Searched refs:chimeraRefSeq (Results 1 – 3 of 3) sorted by relevance
| /dports/biology/mothur/mothur-1.46.1/source/ |
| H A D | refchimeratest.cpp | 85 string chimeraRefSeq = ""; in analyzeAlignedQuery() local
89 chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi); in analyzeAlignedQuery()
93 chimeraRefSeq = referenceSeqs[bestMatchIndex]; in analyzeAlignedQuery()
96 bestRefAlignment = chimeraRefSeq; in analyzeAlignedQuery()
625 …string chimeraRefSeq = referenceSeqs[leftParent].substr(0, breakPoint) + referenceSeqs[rightParent… in stitchBimera() local
626 return chimeraRefSeq; in stitchBimera()
636 return chimeraRefSeq; in stitchTrimera()
641 double RefChimeraTest::calcDistToChimera(string& querySeq, string& chimeraRefSeq){ in calcDistToChimera() argument
648 if(chimeraRefSeq[i] != '.' && querySeq[i] != '.'){ in calcDistToChimera()
649 if(querySeq[i] == '-' && chimeraRefSeq[i] == '-' && chimeraRefSeq[i] != 'N'){ /* do nothing */ } in calcDistToChimera()
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| /dports/biology/mothur/mothur-1.46.1/source/chimera/ |
| H A D | myPerseus.cpp | 689 string chimeraRefSeq; in stitchTrimera() local
691 if (m->getControl_pressed()) { return chimeraRefSeq; } in stitchTrimera()
693 chimeraRefSeq += alignments[leftParent].reference[i]; in stitchTrimera()
698 if (m->getControl_pressed()) { return chimeraRefSeq; } in stitchTrimera()
700 chimeraRefSeq += alignments[middleParent].reference[i]; in stitchTrimera()
705 if (m->getControl_pressed()) { return chimeraRefSeq; } in stitchTrimera()
707 chimeraRefSeq += alignments[rightParent].reference[i]; in stitchTrimera()
711 return chimeraRefSeq; in stitchTrimera()
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| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | chimeraperseuscommand.cpp | 293 string chimeraRefSeq; in driver() local
297 …chimeraRefSeq = myPerseus.stitchTrimera(alignments, leftParentTri, middleParentTri, rightParentTri… in driver()
301 …chimeraRefSeq = myPerseus.stitchBimera(alignments, leftParentBi, rightParentBi, breakPointBi, left… in driver()
306 …t = myPerseus.modeledPairwiseAlignSeqs(params->sequences[i].sequence, chimeraRefSeq, dummyA, dummy… in driver()
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