/dports/biology/wise/wise2.4.1/src/models/ |
H A D | transregion.dy | 217 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 …]
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H A D | transregion.c | 187 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()
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/dports/biology/ugene/ugene-40.1/data/workflow_samples/NGS/cistrome/ |
H A D | chip_seq.uwl | 24 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 …]
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H A D | chip_seq_with_control.uwl | 24 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 …]
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/dports/biology/wise/wise2.4.1/src/other_programs/ |
H A D | orthoset.dy | 52 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 …]
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/dports/misc/py-mxnet/incubator-mxnet-1.9.0/src/operator/ |
H A D | sequence_mask.cu | 39 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()
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H A D | sequence_mask.cc | 37 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()
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H A D | sequence_last-inl.h | 72 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()
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/dports/misc/mxnet/incubator-mxnet-1.9.0/src/operator/ |
H A D | sequence_mask.cu | 39 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()
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H A D | sequence_mask.cc | 37 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()
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H A D | sequence_last-inl.h | 72 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()
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/dports/biology/cdbfasta/cdbfasta/ |
H A D | cdbyank.cpp | 198 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()
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/dports/biology/canu/canu-2.2/src/utgcns/libNDalign/ |
H A D | NDalign.C | 281 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()
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | urkptpf.c | 1356 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 …]
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H A D | urkptpf.h | 122 extern SeqAlignPtr PatternMatch (Uint1Ptr seq, Int4 seqpos, Uint1 strand, 145 extern SeqAlignPtr ProfileMatch (Uint1Ptr seq, Int4 seqpos, FloatHi cutoff,
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/dports/biology/jalview/jalview/src/jalview/structure/ |
H A D | StructureMapping.java | 107 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()
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/dports/games/enygma/enigma-1.04/ |
H A D | savefile.c | 30 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()
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/dports/editors/fte/fte/src/ |
H A D | con_slang.cpp | 475 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()
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/dports/audio/deadbeef/deadbeef-0.7.2/plugins/adplug/adplug/ |
H A D | jbm.cpp | 141 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()
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H A D | jbm.h | 63 unsigned short trkpos, trkstart, seqpos; member
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/dports/audio/libadplug/adplug-adplug-2.3.3/src/ |
H A D | jbm.cpp | 141 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()
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H A D | jbm.h | 63 unsigned short trkpos, trkstart, seqpos; member
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/ |
H A D | external_tool_support.pro | 155 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 \
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/dports/biology/jalview/jalview/src/MCview/ |
H A D | PDBChain.java | 188 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()
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/dports/emulators/mess/mame-mame0226/src/mame/machine/ |
H A D | seibucop.cpp | 420 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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