue]
clustalw-2.1/src/interface/CommandLineParser.cpp:2696:61: style: Parameter 'list' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/multipleAlign/Iteration.cpp:100:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/Iteration.cpp:193:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/Iteration.h:22:14: style: Unused private function: 'Iteration::printSeqArray' [unusedPrivateFunction]
clustalw-2.1/src/multipleAlign/Iteration.h:20:14: performance:inconclusive: Technically the member function 'clustalw::Iteration::removeFirstIterate' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/multipleAlign/Iteration.cpp:142:17: note: Technically the member function 'clustalw::Iteration::removeFirstIterate' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/Iteration.h:20:14: note: Technically the member function 'clustalw::Iteration::removeFirstIterate' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/Iteration.h:22:14: performance:inconclusive: Technically the member function 'clustalw::Iteration::printSeqArray' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/multipleAlign/Iteration.cpp:98:17: note: Technically the member function 'clustalw::Iteration::printSeqArray' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/Iteration.h:22:14: note: Technically the member function 'clustalw::Iteration::printSeqArray' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/Iteration.cpp:72:23: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
clustalw-2.1/src/multipleAlign/Iteration.cpp:63:27: note: outer condition: j<numSeqsProf1+numSeqsProf2
clustalw-2.1/src/multipleAlign/Iteration.cpp:72:23: note: identical inner condition: j<numSeqsProf1+numSeqsProf2
clustalw-2.1/src/multipleAlign/Iteration.cpp:214:26: style: Condition 'nSeqs-1>=2' is always true [knownConditionTrueFalse]
clustalw-2.1/src/multipleAlign/Iteration.cpp:154:14: note: Assuming that condition 'nSeqs<=2' is not redundant
clustalw-2.1/src/multipleAlign/Iteration.cpp:214:26: note: Condition 'nSeqs-1>=2' is always true
clustalw-2.1/src/multipleAlign/Iteration.cpp:170:9: style: The scope of the variable 'count' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/Iteration.cpp:171:10: style: The scope of the variable 'scoreImproved' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/Iteration.cpp:313:13: style: The scope of the variable 'seqId' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/Iteration.cpp:314:28: style: The scope of the variable 'improvedSeq' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/Iteration.cpp:216:26: style: Local variable 'i' shadows outer variable [shadowVariable]
clustalw-2.1/src/multipleAlign/Iteration.cpp:194:17: note: Shadowed declaration
clustalw-2.1/src/multipleAlign/Iteration.cpp:216:26: note: Shadow variable
clustalw-2.1/src/multipleAlign/Iteration.cpp:59:24: style: Variable 'aaCodes' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/Iteration.cpp:167:18: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/Iteration.cpp:171:24: style: Variable 'scoreImproved' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/Iteration.cpp:277:19: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/Iteration.cpp:107:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/multipleAlign/Iteration.cpp:113:33: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/multipleAlign/MSA.cpp:117:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/MSA.cpp:504:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_SCALE_FACTOR [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/MSA.cpp:566:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_SCALE_FACTOR [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/MSA.cpp:694:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_SCALE_FACTOR [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:347:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:533:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:851:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:1033:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/MSA.h:24:13: performance:inconclusive: Technically the member function 'clustalw::MSA::multiSeqAlign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/multipleAlign/MSA.cpp:32:10: note: Technically the member function 'clustalw::MSA::multiSeqAlign' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/MSA.h:24:13: note: Technically the member function 'clustalw::MSA::multiSeqAlign' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/MSA.h:26:13: performance:inconclusive: Technically the member function 'clustalw::MSA::seqsAlignToProfile' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/multipleAlign/MSA.cpp:358:10: note: Technically the member function 'clustalw::MSA::seqsAlignToProfile' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/MSA.h:26:13: note: Technically the member function 'clustalw::MSA::seqsAlignToProfile' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/MSA.h:28:13: performance:inconclusive: Technically the member function 'clustalw::MSA::calcPairwiseForProfileAlign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/multipleAlign/MSA.cpp:547:10: note: Technically the member function 'clustalw::MSA::calcPairwiseForProfileAlign' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/MSA.h:28:13: note: Technically the member function 'clustalw::MSA::calcPairwiseForProfileAlign' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/MSA.h:29:13: performance:inconclusive: Technically the member function 'clustalw::MSA::doProfileAlign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/multipleAlign/MSA.cpp:626:10: note: Technically the member function 'clustalw::MSA::doProfileAlign' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/MSA.h:29:13: note: Technically the member function 'clustalw::MSA::doProfileAlign' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:19:12: style: The destructor '~MyersMillerProfileAlign' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/multipleAlign/ProfileAlignAlgorithm.h:17:12: note: Virtual destructor in base class
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:19:12: note: Destructor in derived class
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:23:21: style: The function 'profileAlign' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/multipleAlign/ProfileAlignAlgorithm.h:20:17: note: Virtual function in base class
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:23:21: note: Function in derived class
clustalw-2.1/src/multipleAlign/MSA.cpp:741:5: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
clustalw-2.1/src/multipleAlign/MSA.cpp:47:23: style: The scope of the variable 'set' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/MSA.cpp:367:9: style: The scope of the variable 'max' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/MSA.cpp:369:9: style: The scope of the variable 'sum' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/MSA.cpp:369:18: style: The scope of the variable 'entries' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/MSA.cpp:370:9: style: The scope of the variable 'score' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/MSA.cpp:359:35: performance: Function parameter 'phylipName' should be passed by const reference. [passedByValue]
clustalw-2.1/src/multipleAlign/MSA.cpp:45:13: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:45:22: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:47:18: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:47:27: style: Variable 'set' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:47:37: style: Variable 'iseq' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:48:17: style: Variable 'entries' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:49:15: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:322:15: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:340:26: style: Variable 'alignmentScore' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:367:13: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:368:18: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:369:13: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:369:26: style: Variable 'entries' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MSA.cpp:370:15: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::profileWithSub' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::profileStandard' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::gapcoef1' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::gapcoef2' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::lencoef1' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::lencoef2' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::printPtr' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::lastPrint' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::matrix' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::switchProfiles' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::profile1' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::profile2' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'MyersMillerProfileAlign::alignmentLength' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'ProfileAlignAlgorithm::prfLength1' is not initialized in the constructor. Maybe it should be initialized directly in the class ProfileAlignAlgorithm? [uninitDerivedMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'ProfileAlignAlgorithm::prfLength2' is not initialized in the constructor. Maybe it should be initialized directly in the class ProfileAlignAlgorithm? [uninitDerivedMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'ProfileAlignAlgorithm::nseqs1' is not initialized in the constructor. Maybe it should be initialized directly in the class ProfileAlignAlgorithm? [uninitDerivedMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:21:26: warning: Member variable 'ProfileAlignAlgorithm::nseqs2' is not initialized in the constructor. Maybe it should be initialized directly in the class ProfileAlignAlgorithm? [uninitDerivedMemberVar]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:30:14: style:inconclusive: Technically the member function 'clustalw::MyersMillerProfileAlign::addGGapsMask' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:942:31: note: Technically the member function 'clustalw::MyersMillerProfileAlign::addGGapsMask' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:30:14: note: Technically the member function 'clustalw::MyersMillerProfileAlign::addGGapsMask' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:31:13: style:inconclusive: Technically the member function 'clustalw::MyersMillerProfileAlign::prfScore' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:1000:37: note: Technically the member function 'clustalw::MyersMillerProfileAlign::prfScore' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:31:13: note: Technically the member function 'clustalw::MyersMillerProfileAlign::prfScore' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:37:13: style:inconclusive: Technically the member function 'clustalw::MyersMillerProfileAlign::openPenalty1' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:1124:37: note: Technically the member function 'clustalw::MyersMillerProfileAlign::openPenalty1' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:37:13: note: Technically the member function 'clustalw::MyersMillerProfileAlign::openPenalty1' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:38:13: style:inconclusive: Technically the member function 'clustalw::MyersMillerProfileAlign::extPenalty1' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:1143:37: note: Technically the member function 'clustalw::MyersMillerProfileAlign::extPenalty1' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:38:13: note: Technically the member function 'clustalw::MyersMillerProfileAlign::extPenalty1' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:39:13: style:inconclusive: Technically the member function 'clustalw::MyersMillerProfileAlign::gapPenalty1' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:1164:30: note: Technically the member function 'clustalw::MyersMillerProfileAlign::gapPenalty1' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:39:13: note: Technically the member function 'clustalw::MyersMillerProfileAlign::gapPenalty1' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:40:13: style:inconclusive: Technically the member function 'clustalw::MyersMillerProfileAlign::openPenalty2' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:1196:37: note: Technically the member function 'clustalw::MyersMillerProfileAlign::openPenalty2' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:40:13: note: Technically the member function 'clustalw::MyersMillerProfileAlign::openPenalty2' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:41:13: style:inconclusive: Technically the member function 'clustalw::MyersMillerProfileAlign::extPenalty2' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:1216:37: note: Technically the member function 'clustalw::MyersMillerProfileAlign::extPenalty2' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:41:13: note: Technically the member function 'clustalw::MyersMillerProfileAlign::extPenalty2' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:42:13: style:inconclusive: Technically the member function 'clustalw::MyersMillerProfileAlign::gapPenalty2' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:1237:30: note: Technically the member function 'clustalw::MyersMillerProfileAlign::gapPenalty2' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:42:13: note: Technically the member function 'clustalw::MyersMillerProfileAlign::gapPenalty2' can be const.
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:524:16: style: The scope of the variable 't' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:524:19: style: The scope of the variable 'tl' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:524:23: style: The scope of the variable 'g' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:524:26: style: The scope of the variable 'h' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:50:9: style: Local variable 'matrix' shadows outer variable [shadowVariable]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h:60:13: note: Shadowed declaration
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:50:9: note: Shadow variable
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:53:13: style: Local variable 'i' shadows outer variable [shadowVariable]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:40:9: note: Shadowed declaration
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:53:13: note: Shadow variable
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:55:17: style: Local variable 'j' shadows outer variable [shadowVariable]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:40:16: note: Shadowed declaration
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:55:17: note: Shadow variable
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:942:86: style: Parameter 'path1' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:943:57: style: Parameter 'path2' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:43:13: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:43:41: style: Variable 'is' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:46:11: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:48:19: style: Variable 'logmin' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp:48:34: style: Variable 'logdiff' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:282:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/multipleAlign/ProfileStandard.cpp:45:15: style: The scope of the variable 'sum2' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/ProfileStandard.cpp:41:53: style:inconclusive: Function 'calcStandardProfile' argument 1 names different: declaration 'alignment' definition 'seqArray'. [funcArgNamesDifferent]
clustalw-2.1/src/multipleAlign/ProfileStandard.h:21:44: note: Function 'calcStandardProfile' argument 1 names different: declaration 'alignment' definition 'seqArray'.
clustalw-2.1/src/multipleAlign/ProfileStandard.cpp:41:53: note: Function 'calcStandardProfile' argument 1 names different: declaration 'alignment' definition 'seqArray'.
clustalw-2.1/src/multipleAlign/ProfileStandard.cpp:41:53: style: Parameter 'seqArray' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:433:28: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:20:14: warning: Member variable 'ProfileBase::nVarPen' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:20:14: warning: Member variable 'ProfileBase::nHydPen' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:20:14: warning: Member variable 'ProfileBase::nPrefPen' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:20:14: warning: Member variable 'ProfileBase::gdist' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/multipleAlign/ProfileBase.h:37:14: style:inconclusive: Technically the member function 'clustalw::ProfileBase::calcVPenalties' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:310:19: note: Technically the member function 'clustalw::ProfileBase::calcVPenalties' can be const.
clustalw-2.1/src/multipleAlign/ProfileBase.h:37:14: note: Technically the member function 'clustalw::ProfileBase::calcVPenalties' can be const.
clustalw-2.1/src/multipleAlign/ProfileBase.h:38:14: style:inconclusive: Technically the member function 'clustalw::ProfileBase::calcResidueSpecificPen' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:355:19: note: Technically the member function 'clustalw::ProfileBase::calcResidueSpecificPen' can be const.
clustalw-2.1/src/multipleAlign/ProfileBase.h:38:14: note: Technically the member function 'clustalw::ProfileBase::calcResidueSpecificPen' can be const.
clustalw-2.1/src/multipleAlign/ProfileBase.h:40:13: style:inconclusive: Technically the member function 'clustalw::ProfileBase::localPenalty' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:466:18: note: Technically the member function 'clustalw::ProfileBase::localPenalty' can be const.
clustalw-2.1/src/multipleAlign/ProfileBase.h:40:13: note: Technically the member function 'clustalw::ProfileBase::localPenalty' can be const.
clustalw-2.1/src/multipleAlign/ProfileBase.h:42:15: style:inconclusive: Technically the member function 'clustalw::ProfileBase::percentId' can be const. [functionConst]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:511:20: note: Technically the member function 'clustalw::ProfileBase::percentId' can be const.
clustalw-2.1/src/multipleAlign/ProfileBase.h:42:15: note: Technically the member function 'clustalw::ProfileBase::percentId' can be const.
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:57:9: style: The scope of the variable 'is' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:57:13: style: The scope of the variable 'ie' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:313:15: style: The scope of the variable 't' can be reduced. [variableScope]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:467:44: style: Parameter 'hydWeight' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:511:43: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/multipleAlign/ProfileBase.cpp:511:60: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/multipleAlign/ProfileWithSub.cpp:42:51: style: Parameter 'seqArray' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:27:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:49:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:15:20: warning: Member variable 'FastPairwiseAlign::next' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:15:20: warning: Member variable 'FastPairwiseAlign::currFrag' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:15:20: warning: Member variable 'FastPairwiseAlign::maxSoFar' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:15:20: warning: Member variable 'FastPairwiseAlign::vatend' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:28:14: performance:inconclusive: Technically the member function 'clustalw::FastPairwiseAlign::makePPtrs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:404:25: note: Technically the member function 'clustalw::FastPairwiseAlign::makePPtrs' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:28:14: note: Technically the member function 'clustalw::FastPairwiseAlign::makePPtrs' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:30:14: performance:inconclusive: Technically the member function 'clustalw::FastPairwiseAlign::makeNPtrs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:464:25: note: Technically the member function 'clustalw::FastPairwiseAlign::makeNPtrs' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:30:14: note: Technically the member function 'clustalw::FastPairwiseAlign::makeNPtrs' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:33:13: performance:inconclusive: Technically the member function 'clustalw::FastPairwiseAlign::fragRelPos' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:561:31: note: Technically the member function 'clustalw::FastPairwiseAlign::fragRelPos' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:33:13: note: Technically the member function 'clustalw::FastPairwiseAlign::fragRelPos' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:34:14: performance:inconclusive: Technically the member function 'clustalw::FastPairwiseAlign::desQuickSort' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:584:25: note: Technically the member function 'clustalw::FastPairwiseAlign::desQuickSort' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/pairwise/FastPairwiseAlign.h:34:14: note: Technically the member function 'clustalw::FastPairwiseAlign::desQuickSort' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:77:20: style: The scope of the variable '_score' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:173:46: style: The scope of the variable 'vn1' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:174:19: style: The scope of the variable 'encrypt' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:175:10: style: The scope of the variable 'flag' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:407:22: style: The scope of the variable 'code' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:408:10: style: The scope of the variable 'flag' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:470:22: style: The scope of the variable 'code' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:471:10: style: The scope of the variable 'flag' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:525:9: style: The scope of the variable 'end' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:466:9: style: Variable 'pot' can be declared as const array [constVariable]
clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp:304:22: style: Variable 'flag' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:15:20: warning: Member variable 'FullPairwiseAlign::_ptrToSeq1' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:15:20: warning: Member variable 'FullPairwiseAlign::_ptrToSeq2' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:15:20: warning: Member variable 'FullPairwiseAlign::matrix' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:34:13: style: Unused private function: 'FullPairwiseAlign::gap' [unusedPrivateFunction]
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:28:13: style:inconclusive: Technically the member function 'clustalw::FullPairwiseAlign::calcScore' can be const. [functionConst]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:220:31: note: Technically the member function 'clustalw::FullPairwiseAlign::calcScore' can be const.
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:28:13: note: Technically the member function 'clustalw::FullPairwiseAlign::calcScore' can be const.
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:29:15: style:inconclusive: Technically the member function 'clustalw::FullPairwiseAlign::tracePath' can be const. [functionConst]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:225:26: note: Technically the member function 'clustalw::FullPairwiseAlign::tracePath' can be const.
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:29:15: note: Technically the member function 'clustalw::FullPairwiseAlign::tracePath' can be const.
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:34:13: style:inconclusive: Technically the member function 'clustalw::FullPairwiseAlign::gap' can be const. [functionConst]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:620:24: note: Technically the member function 'clustalw::FullPairwiseAlign::gap' can be const.
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:34:13: note: Technically the member function 'clustalw::FullPairwiseAlign::gap' can be const.
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:35:13: style:inconclusive: Technically the member function 'clustalw::FullPairwiseAlign::tbgap' can be const. [functionConst]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:632:24: note: Technically the member function 'clustalw::FullPairwiseAlign::tbgap' can be const.
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:35:13: note: Technically the member function 'clustalw::FullPairwiseAlign::tbgap' can be const.
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:36:13: style:inconclusive: Technically the member function 'clustalw::FullPairwiseAlign::tegap' can be const. [functionConst]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:644:24: note: Technically the member function 'clustalw::FullPairwiseAlign::tegap' can be const.
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:36:13: note: Technically the member function 'clustalw::FullPairwiseAlign::tegap' can be const.
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:36:9: style: The scope of the variable 'si' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:36:13: style: The scope of the variable 'sj' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:36:17: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:37:9: style: The scope of the variable 'n' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:37:12: style: The scope of the variable 'm' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:37:15: style: The scope of the variable 'len1' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:37:21: style: The scope of the variable 'len2' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:38:9: style: The scope of the variable 'maxRes' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:40:9: style: The scope of the variable 'res' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:41:12: style: The scope of the variable '_score' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:42:11: style: The scope of the variable 'gapOpenScale' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:42:25: style: The scope of the variable 'gapExtendScale' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:277:9: style: The scope of the variable 'f' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:277:12: style: The scope of the variable 'hh' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:277:16: style: The scope of the variable 'p' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:340:9: style: The scope of the variable 'f' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:340:12: style: The scope of the variable 'hh' can be reduced. [variableScope]
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:337:56: style:inconclusive: Function 'reversePass' argument 1 names different: declaration 'ia' definition 'seq1'. [funcArgNamesDifferent]
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:31:45: note: Function 'reversePass' argument 1 names different: declaration 'ia' definition 'seq1'.
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:337:56: note: Function 'reversePass' argument 1 names different: declaration 'ia' definition 'seq1'.
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:337:81: style:inconclusive: Function 'reversePass' argument 2 names different: declaration 'ib' definition 'seq2'. [funcArgNamesDifferent]
clustalw-2.1/src/pairwise/FullPairwiseAlign.h:31:68: note: Function 'reversePass' argument 2 names different: declaration 'ib' definition 'seq2'.
clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp:337:81: note: Function 'reversePass' argument 2 names different: declaration 'ib' definition 'seq2'.
clustalw-2.1/src/tree/AlignmentSteps.cpp:45:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/AlignmentSteps.h:34:13: style:inconclusive: Technically the member function 'clustalw::AlignmentSteps::getNumSteps' can be const. [functionConst]
clustalw-2.1/src/tree/AlignmentSteps.cpp:33:21: note: Technically the member function 'clustalw::AlignmentSteps::getNumSteps' can be const.
clustalw-2.1/src/tree/AlignmentSteps.h:34:13: note: Technically the member function 'clustalw::AlignmentSteps::getNumSteps' can be const.
clustalw-2.1/src/tree/AlignmentSteps.cpp:14:42: style: Parameter 'groups' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:78:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NUMRES [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:658:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:903:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:929:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1091:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1455:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1518:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTree.cpp:55:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTree.cpp:272:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTree.cpp:535:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTree.cpp:617:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTree.cpp:982:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTree.cpp:20:14: warning: Member variable 'ClusterTree::clusAlgorithm' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/tree/ClusterTree.cpp:20:14: warning: Member variable 'ClusterTree::verbose' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/tree/ClusterTree.cpp:25:5: performance: Variable 'bootstrapPrompt' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/tree/ClusterTree.cpp:26:5: performance: Variable 'bootstrapFileTypeMsg' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
clustalw-2.1/src/tree/ClusterTree.h:40:14: performance:inconclusive: Technically the member function 'clustalw::ClusterTree::overspillMessage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/ClusterTree.cpp:74:19: note: Technically the member function 'clustalw::ClusterTree::overspillMessage' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:40:14: note: Technically the member function 'clustalw::ClusterTree::overspillMessage' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:44:14: performance:inconclusive: Technically the member function 'clustalw::ClusterTree::isAmbiguity' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/ClusterTree.cpp:544:19: note: Technically the member function 'clustalw::ClusterTree::isAmbiguity' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:44:14: note: Technically the member function 'clustalw::ClusterTree::isAmbiguity' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:45:14: performance:inconclusive: Technically the member function 'clustalw::ClusterTree::calcPercIdentity' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/ClusterTree.cpp:568:19: note: Technically the member function 'clustalw::ClusterTree::calcPercIdentity' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:45:14: note: Technically the member function 'clustalw::ClusterTree::calcPercIdentity' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:49:14: performance:inconclusive: Technically the member function 'clustalw::ClusterTree::transition' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/ClusterTree.cpp:737:19: note: Technically the member function 'clustalw::ClusterTree::transition' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:49:14: note: Technically the member function 'clustalw::ClusterTree::transition' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:50:14: style:inconclusive: Technically the member function 'clustalw::ClusterTree::distanceMatrixOutput' can be const. [functionConst]
clustalw-2.1/src/tree/ClusterTree.cpp:40:19: note: Technically the member function 'clustalw::ClusterTree::distanceMatrixOutput' can be const.
clustalw-2.1/src/tree/ClusterTree.h:50:14: note: Technically the member function 'clustalw::ClusterTree::distanceMatrixOutput' can be const.
clustalw-2.1/src/tree/ClusterTree.h:52:14: style:inconclusive: Technically the member function 'clustalw::ClusterTree::openFilesForBootstrap' can be const. [functionConst]
clustalw-2.1/src/tree/ClusterTree.cpp:760:19: note: Technically the member function 'clustalw::ClusterTree::openFilesForBootstrap' can be const.
clustalw-2.1/src/tree/ClusterTree.h:52:14: note: Technically the member function 'clustalw::ClusterTree::openFilesForBootstrap' can be const.
clustalw-2.1/src/tree/ClusterTree.h:54:14: performance:inconclusive: Technically the member function 'clustalw::ClusterTree::openFilesForTreeFromAlignment' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/ClusterTree.cpp:792:19: note: Technically the member function 'clustalw::ClusterTree::openFilesForTreeFromAlignment' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:54:14: note: Technically the member function 'clustalw::ClusterTree::openFilesForTreeFromAlignment' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:64:14: performance:inconclusive: Technically the member function 'clustalw::ClusterTree::printBootstrapHeaderToClustalFile' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/ClusterTree.cpp:943:19: note: Technically the member function 'clustalw::ClusterTree::printBootstrapHeaderToClustalFile' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:64:14: note: Technically the member function 'clustalw::ClusterTree::printBootstrapHeaderToClustalFile' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:65:14: performance:inconclusive: Technically the member function 'clustalw::ClusterTree::promptForBoolSeedAndNumTrials' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/ClusterTree.cpp:963:19: note: Technically the member function 'clustalw::ClusterTree::promptForBoolSeedAndNumTrials' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:65:14: note: Technically the member function 'clustalw::ClusterTree::promptForBoolSeedAndNumTrials' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:66:14: performance:inconclusive: Technically the member function 'clustalw::ClusterTree::printErrorMessageForBootstrap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/ClusterTree.cpp:979:19: note: Technically the member function 'clustalw::ClusterTree::printErrorMessageForBootstrap' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:66:14: note: Technically the member function 'clustalw::ClusterTree::printErrorMessageForBootstrap' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/ClusterTree.h:67:14: style:inconclusive: Technically the member function 'clustalw::ClusterTree::checkIfConditionsMet' can be const. [functionConst]
clustalw-2.1/src/tree/ClusterTree.cpp:1001:19: note: Technically the member function 'clustalw::ClusterTree::checkIfConditionsMet' can be const.
clustalw-2.1/src/tree/ClusterTree.h:67:14: note: Technically the member function 'clustalw::ClusterTree::checkIfConditionsMet' can be const.
clustalw-2.1/src/tree/RandomGenerator.h:26:9: style: Class 'RandomGenerator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/tree/NJTree.h:21:11: style: The destructor '~NJTree' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/tree/ClusterTreeAlgorithm.h:20:12: note: Virtual destructor in base class
clustalw-2.1/src/tree/NJTree.h:21:11: note: Destructor in derived class
clustalw-2.1/src/tree/NJTree.h:39:22: style: The function 'setVerbose' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
clustalw-2.1/src/tree/ClusterTreeAlgorithm.h:24:22: note: Virtual function in base class
clustalw-2.1/src/tree/NJTree.h:39:22: note: Function in derived class
clustalw-2.1/src/tree/ClusterTree.cpp:65:23: style: The if condition is the same as the previous if condition [duplicateCondition]
clustalw-2.1/src/tree/ClusterTree.cpp:61:23: note: First condition
clustalw-2.1/src/tree/ClusterTree.cpp:65:23: note: Second condition
clustalw-2.1/src/tree/ClusterTree.cpp:860:9: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
clustalw-2.1/src/tree/ClusterTree.cpp:864:9: note: Found duplicate branches for 'if' and 'else'.
clustalw-2.1/src/tree/ClusterTree.cpp:860:9: note: Found duplicate branches for 'if' and 'else'.
clustalw-2.1/src/tree/ClusterTree.cpp:580:9: style: The scope of the variable 'rs' can be reduced. [variableScope]
clustalw-2.1/src/tree/ClusterTree.cpp:580:17: style: The scope of the variable 'rl' can be reduced. [variableScope]
clustalw-2.1/src/tree/ClusterTree.cpp:586:9: style: The scope of the variable '_seqLength' can be reduced. [variableScope]
clustalw-2.1/src/tree/ClusterTree.cpp:604:9: style: The scope of the variable '_lenSeqI' can be reduced. [variableScope]
clustalw-2.1/src/tree/ClusterTree.cpp:74:54: style:inconclusive: Function 'overspillMessage' argument 2 names different: declaration 'total_dists' definition 'totalDists'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/ClusterTree.h:40:49: note: Function 'overspillMessage' argument 2 names different: declaration 'total_dists' definition 'totalDists'.
clustalw-2.1/src/tree/ClusterTree.cpp:74:54: note: Function 'overspillMessage' argument 2 names different: declaration 'total_dists' definition 'totalDists'.
clustalw-2.1/src/general/OutputFile.h:18:64: performance: Function parameter 'msg' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/OutputFile.h:19:41: performance: Function parameter 'ext' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/OutputFile.h:19:64: performance: Function parameter 'fileType' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/OutputFile.h:24:57: performance: Function parameter 'prompt' should be passed by const reference. [passedByValue]
clustalw-2.1/src/general/OutputFile.h:25:57: performance: Function parameter 'fileExtension' should be passed by const reference. [passedByValue]
clustalw-2.1/src/tree/ClusterTree.cpp:547:10: style: Variable 'codes' can be declared as const array [constVariable]
clustalw-2.1/src/tree/ClusterTree.cpp:761:99: style: Parameter 'path' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/tree/ClusterTree.cpp:794:69: style: Parameter 'path' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/tree/ClusterTree.cpp:603:12: style: Variable 'nmatch' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/ClusterTreeOutput.cpp:28:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTreeOutput.cpp:51:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTreeOutput.cpp:144:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTreeOutput.cpp:249:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTreeOutput.cpp:343:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/ClusterTreeOutput.cpp:231:9: style: The scope of the variable 'oldRow' can be reduced. [variableScope]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1283:24: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:28:12: warning: Member variable 'SubMatrix::matSeries' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:28:12: warning: Member variable 'SubMatrix::mat' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:28:12: warning: Member variable 'SubMatrix::xref' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:28:12: warning: Member variable 'SubMatrix::_matPtr' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:28:12: warning: Member variable 'SubMatrix::_matXref' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:94:14: style: Unused private function: 'SubMatrix::printGetMatrixResults' [unusedPrivateFunction]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:95:14: style: Unused private function: 'SubMatrix::compareMatrices' [unusedPrivateFunction]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:97:14: style: Unused private function: 'SubMatrix::printVectorToFile' [unusedPrivateFunction]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:61:13: style:inconclusive: Technically the member function 'clustalw::SubMatrix::getMatrixNum' can be const. [functionConst]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1298:16: note: Technically the member function 'clustalw::SubMatrix::getMatrixNum' can be const.
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:61:13: note: Technically the member function 'clustalw::SubMatrix::getMatrixNum' can be const.
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:62:13: style:inconclusive: Technically the member function 'clustalw::SubMatrix::getDNAMatrixNum' can be const. [functionConst]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1307:16: note: Technically the member function 'clustalw::SubMatrix::getDNAMatrixNum' can be const.
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:62:13: note: Technically the member function 'clustalw::SubMatrix::getDNAMatrixNum' can be const.
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:63:13: style:inconclusive: Technically the member function 'clustalw::SubMatrix::getPWMatrixNum' can be const. [functionConst]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1316:16: note: Technically the member function 'clustalw::SubMatrix::getPWMatrixNum' can be const.
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:63:13: note: Technically the member function 'clustalw::SubMatrix::getPWMatrixNum' can be const.
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:64:13: style:inconclusive: Technically the member function 'clustalw::SubMatrix::getPWDNAMatrixNum' can be const. [functionConst]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1325:16: note: Technically the member function 'clustalw::SubMatrix::getPWDNAMatrixNum' can be const.
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:64:13: note: Technically the member function 'clustalw::SubMatrix::getPWDNAMatrixNum' can be const.
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:89:13: performance:inconclusive: Technically the member function 'clustalw::SubMatrix::getArgs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1275:16: note: Technically the member function 'clustalw::SubMatrix::getArgs' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:89:13: note: Technically the member function 'clustalw::SubMatrix::getArgs' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:91:14: performance:inconclusive: Technically the member function 'clustalw::SubMatrix::commentline' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1421:17: note: Technically the member function 'clustalw::SubMatrix::commentline' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:91:14: note: Technically the member function 'clustalw::SubMatrix::commentline' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:94:14: style:inconclusive: Technically the member function 'clustalw::SubMatrix::printGetMatrixResults' can be const. [functionConst]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:924:17: note: Technically the member function 'clustalw::SubMatrix::printGetMatrixResults' can be const.
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:94:14: note: Technically the member function 'clustalw::SubMatrix::printGetMatrixResults' can be const.
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:95:14: performance:inconclusive: Technically the member function 'clustalw::SubMatrix::compareMatrices' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:893:17: note: Technically the member function 'clustalw::SubMatrix::compareMatrices' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:95:14: note: Technically the member function 'clustalw::SubMatrix::compareMatrices' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:96:14: performance:inconclusive: Technically the member function 'clustalw::SubMatrix::printInFormat' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1446:17: note: Technically the member function 'clustalw::SubMatrix::printInFormat' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:96:14: note: Technically the member function 'clustalw::SubMatrix::printInFormat' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:97:14: performance:inconclusive: Technically the member function 'clustalw::SubMatrix::printVectorToFile' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1509:17: note: Technically the member function 'clustalw::SubMatrix::printVectorToFile' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:97:14: note: Technically the member function 'clustalw::SubMatrix::printVectorToFile' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:100:14: performance:inconclusive: Technically the member function 'clustalw::SubMatrix::checkResidueAndAlignType' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1596:17: note: Technically the member function 'clustalw::SubMatrix::checkResidueAndAlignType' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:100:14: note: Technically the member function 'clustalw::SubMatrix::checkResidueAndAlignType' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:110:9: warning: Class 'SubMatrix' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:110:9: warning: Class 'SubMatrix' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1048:17: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:881:22: error: Resource leak: infile [resourceLeak]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:883:5: error: Resource leak: infile [resourceLeak]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:981:22: error: Resource leak: infile [resourceLeak]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:983:5: error: Resource leak: infile [resourceLeak]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1828:9: error: Resource leak: infile [resourceLeak]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1831:5: error: Resource leak: infile [resourceLeak]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1859:9: error: Resource leak: infile [resourceLeak]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1862:5: error: Resource leak: infile [resourceLeak]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1890:9: error: Resource leak: infile [resourceLeak]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1893:5: error: Resource leak: infile [resourceLeak]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:406:10: style: The scope of the variable 'found' can be reduced. [variableScope]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:407:10: style: The scope of the variable 'errorGiven' can be reduced. [variableScope]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:409:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:409:16: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:692:9: style: The scope of the variable 'ggScore' can be reduced. [variableScope]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:693:9: style: The scope of the variable 'grScore' can be reduced. [variableScope]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1719:9: style: The scope of the variable 'max' can be reduced. [variableScope]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1720:9: style: The scope of the variable 'offset' can be reduced. [variableScope]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:689:34: style:inconclusive: Function 'getMatrix' argument 1 names different: declaration 'matPtr' definition 'matptr'. [funcArgNamesDifferent]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:85:31: note: Function 'getMatrix' argument 1 names different: declaration 'matPtr' definition 'matptr'.
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:689:34: note: Function 'getMatrix' argument 1 names different: declaration 'matPtr' definition 'matptr'.
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:261:13: style: Local variable '_matPtr' shadows outer variable [shadowVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:171:17: note: Shadowed declaration
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:261:13: note: Shadow variable
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:262:11: style: Local variable '_matXref' shadows outer variable [shadowVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.h:172:15: note: Shadowed declaration
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:262:11: note: Shadow variable
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1446:46: style: Parameter 'temp' can be declared as reference to const [constParameterReference]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1509:50: style: Parameter 'temp' can be declared as reference to const [constParameterReference]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:842:11: style: Variable 'infile' can be declared as pointer to const [constVariablePointer]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:893:37: style: Parameter 'mat1' can be declared as const array [constParameter]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:893:63: style: Parameter 'mat2' can be declared as const array [constParameter]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:958:11: style: Variable 'infile' can be declared as pointer to const [constVariablePointer]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1421:35: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1446:58: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1509:62: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1800:11: style: Variable 'infile' can be declared as pointer to const [constVariablePointer]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1838:11: style: Variable 'infile' can be declared as pointer to const [constVariablePointer]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1869:11: style: Variable 'infile' can be declared as pointer to const [constVariablePointer]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1102:14: warning: Uninitialized variable: n [uninitvar]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1040:37: note: Assuming condition is false
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1102:14: note: Uninitialized variable: n
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:292:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:292:58: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:298:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:298:61: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:306:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:306:57: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:338:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:338:58: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:344:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:344:56: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:350:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:350:56: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:357:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:357:53: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:363:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:363:54: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:406:16: style: Variable 'found' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:409:11: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:436:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:436:58: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:443:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:443:61: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:449:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:449:55: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:493:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:498:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:503:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:508:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:514:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:520:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:526:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:529:25: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:537:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:542:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:547:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:552:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:557:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:560:25: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:568:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:574:31: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:581:35: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:586:35: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:594:35: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:599:35: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:603:25: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:610:25: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:611:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:634:28: style: Variable 'errorGiven' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:643:25: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:644:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:650:25: style: Variable 'xrefPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:651:27: style: Variable 'matrixPointer' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:735:9: style: Variable 'av1' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:735:15: style: Variable 'av2' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:740:17: style: Variable 'av1' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:743:21: style: Variable 'av2' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:752:9: style: Variable 'av1' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:753:9: style: Variable 'av2' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:860:16: style: Variable 'infile' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:972:16: style: Variable 'infile' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1350:17: style: Variable 'residue' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1350:36: style: Variable 'align' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1356:17: style: Variable 'residue' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1356:36: style: Variable 'align' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1362:17: style: Variable 'residue' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1362:32: style: Variable 'align' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1368:17: style: Variable 'residue' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1368:32: style: Variable 'align' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1709:12: style: Variable 'maxRes' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1740:16: style: Variable 'maxRes' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1792:16: style: Variable 'maxRes' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1809:16: style: Variable 'infile' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1847:16: style: Variable 'infile' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:1878:16: style: Variable 'infile' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:94:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp:105:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
clustalw-2.1/src/tree/NJTree.cpp:223:9: error: Memory leak: sumCols [memleak]
clustalw-2.1/src/tree/NJTree.cpp:223:9: error: Memory leak: sumRows [memleak]
clustalw-2.1/src/tree/NJTree.cpp:223:9: error: Memory leak: join [memleak]
clustalw-2.1/src/tree/NJTree.cpp:268:36: warning: Either the condition 'lpi!=NULL' is redundant or there is possible null pointer dereference: lpi. [nullPointerRedundantCheck]
clustalw-2.1/src/tree/NJTree.cpp:278:18: note: Assuming that condition 'lpi!=NULL' is not redundant
clustalw-2.1/src/tree/NJTree.cpp:268:36: note: Null pointer dereference
clustalw-2.1/src/tree/NJTree.cpp:625:36: warning: Either the condition 'lpj!=NULL' is redundant or there is possible null pointer dereference: lpj. [nullPointerRedundantCheck]
clustalw-2.1/src/tree/NJTree.cpp:632:18: note: Assuming that condition 'lpj!=NULL' is not redundant
clustalw-2.1/src/tree/NJTree.cpp:625:36: note: Null pointer dereference
clustalw-2.1/src/tree/NJTree.cpp:380:13: style: Variable 'dio' is reassigned a value before the old one has been used. [redundantAssignment]
clustalw-2.1/src/tree/NJTree.cpp:377:13: note: dio is assigned
clustalw-2.1/src/tree/NJTree.cpp:380:13: note: dio is overwritten
clustalw-2.1/src/tree/RandomGenerator.h:33:23: style:inconclusive: Technically the member function 'clustalw::RandomGenerator::mult' can be const. [functionConst]
clustalw-2.1/src/tree/RandomGenerator.cpp:54:32: note: Technically the member function 'clustalw::RandomGenerator::mult' can be const.
clustalw-2.1/src/tree/RandomGenerator.h:33:23: note: Technically the member function 'clustalw::RandomGenerator::mult' can be const.
clustalw-2.1/src/tree/NJTree.cpp:167:20: style: The scope of the variable 'fnseqs2' can be reduced. [variableScope]
clustalw-2.1/src/tree/NJTree.cpp:168:27: style: The scope of the variable 'dio' can be reduced. [variableScope]
clustalw-2.1/src/tree/NJTree.cpp:168:32: style: The scope of the variable 'djo' can be reduced. [variableScope]
clustalw-2.1/src/tree/NJTree.cpp:168:37: style: The scope of the variable 'da' can be reduced. [variableScope]
clustalw-2.1/src/tree/NJTree.cpp:169:12: style: The scope of the variable 'tmin' can be reduced. [variableScope]
clustalw-2.1/src/tree/NJTree.cpp:169:25: style: The scope of the variable 'dmin' can be reduced. [variableScope]
clustalw-2.1/src/tree/NJTree.cpp:170:12: style: The scope of the variable 'bi' can be reduced. [variableScope]
clustalw-2.1/src/tree/NJTree.cpp:170:16: style: The scope of the variable 'bj' can be reduced. [variableScope]
clustalw-2.1/src/tree/NJTree.cpp:167:28: style: Variable 'fnseqs2' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/NJTree.cpp:226:10: style: Variable 'mini' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/NJTree.cpp:226:17: style: Variable 'minj' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/NJTree.cpp:262:10: style: Variable 'sumd' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/Tree.cpp:71:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_SCALE_FACTOR [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/Tree.cpp:133:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/Tree.cpp:680:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/Tree.cpp:782:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/Tree.h:19:1: style: The class 'Tree' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
clustalw-2.1/src/tree/TreeInterface.h:92:14: performance:inconclusive: Technically the member function 'clustalw::TreeInterface::treeFromAlignment' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/TreeInterface.cpp:156:16: note: Technically the member function 'clustalw::TreeInterface::treeFromAlignment' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/TreeInterface.h:92:14: note: Technically the member function 'clustalw::TreeInterface::treeFromAlignment' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/TreeInterface.h:99:14: performance:inconclusive: Technically the member function 'clustalw::TreeInterface::bootstrapTree' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/TreeInterface.cpp:171:16: note: Technically the member function 'clustalw::TreeInterface::bootstrapTree' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/TreeInterface.h:99:14: note: Technically the member function 'clustalw::TreeInterface::bootstrapTree' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/TreeInterface.h:113:13: performance:inconclusive: Technically the member function 'clustalw::TreeInterface::readTreeAndCalcWeightsNJ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/TreeInterface.cpp:257:16: note: Technically the member function 'clustalw::TreeInterface::readTreeAndCalcWeightsNJ' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/TreeInterface.h:113:13: note: Technically the member function 'clustalw::TreeInterface::readTreeAndCalcWeightsNJ' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/TreeInterface.h:130:14: performance:inconclusive: Technically the member function 'clustalw::TreeInterface::generateTreeFromDistMatNJ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/TreeInterface.cpp:419:16: note: Technically the member function 'clustalw::TreeInterface::generateTreeFromDistMatNJ' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/TreeInterface.h:130:14: note: Technically the member function 'clustalw::TreeInterface::generateTreeFromDistMatNJ' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/Node.h:17:16: style:inconclusive: Technically the member function 'clustalw::Node::getDist' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.h:21:13: style:inconclusive: Technically the member function 'clustalw::Node::getNumDists' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.h:22:16: style:inconclusive: Technically the member function 'clustalw::Node::getMinDist' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.h:23:13: style:inconclusive: Technically the member function 'clustalw::Node::getIndexToMinDist' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.h:25:13: style:inconclusive: Technically the member function 'clustalw::Node::getOrder' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.h:27:13: style:inconclusive: Technically the member function 'clustalw::Node::getSeqNum' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.h:37:16: style:inconclusive: Technically the member function 'clustalw::Node::getHeight' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.h:40:13: style:inconclusive: Technically the member function 'clustalw::Node::getFirstElement' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.h:42:13: style:inconclusive: Technically the member function 'clustalw::Node::getFirstElem' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.h:43:14: style:inconclusive: Technically the member function 'clustalw::Node::isLeafNode' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.h:28:9: style: Class 'RootedGuideTree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/tree/TreeInterface.cpp:359:9: error: Memory leak: msaObj [memleak]
clustalw-2.1/src/tree/TreeInterface.cpp:371:13: error: Memory leak: msaObj [memleak]
clustalw-2.1/src/tree/TreeInterface.cpp:388:13: error: Memory leak: msaObj [memleak]
clustalw-2.1/src/tree/TreeInterface.cpp:299:75: style:inconclusive: Function 'getWeightsFromDistMatNJ' argument 5 names different: declaration 'nSeqs' definition '_nSeqs'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/TreeInterface.h:122:71: note: Function 'getWeightsFromDistMatNJ' argument 5 names different: declaration 'nSeqs' definition '_nSeqs'.
clustalw-2.1/src/tree/TreeInterface.cpp:299:75: note: Function 'getWeightsFromDistMatNJ' argument 5 names different: declaration 'nSeqs' definition '_nSeqs'.
clustalw-2.1/src/tree/TreeInterface.cpp:258:70: style: Parameter 'treeName' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/tree/TreeInterface.cpp:264:29: performance: Passing the result of c_str() to a function that takes std::string as argument no. 2 is slow and redundant. [stlcstrParam]
clustalw-2.1/src/tree/TreeInterface.cpp:367:29: performance: Passing the result of c_str() to a function that takes std::string as argument no. 2 is slow and redundant. [stlcstrParam]
clustalw-2.1/src/tree/TreeInterface.cpp:384:29: performance: Passing the result of c_str() to a function that takes std::string as argument no. 2 is slow and redundant. [stlcstrParam]
clustalw-2.1/src/tree/TreeInterface.cpp:552:33: performance: Passing the result of c_str() to a function that takes std::string as argument no. 2 is slow and redundant. [stlcstrParam]
clustalw-2.1/src/tree/TreeInterface.cpp:582:33: performance: Passing the result of c_str() to a function that takes std::string as argument no. 2 is slow and redundant. [stlcstrParam]
clustalw-2.1/src/tree/TreeInterface.cpp:655:28: performance: Passing the result of c_str() to a function that takes std::string as argument no. 2 is slow and redundant. [stlcstrParam]
clustalw-2.1/src/tree/TreeInterface.cpp:302:29: style: Variable 'copyOfPhylipName' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/TreeInterface.cpp:363:16: style: Variable 'status' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/TreeInterface.cpp:544:16: style: Variable 'status' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/TreeInterface.cpp:644:29: style: Variable 'copyOfPhylipName' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/TreeInterface.cpp:652:12: style: Variable 'status' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/Tree.cpp:662:5: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
clustalw-2.1/src/tree/Tree.h:50:14: style: Unused private function: 'Tree::debugPrintAllNodes' [unusedPrivateFunction]
clustalw-2.1/src/tree/Tree.h:36:14: style:inconclusive: Technically the member function 'clustalw::Tree::clearTreeNodes' can be const. [functionConst]
clustalw-2.1/src/tree/Tree.cpp:644:12: note: Technically the member function 'clustalw::Tree::clearTreeNodes' can be const.
clustalw-2.1/src/tree/Tree.h:36:14: note: Technically the member function 'clustalw::Tree::clearTreeNodes' can be const.
clustalw-2.1/src/tree/Tree.h:47:19: performance:inconclusive: Technically the member function 'clustalw::Tree::avail' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/Tree.cpp:1234:27: note: Technically the member function 'clustalw::Tree::avail' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/Tree.h:47:19: note: Technically the member function 'clustalw::Tree::avail' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/Tree.h:48:14: performance:inconclusive: Technically the member function 'clustalw::Tree::setInfo' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/Tree.cpp:1255:12: note: Technically the member function 'clustalw::Tree::setInfo' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/Tree.h:48:14: note: Technically the member function 'clustalw::Tree::setInfo' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/Tree.cpp:692:20: style: C-style pointer casting [cstyleCast]
clustalw-2.1/src/tree/Tree.cpp:30:9: style: The scope of the variable 'temp' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:30:15: style: The scope of the variable 'sum' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:31:10: style: The scope of the variable 'weight' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:116:10: style: The scope of the variable 'c' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:117:12: style: The scope of the variable 'name1' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:117:24: style: The scope of the variable 'name2' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:118:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:118:12: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:118:15: style: The scope of the variable 'k' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:119:10: style: The scope of the variable 'found' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:201:9: style: The scope of the variable 'nameLength' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:283:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:283:12: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:334:9: style: The scope of the variable 'depth' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:334:26: style: The scope of the variable 'k' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:334:29: style: The scope of the variable 'n' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:335:10: style: The scope of the variable 'found' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:336:9: style: The scope of the variable 'nerrs' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:336:16: style: The scope of the variable 'seq1' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:336:31: style: The scope of the variable 'seq2' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:338:11: style: The scope of the variable 'dist' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:339:24: style: The scope of the variable 'badDist' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:342:10: style: The scope of the variable 'reply' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:501:15: style: The scope of the variable 'p' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:503:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:676:23: style: The scope of the variable 'p' can be reduced. [variableScope]
clustalw-2.1/src/tree/Tree.cpp:1255:69: performance: Function parameter 'pname' should be passed by const reference. [passedByValue]
clustalw-2.1/src/tree/Tree.cpp:902:46: style: Parameter 'root' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/tree/Tree.cpp:1190:43: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/tree/Tree.cpp:1213:43: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/tree/Tree.cpp:463:14: error: Memory is allocated but not initialized: pathToRoot [uninitdata]
clustalw-2.1/src/tree/Tree.cpp:464:14: error: Memory is allocated but not initialized: distToNode [uninitdata]
clustalw-2.1/src/tree/Tree.cpp:117:18: style: Variable 'name1' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/Tree.cpp:117:30: style: Variable 'name2' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/Tree.cpp:213:19: style: Variable 'name1' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/Tree.cpp:334:15: style: Variable 'depth' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/Tree.cpp:762:10: style: Variable 'diff' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/Tree.cpp:912:10: style: Variable 'dist' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/UPGMA/Node.cpp:85:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/UPGMA/Node.cpp:113:5: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
clustalw-2.1/src/tree/UPGMA/Node.h:32:16: style:inconclusive: Technically the member function 'clustalw::Node::elementsToString' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.cpp:90:14: note: Technically the member function 'clustalw::Node::elementsToString' can be const.
clustalw-2.1/src/tree/UPGMA/Node.h:32:16: note: Technically the member function 'clustalw::Node::elementsToString' can be const.
clustalw-2.1/src/tree/UPGMA/Node.h:57:14: style:inconclusive: Technically the member function 'clustalw::Node::printElements' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/Node.cpp:81:12: note: Technically the member function 'clustalw::Node::printElements' can be const.
clustalw-2.1/src/tree/UPGMA/Node.h:57:14: note: Technically the member function 'clustalw::Node::printElements' can be const.
clustalw-2.1/src/tree/UPGMA/Node.h:59:14: performance:inconclusive: Technically the member function 'clustalw::Node::makeEmpty' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/UPGMA/Node.cpp:105:12: note: Technically the member function 'clustalw::Node::makeEmpty' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/Node.h:59:14: note: Technically the member function 'clustalw::Node::makeEmpty' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/Node.cpp:14:16: style:inconclusive: Function 'Node' argument 1 names different: declaration 'seqNum' definition '_seqNum'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/Node.h:16:18: note: Function 'Node' argument 1 names different: declaration 'seqNum' definition '_seqNum'.
clustalw-2.1/src/tree/UPGMA/Node.cpp:14:16: note: Function 'Node' argument 1 names different: declaration 'seqNum' definition '_seqNum'.
clustalw-2.1/src/tree/UPGMA/Node.cpp:14:33: style:inconclusive: Function 'Node' argument 2 names different: declaration 'aptrToDistMatRow' definition 'dists'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/Node.h:16:34: note: Function 'Node' argument 2 names different: declaration 'aptrToDistMatRow' definition 'dists'.
clustalw-2.1/src/tree/UPGMA/Node.cpp:14:33: note: Function 'Node' argument 2 names different: declaration 'aptrToDistMatRow' definition 'dists'.
clustalw-2.1/src/tree/UPGMA/Node.cpp:14:44: style:inconclusive: Function 'Node' argument 3 names different: declaration 'numDists' definition 'numDist'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/Node.h:16:56: note: Function 'Node' argument 3 names different: declaration 'numDists' definition 'numDist'.
clustalw-2.1/src/tree/UPGMA/Node.cpp:14:44: note: Function 'Node' argument 3 names different: declaration 'numDists' definition 'numDist'.
clustalw-2.1/src/tree/UPGMA/Node.cpp:66:13: style: Variable 'minDistSoFar' can be declared as pointer to const [constVariablePointer]
clustalw-2.1/src/tree/UPGMA/Node.cpp:113:7: style: Variable 't' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/UPGMA/RootedClusterTree.cpp:27:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/UPGMA/RootedClusterTree.cpp:216:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:41:14: performance:inconclusive: Technically the member function 'clustalw::UPGMAAlgorithm::movePtrPastUnusedDistances' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.h:30:9: style: Class 'RootedTreeOutput' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
clustalw-2.1/src/tree/UPGMA/RootedClusterTree.cpp:34:15: style: The scope of the variable 'dist' can be reduced. [variableScope]
clustalw-2.1/src/tree/UPGMA/RootedClusterTree.cpp:121:13: style: The scope of the variable 'totalDists' can be reduced. [variableScope]
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:106:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_SCALE_FACTOR [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.h:36:13: performance:inconclusive: Technically the member function 'clustalw::RootedGuideTree::calcOrderNode' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:45:22: note: Technically the member function 'clustalw::RootedGuideTree::calcOrderNode' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.h:36:13: note: Technically the member function 'clustalw::RootedGuideTree::calcOrderNode' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.h:38:14: performance:inconclusive: Technically the member function 'clustalw::RootedGuideTree::doWeightCalc' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:147:23: note: Technically the member function 'clustalw::RootedGuideTree::doWeightCalc' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.h:38:14: note: Technically the member function 'clustalw::RootedGuideTree::doWeightCalc' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:71:9: style: The scope of the variable 'temp' can be reduced. [variableScope]
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:71:19: style: The scope of the variable 'sum' can be reduced. [variableScope]
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:20:40: style:inconclusive: Function 'RootedGuideTree' argument 1 names different: declaration 'root' definition 'r'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.h:28:31: note: Function 'RootedGuideTree' argument 1 names different: declaration 'root' definition 'r'.
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:20:40: note: Function 'RootedGuideTree' argument 1 names different: declaration 'root' definition 'r'.
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:147:70: style:inconclusive: Function 'doWeightCalc' argument 2 names different: declaration 'seqWeights' definition 'weights'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.h:38:61: note: Function 'doWeightCalc' argument 2 names different: declaration 'seqWeights' definition 'weights'.
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:147:70: note: Function 'doWeightCalc' argument 2 names different: declaration 'seqWeights' definition 'weights'.
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:71:14: style: Variable 'temp' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.cpp:35:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp:71:23: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.cpp:78:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.h:37:14: performance:inconclusive: Technically the member function 'clustalw::RootedTreeOutput::phylipTraverse' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.cpp:95:24: note: Technically the member function 'clustalw::RootedTreeOutput::phylipTraverse' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.h:37:14: note: Technically the member function 'clustalw::RootedTreeOutput::phylipTraverse' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.h:38:14: performance:inconclusive: Technically the member function 'clustalw::RootedTreeOutput::nexusTraverse' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.cpp:125:24: note: Technically the member function 'clustalw::RootedTreeOutput::nexusTraverse' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.h:38:14: note: Technically the member function 'clustalw::RootedTreeOutput::nexusTraverse' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.cpp:95:87: style:inconclusive: Function 'phylipTraverse' argument 3 names different: declaration 'tree' definition 't'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.h:37:77: note: Function 'phylipTraverse' argument 3 names different: declaration 'tree' definition 't'.
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.cpp:95:87: note: Function 'phylipTraverse' argument 3 names different: declaration 'tree' definition 't'.
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.cpp:125:86: style:inconclusive: Function 'nexusTraverse' argument 3 names different: declaration 'tree' definition 't'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.h:38:76: note: Function 'nexusTraverse' argument 3 names different: declaration 'tree' definition 't'.
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.cpp:125:86: note: Function 'nexusTraverse' argument 3 names different: declaration 'tree' definition 't'.
clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.cpp:14:45: style: Parameter 'seqInfo' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:104:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:159:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:181:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:392:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:32:14: style: Unused private function: 'UPGMAAlgorithm::printAllNodes' [unusedPrivateFunction]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:32:14: performance:inconclusive: Technically the member function 'clustalw::UPGMAAlgorithm::printAllNodes' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:98:22: note: Technically the member function 'clustalw::UPGMAAlgorithm::printAllNodes' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:32:14: note: Technically the member function 'clustalw::UPGMAAlgorithm::printAllNodes' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:34:16: performance:inconclusive: Technically the member function 'clustalw::UPGMAAlgorithm::getNodeWithMinDist' can be static (but you may consider moving to unnamed namespace). [functionStatic]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:225:24: note: Technically the member function 'clustalw::UPGMAAlgorithm::getNodeWithMinDist' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:34:16: note: Technically the member function 'clustalw::UPGMAAlgorithm::getNodeWithMinDist' can be static (but you may consider moving to unnamed namespace).
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:40:14: style:inconclusive: Technically the member function 'clustalw::UPGMAAlgorithm::computeDistsForNodesAfterNode2' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:374:22: note: Technically the member function 'clustalw::UPGMAAlgorithm::computeDistsForNodesAfterNode2' can be const.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:40:14: note: Technically the member function 'clustalw::UPGMAAlgorithm::computeDistsForNodesAfterNode2' can be const.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:48:16: style:inconclusive: Technically the member function 'clustalw::UPGMAAlgorithm::calcNewDist' can be const. [functionConst]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:455:24: note: Technically the member function 'clustalw::UPGMAAlgorithm::calcNewDist' can be const.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:48:16: note: Technically the member function 'clustalw::UPGMAAlgorithm::calcNewDist' can be const.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:53:23: style: C-style pointer casting [cstyleCast]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:73:68: style:inconclusive: Function 'initialiseNodes' argument 2 names different: declaration 'firstSeq' definition 'fSeq'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:29:60: note: Function 'initialiseNodes' argument 2 names different: declaration 'firstSeq' definition 'fSeq'.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:73:68: note: Function 'initialiseNodes' argument 2 names different: declaration 'firstSeq' definition 'fSeq'.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:225:50: style:inconclusive: Function 'getNodeWithMinDist' argument 1 names different: declaration 'clusters' definition 'nodes'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:34:42: note: Function 'getNodeWithMinDist' argument 1 names different: declaration 'clusters' definition 'nodes'.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:225:50: note: Function 'getNodeWithMinDist' argument 1 names different: declaration 'clusters' definition 'nodes'.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:321:56: style:inconclusive: Function 'computeDistsUpToNodeToJoin2' argument 1 names different: declaration 'nToJoin1' definition 'nodeToJoin1'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:38:48: note: Function 'computeDistsUpToNodeToJoin2' argument 1 names different: declaration 'nToJoin1' definition 'nodeToJoin1'.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:321:56: note: Function 'computeDistsUpToNodeToJoin2' argument 1 names different: declaration 'nToJoin1' definition 'nodeToJoin1'.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:321:75: style:inconclusive: Function 'computeDistsUpToNodeToJoin2' argument 2 names different: declaration 'nToJoin2' definition 'nodeToJoin2'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:38:64: note: Function 'computeDistsUpToNodeToJoin2' argument 2 names different: declaration 'nToJoin2' definition 'nodeToJoin2'.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:321:75: note: Function 'computeDistsUpToNodeToJoin2' argument 2 names different: declaration 'nToJoin2' definition 'nodeToJoin2'.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:374:59: style:inconclusive: Function 'computeDistsForNodesAfterNode2' argument 1 names different: declaration 'nToJoin2' definition 'nodeToJoin2'. [funcArgNamesDifferent]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h:40:51: note: Function 'computeDistsForNodesAfterNode2' argument 1 names different: declaration 'nToJoin2' definition 'nodeToJoin2'.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:374:59: note: Function 'computeDistsForNodesAfterNode2' argument 1 names different: declaration 'nToJoin2' definition 'nodeToJoin2'.
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:29:52: style: Parameter 'seqInfo' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp:321:75: style: Parameter 'nodeToJoin2' can be declared as pointer to const [constParameterPointer]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:18:22: warning: Member variable 'UnRootedClusterTree::phyloTree' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:18:22: warning: Member variable 'UnRootedClusterTree::outputTree' is not initialized in the constructor. [uninitMemberVar]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:42:13: style: The scope of the variable 'totalDists' can be reduced. [variableScope]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:188:15: style: The scope of the variable 'dist' can be reduced. [variableScope]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:279:9: style: The scope of the variable 'i' can be reduced. [variableScope]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:279:12: style: The scope of the variable 'j' can be reduced. [variableScope]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:280:9: style: The scope of the variable 'ranno' can be reduced. [variableScope]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:284:15: style: The scope of the variable 'ptrToClustalFile' can be reduced. [variableScope]
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:187:19: style: Local variable 'phyloTree' shadows outer variable [shadowVariable]
clustalw-2.1/src/tree/UnRootedClusterTree.h:22:20: note: Shadowed declaration
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:187:19: note: Shadow variable
clustalw-2.1/src/tree/UnRootedClusterTree.cpp:292:19: style: Unused variable: standardTree [unusedVariable]
diff:


DONE