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/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Ddistmat.c57 ajint nseqs);
84 ajint nseqs; in main() local
155 if(nseqs<2) in main()
275 for(j=0;j<nseqs;++j) in distmat_Tamura()
292 for(j=0; j<nseqs; j++) in distmat_Tamura()
520 ajint nseqs) in distmat_KimuraProt() argument
643 for(j=0;j<nseqs;++j) in distmat_calc_match()
808 for(j=0;j<nseqs;++j) in distmat_TajimaNei()
821 for(j=0;j<nseqs;j++) in distmat_TajimaNei()
1064 for(i=0;i<nseqs;i++) in distmat_JinNei()
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H A Dcons.c47 ajint nseqs; in main() local
72 nseqs = ajSeqsetGetSize(seqset); in main()
73 if(nseqs<2) in main()
74 ajFatal("Insufficient sequences (%d) to create a matrix",nseqs); in main()
77 for(i=0;i<nseqs;++i) /* check sequences are same length */ in main()
91 embConsCalc (seqset, cmpmatrix, nseqs, mlen, in main()
H A Dconsambig.c47 ajint nseqs; in main() local
63 nseqs = ajSeqsetGetSize(seqset); in main()
64 if(nseqs<2) in main()
65 ajFatal("Insufficient sequences (%d) to create a matrix",nseqs); in main()
68 for(i=0;i<nseqs;++i) /* check sequences are same length */ in main()
H A Dsizeseq.c39 ajuint nseqs; in main() local
50 nseqs = ajSeqsetGetSize(seqset); in main()
54 for(i=nseqs; i>0; i--) in main()
59 for(i=0; i<nseqs; i++) in main()
H A Daligncopypair.c46 ajuint nseqs; in main() local
60 nseqs = ajSeqsetGetSize(seqset); in main()
70 imax = nseqs-1; in main()
73 for(j=i+1;j<nseqs;j++) in main()
H A Dprophecy.c137 ajuint nseqs; in prophecy_simple_matrix() local
151 nseqs = ajSeqsetGetSize(seqset); in prophecy_simple_matrix()
152 if(nseqs<2) in prophecy_simple_matrix()
158 for(i=0;i<nseqs;++i) in prophecy_simple_matrix()
169 for(i=0;i<nseqs;++i) in prophecy_simple_matrix()
261 ajuint nseqs; in prophecy_gribskov_profile() local
304 for(j=0;j<nseqs;++j) in prophecy_gribskov_profile()
358 for(j=0;j<nseqs;++j) in prophecy_gribskov_profile()
495 ajuint nseqs; in prophecy_henikoff_profile() local
535 for(j=0;j<nseqs;++j) in prophecy_henikoff_profile()
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/dports/biology/clustal-omega/clustal-omega-1.2.4/src/clustal/
H A Dseq.c102 msa = MSAAlloc(prMSeq->nseqs, in AliStat()
268 assert(i<prMSeq->nseqs && j<prMSeq->nseqs); in SeqSwap()
503 if (0 == prMSeq->nseqs) { in ReadSequences()
543 prMSeq->sqinfo[prMSeq->nseqs].name, prMSeq->sqinfo[prMSeq->nseqs].len, in ReadSequences()
551 prMSeq->nseqs++; in ReadSequences()
718 (*prMSeq)->nseqs = 0; in NewMSeq()
751 (*prMSeqDest_p)->nseqs = prMSeqSrc->nseqs; in CopyMSeq()
857 (*mseq)->nseqs = 0; in FreeMSeq()
1124 if (1 == prMSeq->nseqs) { in SeqsAreAligned()
1255 (*prMSeqDest_p)->nseqs++; in AddSeq()
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H A Dmbed.c322 assert(iNumSeeds>0 && iNumSeeds<=prMSeq->nseqs); in SeqToVec()
379 0, iNumSeeds, 0, prMSeq->nseqs, in SeqToVec()
493 iNumSeeds, prMSeq->nseqs); in SeedSelection()
511 iNumSeeds, prMSeq->nseqs); in SeedSelection()
1202 iNumSeeds = (int) NUMBER_OF_SEEDS(prMSeq->nseqs); in Mbed()
1203 if (iNumSeeds >= prMSeq->nseqs) { in Mbed()
1205 iNumSeeds = prMSeq->nseqs-1; in Mbed()
1221 for (iI=0; iI<prMSeq->nseqs; iI++) { in Mbed()
1440 prSubClusterMSeq->nseqs = iNSeqInCluster; in Mbed()
1483 0, prSubClusterMSeq->nseqs, 0, prSubClusterMSeq->nseqs, in Mbed()
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H A Dhhalign_wrapper.c108 for (iS = 0; iS < mseq->nseqs; iS++){ in SanitiseUnknown()
163 for (iS = 0; iS < mseq->nseqs; iS++){ in TranslateUnknown2Ambiguity()
281 assert(prMSeq->nseqs > iProfProfSeparator); in ReAttachLeadingGaps()
284 iSize2 = prMSeq->nseqs - iProfProfSeparator; in ReAttachLeadingGaps()
310 for (i = 0; i < prMSeq->nseqs; i++){ in ReAttachLeadingGaps()
509 int iNseq = prMSeq->nseqs; /* number of sequences */ in PosteriorProbabilities()
658 for (iI = 0; iI < prMSeq->nseqs; iI++){ in PileUp()
671 for (iI = 1; iI < MIN(prMSeq->nseqs, iClustersize); iI++){ in PileUp()
700 while (iI < prMSeq->nseqs){ in PileUp()
986 int iSizeProf2 = prMSeq->nseqs - iProfProfSeparator; in HHalignWrapper()
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/dports/biology/hhsuite/hh-suite-3.3.0/src/cs/
H A Dalignment-inl.h37 Resize(nseqs, ncols); in Alignment()
38 for (size_t k = 0; k < nseqs; ++k) in Alignment()
65 const size_t nseqs = seqs.size(); in Init() local
446 if (nseqs == 0 || ncols == 0) in Resize()
450 seqs_.Resize(ncols, nseqs); in Resize()
454 headers_.resize(nseqs); in Resize()
611 Vector<int> mapping(nseqs()); in Rearrange()
699 const size_t nseqs = ali.nseqs(); in GlobalWeightsAndDiversity() local
739 Normalize(&wg[0], nseqs); in GlobalWeightsAndDiversity()
778 const size_t nseqs = ali.nseqs(); in PositionSpecificWeightsAndDiversity() local
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/dports/biology/mothur/mothur-1.46.1/source/read/
H A Dreadphylip.cpp36 int square, nseqs; square = 0; in read() local
44 else { convert(numTest, nseqs); } in read()
49 list = new ListVector(nseqs); in read()
74 DMatrix->resize(nseqs); in read()
80 for(int i=1;i<nseqs;i++){ in read()
131 int index = nseqs; in read()
133 for(int i=1;i<nseqs;i++){ in read()
236 DMatrix->resize(nseqs); in read()
242 for(int i=1;i<nseqs;i++){ in read()
302 int index = nseqs; in read()
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H A Dreadcluster.cpp94 list = new ListVector(nseqs); in convertPhylip2Column()
108 for(int i=0;i<nseqs;i++){ in convertPhylip2Column()
121 for(int i=1;i<nseqs;i++){ in convertPhylip2Column()
163 for(int i=1;i<nseqs;i++){ in convertPhylip2Column()
170 for(int j=0;j<nseqs;j++){ in convertPhylip2Column()
185 for(int j=0;j<nseqs;j++){ in convertPhylip2Column()
261 int square, nseqs; in convertPhylip2Column() local
286 for(int i=0;i<nseqs;i++){ in convertPhylip2Column()
299 for(int i=1;i<nseqs;i++){ in convertPhylip2Column()
340 for(int i=1;i<nseqs;i++){ in convertPhylip2Column()
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/dports/biology/emboss/EMBOSS-6.6.0/nucleus/
H A Dembcons.c63 ajint nseqs, ajint mlen,float fplural,float setcase, in embConsCalc() argument
94 AJCNEW(seqcharptr,nseqs); in embConsCalc()
105 for(i=0;i<nseqs;i++) /* get sequence as string */ in embConsCalc()
118 for(i=0;i<nseqs;i++) in embConsCalc()
121 for(i=0;i<nseqs;i++) /* generate score for columns */ in embConsCalc()
128 for(j=i+1;j<nseqs;j++) in embConsCalc()
150 for(i=0;i<nseqs;i++) in embConsCalc()
164 for(j=0;j<nseqs;j++) in embConsCalc()
188 for(i=0;i<nseqs;i++) in embConsCalc()
196 for(i=0;i<nseqs;i++) in embConsCalc()
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/dports/biology/mothur/mothur-1.46.1/source/
H A Dclusterclassic.cpp54 list = new ListVector(nseqs); in readPhylipFile()
63 dMatrix.resize(nseqs); in readPhylipFile()
72 for(int i=0;i<nseqs;i++){ in readPhylipFile()
90 for(int i=1;i<nseqs;i++){ in readPhylipFile()
149 int index = nseqs; in readPhylipFile()
151 for(int i=1;i<nseqs;i++){ in readPhylipFile()
157 for(int j=0;j<nseqs;j++){ in readPhylipFile()
245 dMatrix.resize(nseqs); in readPhylipFile()
330 int index = nseqs; in readPhylipFile()
417 for(int i=1;i<nseqs;i++){ in getSmallCell()
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H A Dvenn.cpp61 if (nseqs) { in getPic()
126 if (nseqs) { in getPic()
186 if (nseqs) { in getPic()
275 if (nseqs) { in getPic()
444 if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedVal); } in getPic()
566 if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); } in getPic()
573 if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB); } in getPic()
580 if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsC); } in getPic()
818 if (nseqs) { in getPic()
879 if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); } in getPic()
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/dports/biology/vt/vt-0.57721/
H A Dprofile_chrom.cpp219 int32_t nseqs; in print_pdf() local
220 const char** seq_names = bcf_hdr_seqnames(odr->hdr, &nseqs); in print_pdf()
221 int32_t* len = bcf_hdr_seqlen(odr->hdr, &nseqs); in print_pdf()
223 for (int32_t i=0; i<nseqs; ++i) in print_pdf()
240 if(nseqs) free(seq_names); in print_pdf()
241 if(nseqs) free(len); in print_pdf()
280 int32_t nseqs; in print_stats() local
284 int32_t* len = bcf_hdr_seqlen(odr->hdr, &nseqs); in print_stats()
287 for (int32_t i=0; i<nseqs; ++i) in print_stats()
305 if(nseqs) free(seq_names); in print_stats()
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H A Dbcf_synced_reader.cpp114 int32_t nseqs; in BCFSyncedReader() local
115 const char ** seqnames = bcf_hdr_seqnames(hdrs[i], &nseqs); in BCFSyncedReader()
117 if (nseqs0==0 || nseqs==0 || nseqs0!=nseqs) in BCFSyncedReader()
123 for (size_t j=0; j<nseqs; ++j) in BCFSyncedReader()
151 int32_t nseqs = 0; in add_interval() local
156 seq_names = bcf_hdr_seqnames(hdrs[i], &nseqs); in add_interval()
157 for (size_t j=0; j<nseqs; ++j) in add_interval()
171 seq_names = tbx_seqnames(tbxs[i], &nseqs); in add_interval()
172 for (size_t j=0; j<nseqs; ++j) in add_interval()
/dports/biology/emboss/EMBOSS-6.6.0/jemboss/org/emboss/jemboss/editor/
H A DConsensus.java126 int nseqs = seqs.size(); in calculateCons() local
138 float score[] = new float[nseqs]; in calculateCons()
158 for(i=0;i<nseqs;i++) in calculateCons()
161 for(i=0;i<nseqs;i++) /* generate score for columns */ in calculateCons()
168 for(j=i+1;j<nseqs;j++) in calculateCons()
184 for(i=0;i<nseqs;i++) in calculateCons()
197 for(i=0;i<nseqs;i++) /* find +ve matches in the column */ in calculateCons()
215 for(j=0;j<nseqs;j++) in calculateCons()
231 for(i=0;i<nseqs;i++) in calculateCons()
243 for(i=0;i<nseqs;i++) in calculateCons()
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/dports/biology/mothur/mothur-1.46.1/source/datastructures/
H A Doptimatrix.cpp35 long long nseqs; in readPhylip() local
49 else { convert(numTest, nseqs); } in readPhylip()
58 vector<bool> singleton; singleton.resize(nseqs, true); in readPhylip()
62 for(long long i=1;i<nseqs;i++){ in readPhylip()
80 for(long long i=1;i<nseqs;i++){ in readPhylip()
85 for(long long j=0;j<nseqs;j++){ in readPhylip()
123 in >> nseqs >> name; in readPhylip()
133 for(long long i=1;i<nseqs;i++){ in readPhylip()
158 long long index = nseqs; in readPhylip()
162 for(long long i=1;i<nseqs;i++){ in readPhylip()
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/dports/biology/tRNAscan-SE/tRNAscan-SE-2.0/src/
H A Dseqstat_main.c40 int nseqs; in main() local
95 nseqs = 0; in main()
106 nseqs++; in main()
112 printf("Number of sequences: %d\n", nseqs); in main()
116 printf("Average length: %.1f\n", (float) total / (float) nseqs); in main()
/dports/biology/emboss/EMBOSS-6.6.0/jemboss/org/emboss/jemboss/gui/form/
H A DListFilePanel.java119 int nseqs = 0; in getArrayListFile() local
123 nseqs++; in getArrayListFile()
126 String list[] = new String[nseqs]; in getArrayListFile()
172 int nseqs = 0; in getSequence() local
177 nseqs++; in getSequence()
178 if(nseqs == n) in getSequence()
/dports/biology/jalview/jalview/test/jalview/io/
H A DNewickFileTests.java127 Vector<SequenceNode> oseqs, nseqs; in testTreeIO() local
137 nseqs = new TreeModel(new SequenceI[0], null, nf_regen) in testTreeIO()
141 nseqs.size() > 0); in testTreeIO()
142 SequenceI[] nsqs = new SequenceI[nseqs.size()]; in testTreeIO()
143 for (int i = 0, iSize = nseqs.size(); i < iSize; i++) in testTreeIO()
145 nsqs[i] = (SequenceI) nseqs.get(i).element(); in testTreeIO()
157 for (int i = 0, iSize = nseqs.size(); i < iSize; i++) in testTreeIO()
/dports/biology/mothur/mothur-1.46.1/source/commands/
H A Dremovedistscommand.cpp186 int square, nseqs; in readPhylip() local
196 else { convert(numTest, nseqs); } in readPhylip()
209 for(int i=0;i<nseqs;i++){ in readPhylip()
222 for(int i=1;i<nseqs;i++){ in readPhylip()
234 for(int i=1;i<nseqs;i++){ in readPhylip()
238 for(int j=0;j<nseqs;j++){ in readPhylip()
257 out << (nseqs-names.size()) << endl; in readPhylip()
262 for(int i=0;i<nseqs;i++){ in readPhylip()
281 for(int i=0;i<nseqs;i++){ in readPhylip()
289 for(int j=0;j<nseqs;j++){ in readPhylip()
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H A Dgetdistscommand.cpp185 int square, nseqs; square = 0; in readPhylip() local
195 else { convert(numTest, nseqs); } in readPhylip()
207 for(int i=0;i<nseqs;i++){ in readPhylip()
220 for(int i=1;i<nseqs;i++){ in readPhylip()
232 for(int i=1;i<nseqs;i++){ in readPhylip()
236 for(int j=0;j<nseqs;j++){ in readPhylip()
259 for(int i=0;i<nseqs;i++){ in readPhylip()
278 for(int i=0;i<nseqs;i++){ in readPhylip()
286 for(int j=0;j<nseqs;j++){ in readPhylip()
311 in3 >> nseqs; util.gobble(in3); in readPhylip()
/dports/biology/mothur/mothur-1.46.1/source/clearcut/
H A Dfasta.cpp309 long int bufsize, nseqs = NJ_INITIAL_NSEQS; in NJ_read_fasta() local
431 if(seq == nseqs) { in NJ_read_fasta()
435 nseqs *= 2; in NJ_read_fasta()
437 alignment->titles = (char **)realloc(alignment->titles, nseqs*sizeof(char *)); in NJ_read_fasta()
443 alignment->data = (char *)realloc(alignment->data, alignment->length*nseqs*sizeof(char)); in NJ_read_fasta()
488 nseqs = NJ_INITIAL_NSEQS; in NJ_read_fasta()
489 alignment->data = (char *)calloc(alignment->length*nseqs, sizeof(char)); in NJ_read_fasta()

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