| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/kalign/src/ |
| H A D | KalignTask.cpp | 114 bool KalignTask::isAlphabetSupported(const QString &alphabetId) { in isAlphabetSupported() argument
115 return (alphabetId == BaseDNAAlphabetIds::NUCL_DNA_DEFAULT() || in isAlphabetSupported()
116 alphabetId == BaseDNAAlphabetIds::NUCL_RNA_DEFAULT() || in isAlphabetSupported()
117 alphabetId == BaseDNAAlphabetIds::NUCL_DNA_EXTENDED() || in isAlphabetSupported()
118 alphabetId == BaseDNAAlphabetIds::NUCL_RNA_EXTENDED() || in isAlphabetSupported()
119 alphabetId == BaseDNAAlphabetIds::AMINO_DEFAULT()); in isAlphabetSupported()
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| H A D | PairwiseAlignmentHirschbergGUIExtensionFactory.cpp | 48 …QString alphabetId = externSettings->value(PairwiseAlignmentTaskSettings::ALPHABET, "").toString(); in initParameters() local
49 const DNAAlphabet *alphabet = alphabetReg->findById(alphabetId); in initParameters()
50 SAFE_POINT(NULL != alphabet, QString("Alphabet %1 not found").arg(alphabetId), ); in initParameters()
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| H A D | KalignTask.h | 75 static bool isAlphabetSupported(const QString &alphabetId);
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/ |
| H A D | MSAEditor.cpp | 182 auto alphabetId = maObject->getAlphabet()->getId(); in updateActions() local
183 …convertDnaToRnaAction->setEnabled(!isReadOnly && alphabetId == BaseDNAAlphabetIds::NUCL_DNA_DEFAUL… in updateActions()
185 convertRawToDnaAction->setEnabled(!isReadOnly && alphabetId == BaseDNAAlphabetIds::RAW()); in updateActions()
186 convertRawToAminoAction->setEnabled(!isReadOnly && alphabetId == BaseDNAAlphabetIds::RAW()); in updateActions()
775 auto alphabetId = maObject->getAlphabet()->getId(); in sl_convertBetweenDnaAndRnaAlphabets()
776 bool isDnaAlphabet = alphabetId == BaseDNAAlphabetIds::NUCL_DNA_DEFAULT(); in sl_convertBetweenDnaAndRnaAlphabets()
777 bool isRnaAlphabet = alphabetId == BaseDNAAlphabetIds::NUCL_RNA_DEFAULT(); in sl_convertBetweenDnaAndRnaAlphabets()
793 auto alphabetId = maObject->getAlphabet()->getId(); in sl_convertRawToDnaAlphabet()
794 CHECK(alphabetId == BaseDNAAlphabetIds::RAW(), ); in sl_convertRawToDnaAlphabet()
809 auto alphabetId = maObject->getAlphabet()->getId(); in sl_convertRawToAminoAlphabet()
[all …]
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/util/ |
| H A D | U2SequenceUtils.h | 61 …s, const U2DbiRef &dbiRef, const DNASequence &seq, const U2AlphabetId &alphabetId = U2AlphabetId()…
62 …ef, const QString &folder, const DNASequence &seq, const U2AlphabetId &alphabetId = U2AlphabetId()…
79 …&folder, const QString &visualName, bool circular, const U2AlphabetId &alphabetId = U2AlphabetId()…
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| H A D | MultipleChromatogramAlignmentImporter.cpp | 131 const U2AlphabetId alphabetId = alphabet->getId(); in importRowChildObjects() local
139 …aRowDatabaseData.sequence = importSequence(os, connection, folder, row->getSequence(), alphabetId); in importRowChildObjects()
195 const U2AlphabetId &alphabetId) { in importSequence() argument
196 …quenceRef = U2SequenceUtils::import(os, connection.dbi->getDbiRef(), folder, sequence, alphabetId); in importSequence()
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| H A D | U2SequenceUtils.cpp | 220 …t(U2OpStatus &os, const U2DbiRef &dbiRef, const DNASequence &seq, const U2AlphabetId &alphabetId) { in import() argument
221 return import(os, dbiRef, U2ObjectDbi::ROOT_FOLDER, seq, alphabetId); in import()
224 … U2DbiRef &dbiRef, const QString &folder, const DNASequence &seq, const U2AlphabetId &alphabetId) { in import() argument
228 i.startSequence(os, dbiRef, folder, seq.getName(), seq.circular, alphabetId); in import()
430 const U2AlphabetId &alphabetId) { in startSequence() argument
440 sequence.alphabet.id = alphabetId.id; in startSequence()
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| H A D | MultipleChromatogramAlignmentImporter.h | 44 …n &connection, const QString &folder, const DNASequence &sequence, const U2AlphabetId &alphabetId);
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/datatype/ |
| H A D | SMatrix.cpp | 107 QString alphabetId = list.at(n++).toString(); in fromQVariant() local
108 m.alphabet = AppContext::getDNAAlphabetRegistry()->findById(alphabetId); in fromQVariant()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/ |
| H A D | NEXUSFormat.cpp | 780 const QString &alphabetId = ma->getAlphabet()->getId(); in writeMAligment() local
781 …if (alphabetId == BaseDNAAlphabetIds::NUCL_DNA_DEFAULT() || alphabetId == BaseDNAAlphabetIds::NUCL… in writeMAligment()
783 …} else if (alphabetId == BaseDNAAlphabetIds::NUCL_RNA_DEFAULT() || alphabetId == BaseDNAAlphabetId… in writeMAligment()
785 } else if (alphabetId == BaseDNAAlphabetIds::AMINO_DEFAULT()) { in writeMAligment()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/smith_waterman/ |
| H A D | SmithWatermanReportCallback.cpp | 141 const U2AlphabetId alphabetId = msaDbi->getMsaObject(sourceMsaRef.entityId, os).alphabet; in SmithWatermanReportCallbackMAImpl() local
143 alphabet = U2AlphabetUtils::getById(alphabetId); in SmithWatermanReportCallbackMAImpl()
164 const U2AlphabetId alphabetId = msaDbi->getMsaObject(sourceMsaRef.entityId, os).alphabet; in SmithWatermanReportCallbackMAImpl() local
168 alphabet = U2AlphabetUtils::getById(alphabetId); in SmithWatermanReportCallbackMAImpl()
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| /dports/biology/ugene/ugene-40.1/src/plugins/CoreTests/src/ |
| H A D | DNASequenceObjectTests.h | 55 QString alphabetId; variable
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| H A D | DNASequenceObjectTests.cpp | 91 alphabetId = el.attribute(VALUE_ATTR); in init()
92 if (alphabetId.isEmpty()) { in init()
114 if (tempAlphabet->getId() != alphabetId) { in report()
115 …rror(QString("Alphabet not matched: %1, expected %2 ").arg(tempAlphabet->getId()).arg(alphabetId)); in report()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_sequence/sequence_info/ |
| H A D | SequenceInfo.cpp | 199 const QString alphabetId = activeSequenceAlphabet->getId(); in updateDinuclLayout() local
200 …if ((alphabetId == BaseDNAAlphabetIds::NUCL_DNA_DEFAULT()) || (alphabetId == BaseDNAAlphabetIds::N… in updateDinuclLayout()
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