| /dports/biology/clustal-omega/clustal-omega-1.2.4/src/squid/ |
| H A D | msa.c | 62 MSA *msa; in MSAAlloc() local
155 MSAExpand(MSA *msa) in MSAExpand()
250 MSAFree(MSA *msa) in MSAFree()
355 MSAAddComment(MSA *msa, char *s) in MSAAddComment()
561 MSAGetGC(MSA *msa, char *tag) in MSAGetGC()
662 MSAVerifyParse(MSA *msa) in MSAVerifyParse()
736 MSAVerifyParseDub(MSA *msa) in MSAVerifyParseDub()
980 MSA *msa = NULL; in MSAFileRead() local
1110 MSA *msa; in MSAFromAINFO() local
1226 MSAMingap(MSA *msa) in MSAMingap()
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| H A D | stockholm.c | 52 MSA *msa; in main() local
93 MSA *msa; in ReadStockholm() local
180 MSA *msa; in ReadDublin() local
257 WriteStockholm(FILE *fp, MSA *msa) in WriteStockholm()
275 WriteStockholmOneBlock(FILE *fp, MSA *msa) in WriteStockholmOneBlock()
479 parse_gf(MSA *msa, char *buf) in parse_gf()
544 parse_gs(MSA *msa, char *buf) in parse_gs()
587 parse_gc(MSA *msa, char *buf) in parse_gc()
616 parse_gr(MSA *msa, char *buf) in parse_gr()
689 parse_comment(MSA *msa, char *buf) in parse_comment()
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| H A D | phylip.c | 35 MSA *msa; in main() local
75 MSA *msa; in ReadPhylip() local
143 WritePhylip(FILE *fp, MSA *msa) in WritePhylip()
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| H A D | msf.c | 38 MSA *msa; in main() local
81 MSA *msa; in ReadMSF() local
242 WriteMSF(FILE *fp, MSA *msa) in WriteMSF()
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| /dports/biology/infernal/infernal-1.1.3/easel/ |
| H A D | esl_msa.c | 89 ESL_MSA *msa; in esl_msa_Create() local
136 esl_msa_Expand(ESL_MSA *msa) in esl_msa_Expand()
444 esl_msa_Sizeof(ESL_MSA *msa) in esl_msa_Sizeof()
505 esl_msa_Destroy(ESL_MSA *msa) in esl_msa_Destroy()
587 ESL_MSA *msa = NULL; in msa_create_mostly() local
814 ESL_MSA *msa; in esl_msa_CreateDigital() local
3050 esl_msa_Hash(ESL_MSA *msa) in esl_msa_Hash()
3330 ESL_MSA *msa = NULL; in esl_msa_Sample() local
3447 ESL_MSA *msa = NULL; in utest_Create() local
3478 ESL_MSA *msa = NULL; in utest_Destroy() local
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| H A D | esl_msaweight.c | 144 esl_msaweight_PB(ESL_MSA *msa) in esl_msaweight_PB()
476 msaweight_PB_txt(ESL_MSA *msa) in msaweight_PB_txt()
701 esl_msaweight_GSC(ESL_MSA *msa) in esl_msaweight_GSC()
850 esl_msaweight_BLOSUM(ESL_MSA *msa, double maxid) in esl_msaweight_BLOSUM()
950 esl_msaweight_IDFilter(const ESL_MSA *msa, double maxid, ESL_MSA **ret_newmsa) in esl_msaweight_IDFilter()
1158 msaweight_IDFilter_txt(const ESL_MSA *msa, double maxid, ESL_MSA **ret_newmsa) in msaweight_IDFilter_txt()
1259 ESL_MSA *msa; in main() local
1365 ESL_MSA *msa; in main() local
1452 do_GSC(ESL_ALPHABET *abc, ESL_MSA *msa, double *expect, char *msg) in do_GSC()
1470 do_PB(ESL_ALPHABET *abc, ESL_MSA *msa, double *expect, char *msg) in do_PB()
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| /dports/biology/hmmer/hmmer-3.3/easel/ |
| H A D | esl_msa.c | 89 ESL_MSA *msa; in esl_msa_Create() local
136 esl_msa_Expand(ESL_MSA *msa) in esl_msa_Expand()
444 esl_msa_Sizeof(ESL_MSA *msa) in esl_msa_Sizeof()
505 esl_msa_Destroy(ESL_MSA *msa) in esl_msa_Destroy()
587 ESL_MSA *msa = NULL; in msa_create_mostly() local
814 ESL_MSA *msa; in esl_msa_CreateDigital() local
3050 esl_msa_Hash(ESL_MSA *msa) in esl_msa_Hash()
3330 ESL_MSA *msa = NULL; in esl_msa_Sample() local
3447 ESL_MSA *msa = NULL; in utest_Create() local
3478 ESL_MSA *msa = NULL; in utest_Destroy() local
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| H A D | esl_msaweight.c | 144 esl_msaweight_PB(ESL_MSA *msa) in esl_msaweight_PB()
476 msaweight_PB_txt(ESL_MSA *msa) in msaweight_PB_txt()
701 esl_msaweight_GSC(ESL_MSA *msa) in esl_msaweight_GSC()
850 esl_msaweight_BLOSUM(ESL_MSA *msa, double maxid) in esl_msaweight_BLOSUM()
950 esl_msaweight_IDFilter(const ESL_MSA *msa, double maxid, ESL_MSA **ret_newmsa) in esl_msaweight_IDFilter()
1158 msaweight_IDFilter_txt(const ESL_MSA *msa, double maxid, ESL_MSA **ret_newmsa) in msaweight_IDFilter_txt()
1259 ESL_MSA *msa; in main() local
1365 ESL_MSA *msa; in main() local
1452 do_GSC(ESL_ALPHABET *abc, ESL_MSA *msa, double *expect, char *msg) in do_GSC()
1470 do_PB(ESL_ALPHABET *abc, ESL_MSA *msa, double *expect, char *msg) in do_PB()
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/hmmer2/ |
| H A D | msa.cpp | 64 MSA *msa; in MSAAlloc() local
117 MSAFree(MSA *msa) in MSAFree()
151 MSAMingap(MSA *msa) in MSAMingap()
183 MSANogap(MSA *msa) in MSANogap()
219 MSAShorterAlignment(MSA *msa, int *useme) in MSAShorterAlignment()
297 MSASmallerAlignment(MSA *msa, int *useme, MSA **ret_new) in MSASmallerAlignment()
364 MSASetSeqAccession(MSA *msa, int seqidx, char *acc) in MSASetSeqAccession()
382 MSASetSeqDescription(MSA *msa, int seqidx, char *desc) in MSASetSeqDescription()
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| /dports/biology/jalview/jalview/src/vamsas/objects/simple/ |
| H A D | MsaResult.java | 26 private vamsas.objects.simple.Alignment msa; field in MsaResult
36 public MsaResult(vamsas.objects.simple.Alignment msa) in MsaResult()
56 public void setMsa(vamsas.objects.simple.Alignment msa) in setMsa()
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| /dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
| H A D | build.c | 81 p7_Handmodelmaker(ESL_MSA *msa, P7_BUILDER *bld, P7_HMM **ret_hmm, P7_TRACE ***opt_tr) in p7_Handmodelmaker()
155 p7_Fastmodelmaker(ESL_MSA *msa, float symfrac, P7_BUILDER *bld, P7_HMM **ret_hmm, P7_TRACE ***opt_t… in p7_Fastmodelmaker()
223 do_modelmask( ESL_MSA *msa) in do_modelmask()
258 matassign2hmm(ESL_MSA *msa, int *matassign, P7_HMM **ret_hmm, P7_TRACE ***opt_tr) in matassign2hmm()
339 annotate_model(P7_HMM *hmm, int *matassign, ESL_MSA *msa) in annotate_model()
417 ESL_MSA *msa = NULL; in utest_basic() local
459 ESL_MSA *msa = NULL; in utest_fragments() local
586 ESL_MSA *msa = NULL; in main() local
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| H A D | tracealign.c | 99 ESL_MSA *msa = NULL; /* RETURN: new MSA */ in p7_tracealign_Seqs() local
168 ESL_MSA *msa = NULL; /* RETURN: new MSA */ in p7_tracealign_MSA() local
393 ESL_MSA *msa = NULL; /* resulting multiple alignment */ in p7_tracealign_getMSAandStats() local
606 ESL_MSA *msa = NULL; in make_digital_msa() local
708 ESL_MSA *msa = NULL; in make_text_msa() local
818 annotate_rf(ESL_MSA *msa, int M, const int *matuse, const int *matmap) in annotate_rf()
860 annotate_mm(ESL_MSA *msa, P7_HMM * hmm, const int *matuse, const int *matmap) in annotate_mm()
885 annotate_posterior_probability(ESL_MSA *msa, P7_TRACE **tr, const int *matmap, int M, int optflags) in annotate_posterior_probability()
1003 rejustify_insertions_digital(ESL_MSA *msa, const int *inserts, const int *matmap, const int *matuse… in rejustify_insertions_digital()
1043 rejustify_insertions_text(const ESL_ALPHABET *abc, ESL_MSA *msa, const int *inserts, const int *mat… in rejustify_insertions_text()
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| /dports/biology/hmmer/hmmer-3.3/src/ |
| H A D | build.c | 81 p7_Handmodelmaker(ESL_MSA *msa, P7_BUILDER *bld, P7_HMM **ret_hmm, P7_TRACE ***opt_tr) in p7_Handmodelmaker()
155 p7_Fastmodelmaker(ESL_MSA *msa, float symfrac, P7_BUILDER *bld, P7_HMM **ret_hmm, P7_TRACE ***opt_t… in p7_Fastmodelmaker()
223 do_modelmask( ESL_MSA *msa) in do_modelmask()
258 matassign2hmm(ESL_MSA *msa, int *matassign, P7_HMM **ret_hmm, P7_TRACE ***opt_tr) in matassign2hmm()
339 annotate_model(P7_HMM *hmm, int *matassign, ESL_MSA *msa) in annotate_model()
417 ESL_MSA *msa = NULL; in utest_basic() local
459 ESL_MSA *msa = NULL; in utest_fragments() local
586 ESL_MSA *msa = NULL; in main() local
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| /dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
| H A D | blast_psi_priv.c | 183 _PSIPackedMsaFree(_PSIPackedMsa* msa) in _PSIPackedMsaFree()
247 PrintMsaFP(FILE* fp, const PSIMsa* msa) in PrintMsaFP()
389 _PSIMsaFree(_PSIMsa* msa) in _PSIMsaFree()
948 _PSIPurgeBiasedSegments(_PSIPackedMsa* msa) in _PSIPurgeBiasedSegments()
961 s_PSIPurgeSelfHits(_PSIPackedMsa* msa) in s_PSIPurgeSelfHits()
991 _PSIUpdatePositionCounts(_PSIMsa* msa) in _PSIUpdatePositionCounts()
1751 const _PSIMsa* msa,
1876 const _PSIMsa* msa, /* [in] */
1932 _PSISpreadGapWeights(const _PSIMsa* msa,
2071 _PSIComputeFreqRatios(const _PSIMsa* msa,
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
| H A D | blast_psi_priv.c | 183 _PSIPackedMsaFree(_PSIPackedMsa* msa) in _PSIPackedMsaFree()
247 PrintMsaFP(FILE* fp, const PSIMsa* msa) in PrintMsaFP()
389 _PSIMsaFree(_PSIMsa* msa) in _PSIMsaFree()
948 _PSIPurgeBiasedSegments(_PSIPackedMsa* msa) in _PSIPurgeBiasedSegments()
961 s_PSIPurgeSelfHits(_PSIPackedMsa* msa) in s_PSIPurgeSelfHits()
991 _PSIUpdatePositionCounts(_PSIMsa* msa) in _PSIUpdatePositionCounts()
1751 const _PSIMsa* msa,
1876 const _PSIMsa* msa, /* [in] */
1932 _PSISpreadGapWeights(const _PSIMsa* msa,
2071 _PSIComputeFreqRatios(const _PSIMsa* msa,
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
| H A D | blast_psi_priv.c | 183 _PSIPackedMsaFree(_PSIPackedMsa* msa) in _PSIPackedMsaFree()
247 PrintMsaFP(FILE* fp, const PSIMsa* msa) in PrintMsaFP()
389 _PSIMsaFree(_PSIMsa* msa) in _PSIMsaFree()
948 _PSIPurgeBiasedSegments(_PSIPackedMsa* msa) in _PSIPurgeBiasedSegments()
961 s_PSIPurgeSelfHits(_PSIPackedMsa* msa) in s_PSIPurgeSelfHits()
991 _PSIUpdatePositionCounts(_PSIMsa* msa) in _PSIUpdatePositionCounts()
1751 const _PSIMsa* msa,
1876 const _PSIMsa* msa, /* [in] */
1932 _PSISpreadGapWeights(const _PSIMsa* msa,
2071 _PSIComputeFreqRatios(const _PSIMsa* msa,
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| /dports/biology/muscle/muscle-3.8.1551/ |
| H A D | validateids.cpp | 10 void SetMuscleInputMSA(MSA &msa) in SetMuscleInputMSA()
20 void ValidateMuscleIdsSeqVect(const MSA &msa) in ValidateMuscleIdsSeqVect()
33 void ValidateMuscleIdsMSA(const MSA &msa) in ValidateMuscleIdsMSA()
55 void ValidateMuscleIds(const MSA &msa) in ValidateMuscleIds()
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| H A D | treefrommsa.cpp | 8 static void SaveMSADist(const MSA &msa, MSADist &d, const char *FileName) in SaveMSADist()
25 static void TreeFromMSA_NJ(const MSA &msa, Tree &tree, CLUSTER Cluster, in TreeFromMSA_NJ()
60 static void TreeFromMSA_UPGMA(const MSA &msa, Tree &tree, CLUSTER Cluster, in TreeFromMSA_UPGMA()
89 void TreeFromMSA(const MSA &msa, Tree &tree, CLUSTER Cluster, in TreeFromMSA()
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| H A D | scoredist.cpp | 26 static double Sigma(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2, in Sigma()
47 static double Sigma_N(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2) in Sigma_N()
56 static double Sigma_U(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2, in Sigma_U()
65 static double Sigma_UN(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2) in Sigma_UN()
73 double GetScoreDist(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2) in GetScoreDist()
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| H A D | muscleout.cpp | 6 static void DoOutput(MSA &msa) in DoOutput()
104 void MuscleOutput(MSA &msa) in MuscleOutput()
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/ |
| H A D | treefrommsa.cpp | 8 static void SaveMSADist(const MSA &msa, MSADist &d, const char *FileName) in SaveMSADist()
25 static void TreeFromMSA_NJ(const MSA &msa, Tree &tree, CLUSTER Cluster, in TreeFromMSA_NJ()
60 static void TreeFromMSA_UPGMA(const MSA &msa, Tree &tree, CLUSTER Cluster, in TreeFromMSA_UPGMA()
89 void TreeFromMSA(const MSA &msa, Tree &tree, CLUSTER Cluster, in TreeFromMSA()
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| H A D | scoredist.cpp | 24 static double Sigma(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2, in Sigma()
46 static double Sigma_N(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2) in Sigma_N()
55 static double Sigma_U(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2, in Sigma_U()
64 static double Sigma_UN(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2) in Sigma_UN()
72 double GetScoreDist(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2) in GetScoreDist()
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| H A D | validateids.cpp | 9 void SetMuscleInputMSA(MSA &msa) in SetMuscleInputMSA()
19 void ValidateMuscleIdsSeqVect(const MSA &msa) in ValidateMuscleIdsSeqVect()
33 void ValidateMuscleIdsMSA(const MSA &msa) in ValidateMuscleIdsMSA()
57 void ValidateMuscleIds(const MSA &msa) in ValidateMuscleIds()
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| H A D | muscleout.cpp | 7 static void DoOutput(MSA &msa) in DoOutput()
106 void MuscleOutput(MSA &msa) in MuscleOutput()
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| /dports/science/nwchem-data/nwchem-7.0.2-release/src/qhop/ |
| H A D | qhop_pindex.F | 1 subroutine qhop_pindex(msa,nsa,isgm,ihop,ips) argument
19 subroutine qhop_pindex2(msa,nsa,isgm,ihop,ips, argument
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