| /dports/biology/muscle/muscle-3.8.1551/ |
| H A D | profile.cpp | 34 void ProfileProfile(MSA &msa1, MSA &msa2, MSA &msaOut) in ProfileProfile()
95 MSA msa1; in Profile() local
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| H A D | objscore2.cpp | 41 SCORE ScoreSeqPairLetters(const MSA &msa1, unsigned uSeqIndex1, in ScoreSeqPairLetters()
115 SCORE ScoreSeqPairGaps(const MSA &msa1, unsigned uSeqIndex1, in ScoreSeqPairGaps()
307 SCORE ObjScoreDP(const MSA &msa1, const MSA &msa2, SCORE MatchScore[]) in ObjScoreDP()
376 const MSA &msa1 = *g_ptrPPScoreMSA1; in ObjScoreDP_Profs() local
470 SCORE ObjScoreXP(const MSA &msa1, const MSA &msa2) in ObjScoreXP()
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| H A D | aligntwomsas.cpp | 8 SCORE AlignTwoMSAs(const MSA &msa1, const MSA &msa2, MSA &msaOut, PWPath &Path, in AlignTwoMSAs()
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| H A D | profdb.cpp | 24 MSA msa1; in ProfDB() local
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| H A D | distpwkimura.cpp | 21 MSA msa1; in DistPWKimura() local
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| H A D | msa2.cpp | 296 void AssertMSAEqIgnoreCaseAndGaps(const MSA &msa1, const MSA &msa2) in AssertMSAEqIgnoreCaseAndGaps()
325 void AssertMSAEq(const MSA &msa1, const MSA &msa2) in AssertMSAEq()
470 void MSAAppend(MSA &msa1, const MSA &msa2) in MSAAppend()
495 void MSACat(const MSA &msa1, const MSA &msa2, MSA &msaCat) in MSACat()
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| H A D | ppscore.cpp | 33 MSA msa1; in PPScore() local
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| H A D | local.cpp | 34 MSA msa1; in Local() local
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| H A D | objscore.cpp | 28 MSA msa1; in ObjScore() local
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/ |
| H A D | profile.cpp | 36 void ProfileProfile(MSA &msa1, MSA &msa2, MSA &msaOut) in ProfileProfile()
99 MSA msa1; in Profile() local
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| H A D | aligntwomsas.cpp | 8 SCORE AlignTwoMSAs(const MSA &msa1, const MSA &msa2, MSA &msaOut, PWPath &Path, in AlignTwoMSAs()
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| H A D | profdb.cpp | 30 MSA msa1; in ProfDB() local
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| H A D | objscore2.cpp | 43 SCORE ScoreSeqPairLetters(const MSA &msa1, unsigned uSeqIndex1, in ScoreSeqPairLetters()
118 SCORE ScoreSeqPairGaps(const MSA &msa1, unsigned uSeqIndex1, in ScoreSeqPairGaps()
317 SCORE ObjScoreDP(const MSA &msa1, const MSA &msa2, SCORE MatchScore[]) in ObjScoreDP()
488 SCORE ObjScoreXP(const MSA &msa1, const MSA &msa2) in ObjScoreXP()
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| H A D | distpwkimura.cpp | 21 MSA msa1; in DistPWKimura() local
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| H A D | msa2.cpp | 308 void AssertMSAEqIgnoreCaseAndGaps(const MSA &msa1, const MSA &msa2) in AssertMSAEqIgnoreCaseAndGaps()
337 void AssertMSAEq(const MSA &msa1, const MSA &msa2) in AssertMSAEq()
501 void MSAAppend(MSA &msa1, const MSA &msa2) in MSAAppend()
525 void MSACat(const MSA &msa1, const MSA &msa2, MSA &msaCat) in MSACat()
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| H A D | ppscore.cpp | 32 MSA msa1; in PPScore() local
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| H A D | local.cpp | 37 MSA msa1; in Local() local
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| H A D | objscore.cpp | 31 MSA msa1; in ObjScore() local
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| /dports/biology/infernal/infernal-1.1.3/easel/miniapps/ |
| H A D | esl-alimap.c | 68 ESL_MSA *msa1 = NULL; /* multiple sequence alignment 1 */ in main() local
183 map_msas(const ESL_GETOPTS *go, char *errbuf, ESL_MSA *msa1, ESL_MSA *msa2, int **ret_msa1_to_msa2_… in map_msas()
463 map_sub_msas(const ESL_GETOPTS *go, char *errbuf, ESL_MSA *msa1, ESL_MSA *msa2, char **ret_msa1_to_… in map_sub_msas()
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| /dports/biology/hmmer/hmmer-3.3/easel/miniapps/ |
| H A D | esl-alimap.c | 68 ESL_MSA *msa1 = NULL; /* multiple sequence alignment 1 */ in main() local
183 map_msas(const ESL_GETOPTS *go, char *errbuf, ESL_MSA *msa1, ESL_MSA *msa2, int **ret_msa1_to_msa2_… in map_msas()
463 map_sub_msas(const ESL_GETOPTS *go, char *errbuf, ESL_MSA *msa1, ESL_MSA *msa2, char **ret_msa1_to_… in map_sub_msas()
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| /dports/biology/ugene/ugene-40.1/src/plugins/CoreTests/src/ |
| H A D | MsaObjectTests.cpp | 58 …MultipleSequenceAlignmentObject *msa1 = qobject_cast<MultipleSequenceAlignmentObject *>(objs1.firs… in report() local
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| /dports/biology/infernal/infernal-1.1.3/easel/ |
| H A D | esl_msafile_afa.c | 349 ESL_MSA *msa1 = NULL; in utest_goodfile() local
440 ESL_MSA *msa1, *msa2, *msa3, *msa4; in read_test_msas_digital() local
489 ESL_MSA *msa1, *msa2, *msa3, *msa4; in read_test_msas_text() local
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| H A D | esl_msafile_psiblast.c | 442 ESL_MSA *msa1 = NULL; in utest_goodfile() local
528 ESL_MSA *msa1, *msa2, *msa3, *msa4; in read_test_msas_digital() local
577 ESL_MSA *msa1, *msa2, *msa3, *msa4; in read_test_msas_text() local
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| /dports/biology/hmmer/hmmer-3.3/easel/ |
| H A D | esl_msafile_afa.c | 349 ESL_MSA *msa1 = NULL; in utest_goodfile() local
440 ESL_MSA *msa1, *msa2, *msa3, *msa4; in read_test_msas_digital() local
489 ESL_MSA *msa1, *msa2, *msa3, *msa4; in read_test_msas_text() local
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| H A D | esl_msafile_psiblast.c | 442 ESL_MSA *msa1 = NULL; in utest_goodfile() local
528 ESL_MSA *msa1, *msa2, *msa3, *msa4; in read_test_msas_digital() local
577 ESL_MSA *msa1, *msa2, *msa3, *msa4; in read_test_msas_text() local
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