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Searched refs:seqarray (Results 1 – 9 of 9) sorted by relevance

/dports/biology/p5-BioPerl/BioPerl-1.7.7/bin/
H A Dbp_gccalc67 my @seqarray = split('',$seq);
69 foreach my $base (@seqarray) {
73 my $len = $#seqarray+1;
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Align/
H A DDNAStatistics.pm1382 my @seqarray = @$seq_ref;
1386 for (my $i = 0; $i < scalar @seqarray; $i++) {
1387 for (my $j = $i +1; $j<scalar @seqarray; $j++ ){
1389 if (length($seqarray[$i]{'seq'}) != length($seqarray[$j]{'seq'})) {
1394 my $syn_site_count = count_syn_sites($seqarray[$i]{'seq'}, $synsites);
1395 my $syn_site_count2 = count_syn_sites($seqarray[$j]{'seq'}, $synsites);
1397 …my ($syn_count, $non_syn_count, $gap_cnt) = analyse_mutations($seqarray[$i]{'seq'}, $seqarray[$j]{…
1422 my $d_nc_var = jk_var($nc_prop, length ($seqarray[$i]{'seq'}) - $gap_cnt);
1435 Seq1 => $seqarray[$i]{'id'},
1436 Seq2 => $seqarray[$j]{'id'},
[all …]
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/PerlLib/
H A DPWM.pm273 my @seqarray = split(//, $target_sequence);
286 my $char = $seqarray[$i];
348 my @seqarray = split(//, $target_sequence);
362 my $char = $seqarray[$i];
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/util/PWM/
H A Dbuild_atgPWM_+-.pl172 my @seqarray = split(//, $sequence);
183 my $feature_seq = &get_feature_seq(\@seqarray, $start_pos);
/dports/biology/jalview/jalview/src/jalview/ws/jws1/
H A DSeqSearchWSThread.java110 vamsas.objects.simple.Sequence[] seqarray = (valid) in prepareInput() local
126 seqarray[n] = new vamsas.objects.simple.Sequence(); in prepareInput()
127 seqarray[n].setId(newname); in prepareInput()
128 seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString() in prepareInput()
149 this.seqs.setSeqs(seqarray); in prepareInput()
H A DMsaWSThread.java110 vamsas.objects.simple.Sequence[] seqarray = (valid) in prepareInput() local
124 seqarray[n] = new vamsas.objects.simple.Sequence(); in prepareInput()
125 seqarray[n].setId(newname); in prepareInput()
126 seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString() in prepareInput()
143 this.seqs.setSeqs(seqarray); in prepareInput()
/dports/math/py-pynleq2/pysces-0.9.8/pysces/
H A DPyscesParScan.py289 def Analyze(partition,seqarray,GenOrder,mode,UserOutputList,mod): argument
310 invalid_state_list_idx.append(seqarray[i])
/dports/biology/py-PySCeS/pysces-1.0.0/pysces/
H A DPyscesParScan.py332 def Analyze(partition, seqarray, GenOrder, mode, UserOutputList, mod): argument
353 invalid_state_list_idx.append(seqarray[i])
/dports/graphics/blender/blender-2.91.0/source/blender/sequencer/intern/
H A Dsequencer.c702 Sequence ***seqarray, in seq_array() argument
708 *seqarray = NULL; in seq_array()
726 *seqarray = array = MEM_mallocN(sizeof(Sequence *) * (*tot), "SeqArray"); in seq_array()