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Searched refs:seqpos (Results 1 – 25 of 54) sorted by relevance

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/dports/biology/wise/wise2.4.1/src/models/
H A Dtransregion.dy217 int seqpos;
249 for(seqpos = tfms->match[0]->start,motifpos = 0;seqpos < end && motifpos < tfms->len;) {
252 last_covered_base = seqpos;
253 …for(seq_trial = seqpos, motif_trial = motifpos; seq_trial < end && seq_trial - seqpos < tfrp->min_…
270 if( seq_trial - seqpos < tfrp->min_window ) {
277 if( (double) covered_bases / (double) (seq_trial - seqpos) < tfrp->min_density ) {
282 seqpos = tfms->match[motifpos]->start;
309 /* we have a match! from seqpos to seq_trial and from motifpos to motiftrial */
312 region->start = seqpos;
314 region->density = (double) covered_bases / (double) (seq_trial - seqpos);
[all …]
H A Dtransregion.c187 int seqpos; in new_window_TransFactorRegionSet() local
219 for(seqpos = tfms->match[0]->start,motifpos = 0;seqpos < end && motifpos < tfms->len;) { in new_window_TransFactorRegionSet()
222 last_covered_base = seqpos; in new_window_TransFactorRegionSet()
223 …for(seq_trial = seqpos, motif_trial = motifpos; seq_trial < end && seq_trial - seqpos < tfrp->min_… in new_window_TransFactorRegionSet()
240 if( seq_trial - seqpos < tfrp->min_window ) { in new_window_TransFactorRegionSet()
247 if( (double) covered_bases / (double) (seq_trial - seqpos) < tfrp->min_density ) { in new_window_TransFactorRegionSet()
252 seqpos = tfms->match[motifpos]->start; in new_window_TransFactorRegionSet()
282 region->start = seqpos; in new_window_TransFactorRegionSet()
284 region->density = (double) covered_bases / (double) (seq_trial - seqpos); in new_window_TransFactorRegionSet()
295 seqpos = tfms->match[motifpos]->start; in new_window_TransFactorRegionSet()
/dports/biology/ugene/ugene-40.1/data/workflow_samples/NGS/cistrome/
H A Dchip_seq.uwl24 seqpos-id {
25 type:seqpos-id;
96 macs-id.out-data->seqpos-id.in-data
131 seqpos-id.output-dir {
189 seqpos-id {
403 seqpos-id.assembly {
405 seqpos-id.de_novo {
407 seqpos-id.motif_db {
409 seqpos-id.reg_width {
411 seqpos-id.p_val {
[all …]
H A Dchip_seq_with_control.uwl24 seqpos-id {
25 type:seqpos-id;
144 macs-id.out-data->seqpos-id.in-data
182 seqpos-id.output-dir {
245 seqpos-id {
468 seqpos-id.assembly {
470 seqpos-id.de_novo {
472 seqpos-id.motif_db {
474 seqpos-id.reg_width {
476 seqpos-id.p_val {
[all …]
/dports/biology/wise/wise2.4.1/src/other_programs/
H A Dorthoset.dy52 OrthoSeqPos * seqpos !link
301 OrthoSeqPos * seqpos;
318 if( strcmp(owl->w[j]->seqpos->seq_name,owl->w[j-1]->seqpos->seq_name) != 0 ) {
321 if( owl->w[j-1]->seqpos->end + p->max_internode_size < owl->w[j]->seqpos->start ) {
376 seqpos->seq_name = stringalloc(owl->w[j-1]->seqpos->seq_name);
377 seqpos->start = owl->w[j-1]->seqpos->end;
378 seqpos->end = owl->w[j]->seqpos->start;
379 seqpos->strand = strand;
381 add_OrthoLink(link,seqpos);
400 t = strcmp(one->seqpos->seq_name,two->seqpos->seq_name);
[all …]
/dports/misc/py-mxnet/incubator-mxnet-1.9.0/src/operator/
H A Dsequence_mask.cu39 const index_t seqpos = static_cast<int>(idx[batch]); in Map() local
41 if (seq >= seqpos) { in Map()
55 const index_t seqpos = static_cast<int>(idx[batch]); in Map() local
57 if (seq >= seqpos) { in Map()
H A Dsequence_mask.cc37 const index_t seqpos = static_cast<int>(idx[batch]); in Map() local
39 for (index_t s = seqpos; s < max_s_len; ++s) { in Map()
55 const index_t seqpos = static_cast<int>(idx[batch]); in Map() local
57 for (index_t s = seqpos; s < max_s_len; ++s) { in Map()
H A Dsequence_last-inl.h72 const index_t seqpos = static_cast<index_t>(idx[opos[0]]) - 1; in Map() local
73 const index_t ipos = seqpos * offset1 + opos[0] * offset2 + opos[1]; in Map()
84 const index_t seqpos = static_cast<index_t>(idx[opos[0]]) - 1; in Map() local
85 const index_t ipos = seqpos * offset1 + opos[0] * offset2 + opos[1]; in Map()
/dports/misc/mxnet/incubator-mxnet-1.9.0/src/operator/
H A Dsequence_mask.cu39 const index_t seqpos = static_cast<int>(idx[batch]); in Map() local
41 if (seq >= seqpos) { in Map()
55 const index_t seqpos = static_cast<int>(idx[batch]); in Map() local
57 if (seq >= seqpos) { in Map()
H A Dsequence_mask.cc37 const index_t seqpos = static_cast<int>(idx[batch]); in Map() local
39 for (index_t s = seqpos; s < max_s_len; ++s) { in Map()
55 const index_t seqpos = static_cast<int>(idx[batch]); in Map() local
57 for (index_t s = seqpos; s < max_s_len; ++s) { in Map()
H A Dsequence_last-inl.h72 const index_t seqpos = static_cast<index_t>(idx[opos[0]]) - 1; in Map() local
73 const index_t ipos = seqpos * offset1 + opos[0] * offset2 + opos[1]; in Map()
84 const index_t seqpos = static_cast<index_t>(idx[opos[0]]) - 1; in Map() local
85 const index_t ipos = seqpos * offset1 + opos[0] * offset2 + opos[1]; in Map()
/dports/biology/cdbfasta/cdbfasta/
H A Dcdbyank.cpp198 int seqpos=0; in fetch_record() local
204 seqpos++; in fetch_record()
205 if (seqpos>=r_start && seqpos<=r_end) { in fetch_record()
208 if (linelen==60 || seqpos==r_end) { in fetch_record()
212 if (seqpos==r_end) break; in fetch_record()
241 int seqpos=1; in fetch_record() local
243 while (reclen-- && read(fdb, &c, 1)==1 && seqpos<=r_end) { in fetch_record()
245 if (seqpos>=r_start) { in fetch_record()
246 int written=seqpos-r_start; in fetch_record()
251 seqpos++; in fetch_record()
/dports/biology/canu/canu-2.2/src/utgcns/libNDalign/
H A DNDalign.C281 for (int32 seqpos=bgn; (seqpos < end) && (_aStr[seqpos] != 0); seqpos++) { in fastFindMersA() local
285 mer |= acgtToBit[_aStr[seqpos]]; in fastFindMersA()
286 val |= acgtToVal[_aStr[seqpos]]; in fastFindMersA()
302 _aMap[mer] = seqpos + 1 - _merSize; in fastFindMersA()
330 for (int32 seqpos=bgn; (seqpos < end) && (_bStr[seqpos] != 0); seqpos++) { in fastFindMersB() local
334 mer |= acgtToBit[_bStr[seqpos]]; in fastFindMersB()
335 val |= acgtToVal[_bStr[seqpos]]; in fastFindMersB()
349 int32 bpos = seqpos + 1 - _merSize; in fastFindMersB()
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Durkptpf.c1356 seqpos++; in PatternMatchX()
1372 seqpos++; in PatternMatchX()
1428 seqpos++; in PatternMatchX()
1447 seqpos--; in PatternMatchX()
1472 seqpos++; in PatternMatchX()
2002 seqpos++; in ProfileMatchX()
2033 seqpos--; in ProfileMatchX()
2045 seqpos++; in ProfileMatchX()
2078 seqpos++; in ProfileMatchXInt()
2111 seqpos--; in ProfileMatchXInt()
[all …]
H A Durkptpf.h122 extern SeqAlignPtr PatternMatch (Uint1Ptr seq, Int4 seqpos, Uint1 strand,
145 extern SeqAlignPtr ProfileMatch (Uint1Ptr seq, Int4 seqpos, FloatHi cutoff,
/dports/biology/jalview/jalview/src/jalview/structure/
H A DStructureMapping.java107 public int getAtomNum(int seqpos) in getAtomNum() argument
109 int[] resNumAtomMap = mapping.get(seqpos); in getAtomNum()
126 public int getPDBResNum(int seqpos) in getPDBResNum() argument
128 int[] resNumAtomMap = mapping.get(seqpos); in getPDBResNum()
/dports/games/enygma/enigma-1.04/
H A Dsavefile.c30 int seqpos = 0; in savepos_load() local
79 seqpos = 0; in savepos_load()
85 if (len > state->sequence_size - seqpos) in savepos_load()
86 len = state->sequence_size - seqpos; in savepos_load()
88 memcpy(state->sequence + seqpos, p, len); in savepos_load()
89 seqpos += len; in savepos_load()
/dports/editors/fte/fte/src/
H A Dcon_slang.cpp475 unsigned seqpos = 1; in parseEsc() local
479 while (seqpos < 7 && (seq[seqpos] = (char)getkey(0))) { in parseEsc()
480 if ((unsigned char)seq[seqpos] < ' ') { in parseEsc()
481 SLang_ungetkey((unsigned char)seq[seqpos]); in parseEsc()
484 seqpos++; in parseEsc()
486 seq[seqpos] = 0; in parseEsc()
489 if (seqpos == 5 && seq[0] == '[' && seq[1] == 'M') { in parseEsc()
/dports/audio/deadbeef/deadbeef-0.7.2/plugins/adplug/adplug/
H A Djbm.cpp141 spos = voice[c].seqpos; in update()
157 spos = voice[c].seqpos = sequences[voice[c].seqno]; in update()
174 voice[c].seqpos = spos; in update()
204 voice[c].seqpos = sequences[voice[c].seqno]; in rewind()
H A Djbm.h63 unsigned short trkpos, trkstart, seqpos; member
/dports/audio/libadplug/adplug-adplug-2.3.3/src/
H A Djbm.cpp141 spos = voice[c].seqpos; in update()
157 spos = voice[c].seqpos = sequences[voice[c].seqno]; in update()
174 voice[c].seqpos = spos; in update()
204 voice[c].seqpos = sequences[voice[c].seqno]; in rewind()
H A Djbm.h63 unsigned short trkpos, trkstart, seqpos; member
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/
H A Dexternal_tool_support.pro155 src/seqpos/SeqPosSettings.h \
156 src/seqpos/SeqPosSupport.h \
157 src/seqpos/SeqPosTask.h \
158 src/seqpos/SeqPosWorker.h \
414 src/seqpos/SeqPosSettings.cpp \
415 src/seqpos/SeqPosSupport.cpp \
416 src/seqpos/SeqPosTask.cpp \
417 src/seqpos/SeqPosWorker.cpp \
/dports/biology/jalview/jalview/src/MCview/
H A DPDBChain.java188 int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber); in makeExactMapping() local
190 if (seqpos == StructureMapping.UNASSIGNED_VALUE) in makeExactMapping()
194 char seqchar = ds.getCharAt(seqpos - ds.getStart()); in makeExactMapping()
202 atom.alignmentMapping = seqpos - 1; in makeExactMapping()
/dports/emulators/mess/mame-mame0226/src/mame/machine/
H A Dseibucop.cpp420 int seqpos; in dump_table() local
421 for (seqpos = 0; seqpos < 8; seqpos++) in dump_table()
423 printf("%03x", cop_program[command * 8 + seqpos]); in dump_table()
424 if (seqpos < 7) in dump_table()

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