/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/ |
H A D | roadMap.c | 101 IDnum seqID; in importRoadMapArray() local 148 for (seqID = 1; seqID <= sequenceCount; seqID++) in importRoadMapArray() 149 annotationOffset[seqID] += annotationOffset[seqID - 1]; in importRoadMapArray() 163 seqID = (IDnum) long_var; in importRoadMapArray() 172 if (seqID > 0) in importRoadMapArray() 198 IDnum seqID; in importReferenceRoadMapArray() local 231 if (seqID <= result->referenceCount && seqID >= -result->referenceCount) in importReferenceRoadMapArray() 251 for (seqID = 1; seqID <= sequenceCount; seqID++) in importReferenceRoadMapArray() 252 annotationOffset[seqID] += annotationOffset[seqID - 1]; in importReferenceRoadMapArray() 268 if (seqID <= result->referenceCount && seqID >= -result->referenceCount) in importReferenceRoadMapArray() [all …]
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H A D | splay.c | 42 IDnum seqID; member 208 findOrInsertOccurenceInSplayTree(Kmer * kmer, IDnum * seqID, in findOrInsertOccurenceInSplayTree() argument 216 newNode->seqID = *seqID; in findOrInsertOccurenceInSplayTree() 230 newNode->seqID = *seqID; in findOrInsertOccurenceInSplayTree() 239 printf("1: sequenceID = %d\n", *seqID); in findOrInsertOccurenceInSplayTree() 245 newNode->seqID = *seqID; in findOrInsertOccurenceInSplayTree() 254 printf("2: sequenceID = %d\n", *seqID); in findOrInsertOccurenceInSplayTree() 258 *seqID = (*T)->seqID; in findOrInsertOccurenceInSplayTree() 261 printf("3: sequenceID = %d\n", *seqID); in findOrInsertOccurenceInSplayTree()
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H A D | splayTable.c | 377 *seqID = sequenceIDs[readIndex]; in findOrInsertOccurenceInSplayTable() 379 *seqID = -sequenceIDs[readIndex]; in findOrInsertOccurenceInSplayTable() 395 *seqID = getKmerOccurenceNodeID(hit); in findOrInsertOccurenceInSplayTable() 401 *seqID = getKmerOccurenceNodeID(hit); in findOrInsertOccurenceInSplayTable() 415 FILE * file, boolean second_in_pair, IDnum seqID) in printAnnotations() argument 441 sprintf(lineBuffer, "ROADMAP %li\n", (long)seqID); in printAnnotations() 478 sequenceID = seqID; in printAnnotations() 506 if( sequenceID!=seqID && sequenceID<0 ){ in printAnnotations() 648 tString = getTightStringInArray(array, seqID - 1); in computeClearHSPs() 782 IDnum seqID) in inputSequenceIntoSplayTable() argument [all …]
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/dports/biology/velvet/velvet_1.2.10/src/ |
H A D | roadMap.c | 101 IDnum seqID; in importRoadMapArray() local 148 for (seqID = 1; seqID <= sequenceCount; seqID++) in importRoadMapArray() 149 annotationOffset[seqID] += annotationOffset[seqID - 1]; in importRoadMapArray() 163 seqID = (IDnum) long_var; in importRoadMapArray() 172 if (seqID > 0) in importRoadMapArray() 198 IDnum seqID; in importReferenceRoadMapArray() local 231 if (seqID <= result->referenceCount && seqID >= -result->referenceCount) in importReferenceRoadMapArray() 251 for (seqID = 1; seqID <= sequenceCount; seqID++) in importReferenceRoadMapArray() 252 annotationOffset[seqID] += annotationOffset[seqID - 1]; in importReferenceRoadMapArray() 268 if (seqID <= result->referenceCount && seqID >= -result->referenceCount) in importReferenceRoadMapArray() [all …]
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H A D | splayTable.c | 480 sequenceID = seqID; in printAnnotations() 736 IDnum seqID) in inputSequenceIntoSplayTable() argument 774 currentIndex = seqID; in inputReferenceIntoSplayTable() 1007 IDnum seqID = 0; in inputSequenceArrayIntoSplayTableAndArchive() local 1143 for (seqID = referenceSequenceCount + 1; seqID < sequenceCount + 1; seqID++) { in inputSequenceArrayIntoSplayTableAndArchive() 1191 mapReferenceIDs[seqID] = reallocOrExit(mapReferenceIDs[seqID], maxCount, IDnum); in inputSequenceArrayIntoSplayTableAndArchive() 1192 mapCoords[seqID] = reallocOrExit(mapCoords[seqID], maxCount, Coordinate); in inputSequenceArrayIntoSplayTableAndArchive() 1204 mapCount[seqID] = counter; in inputSequenceArrayIntoSplayTableAndArchive() 1209 seqID = (IDnum) long_var; in inputSequenceArrayIntoSplayTableAndArchive() 1220 mapReferenceIDs[seqID] = reallocOrExit(mapReferenceIDs[seqID], maxCount, IDnum); in inputSequenceArrayIntoSplayTableAndArchive() [all …]
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H A D | splay.c | 42 IDnum seqID; member 208 findOrInsertOccurenceInSplayTree(Kmer * kmer, IDnum * seqID, in findOrInsertOccurenceInSplayTree() argument 216 newNode->seqID = *seqID; in findOrInsertOccurenceInSplayTree() 230 newNode->seqID = *seqID; in findOrInsertOccurenceInSplayTree() 243 newNode->seqID = *seqID; in findOrInsertOccurenceInSplayTree() 254 *seqID = (*T)->seqID; in findOrInsertOccurenceInSplayTree()
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/dports/devel/fbthrift/fbthrift-2021.12.27.00/thrift/lib/go/thrift/ |
H A D | serial_channel.go | 29 seqID int32 member 42 c.seqID++ 43 seqID := c.seqID 45 if err := c.protocol.WriteMessageBegin(method, msgType, seqID); err != nil { 46 return seqID, err 50 return seqID, err 54 return seqID, err 57 return seqID, c.protocol.Flush() 72 if msgSeqID != seqID { 122 seqID, err := c.sendMsg(method, request, CALL) [all …]
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H A D | clientconn_test.go | 45 seqID int32 member 63 func (f *fakeOproto) WriteMessageBegin(method string, typeID MessageType, seqID int32) error { 84 func (f *fakeIproto) ReadMessageBegin() (method string, typeID MessageType, seqID int32, err error)… 90 return f.method, f.typeID, f.seqID, nil 161 iproto: &fakeIproto{method: "foobar", seqID: -1}, 167 iproto: &fakeIproto{method: "foobar", seqID: 0, typeID: -1}, 173 iproto: &fakeIproto{method: "foobar", seqID: 0, typeID: REPLY},
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H A D | clientconn.go | 29 seqID int32 member 85 cc.seqID++ 87 if err := cc.oproto.WriteMessageBegin(method, msgType, cc.seqID); err != nil { 104 recvMethod, mTypeID, seqID, err := cc.iproto.ReadMessageBegin() 114 if cc.seqID != seqID {
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H A D | processor.go | 51 Write(seqID int32, result WritableStruct, oprot Protocol) Exception 91 Write(seqID int32, result WritableStruct, oprot Protocol) Exception 116 name, messageType, seqID, rerr := iprot.ReadMessageBegin() 154 if e2 := sendException(oprot, name, seqID, err); e2 != nil { 201 if e2 := pfunc.Write(seqID, result, oprot); e2 != nil {
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/dports/biology/py-crossmap/CrossMap-0.5.4/lib/cmmodule/ |
H A D | fasta.py | 68 def getSeq(self,seqID=None): argument 70 if seqID is None: 73 return self.seqs[seqID] 83 def getSeqLen(self,seqID=None): argument 85 if seqID is None: 90 seqlen[seqID]=len(self.seqs[seqID]) 115 def revComp(self,seqID=None): argument 118 if seqID is None: 144 def findPattern(self,pat,outfile,seqID=None,rev=True): argument 154 if seqID is None: [all …]
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/ |
H A D | splay.c | 37 IDnum seqID; member 201 newNode->seqID = *seqID; in findOrInsertOccurenceInSplayTree() 215 newNode->seqID = *seqID; in findOrInsertOccurenceInSplayTree() 228 newNode->seqID = *seqID; in findOrInsertOccurenceInSplayTree() 239 *seqID = (*T)->seqID; in findOrInsertOccurenceInSplayTree() 251 IDnum newID = *seqID; in placeOccurenceInSplayTree() 257 newNode->seqID = *seqID; in placeOccurenceInSplayTree() 271 newNode->seqID = *seqID; in placeOccurenceInSplayTree() 284 newNode->seqID = *seqID; in placeOccurenceInSplayTree() 295 *seqID = (*T)->seqID; in placeOccurenceInSplayTree() [all …]
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/ |
H A D | SimilarityPlot.bf | 57 for (seqID = 0; seqID < ds.species; seqID = seqID + 1) 59 if (seqID != whichSequence) 61 columnHeaders[columnIdx] = seqNames[seqID]; 63 columnPlots = columnPlots + seqNames[seqID] + ";"; 85 for (seqID = 0; seqID < ds.species; seqID = seqID + 1) 87 if (seqID != whichSequence) 89 gdInfo[aStep][columnIdx] = ComputeDistanceFormula (seqID, whichSequence);
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/RNAforester/src/ |
H A D | parser.cpp | 14 int seqID = 0; in parseXMLFile() local 25 seqID++; in parseXMLFile() 27 ss << ">" << seqID << "\n"; in parseXMLFile() 38 std::cout << "seqID: " << seqID << std::endl; in parseXMLFile() 40 idMapping[seqID] = elemSeq->get_attribute("seqID")->get_value(); in parseXMLFile() 46 names[seqID] = ((xmlpp::Element*)(*it3))->get_child_text()->get_content(); in parseXMLFile() 50 … synonyms[seqID] = ((xmlpp::Element*)(*it3))->get_child_text()->get_content(); in parseXMLFile() 54 … descriptions[seqID] = ((xmlpp::Element*)(*it3))->get_child_text()->get_content(); in parseXMLFile() 66 comments[seqID] = ((xmlpp::Element*)(*it2))->get_child_text()->get_content(); in parseXMLFile()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/ |
H A D | cuSequence.cpp | 860 if (!seqID) { in GetAccessionAndDatabaseSource() 867 if (seqID->IsGi()) { in GetAccessionAndDatabaseSource() 870 else if (seqID->IsPdb()) { in GetAccessionAndDatabaseSource() 871 const CPDB_seq_id& pPDB_ID = seqID->GetPdb(); in GetAccessionAndDatabaseSource() 878 else if (seqID->IsLocal()) { in GetAccessionAndDatabaseSource() 887 else if (seqID->IsGeneral()) { in GetAccessionAndDatabaseSource() 902 else if (seqID->IsGibbsq()) { in GetAccessionAndDatabaseSource() 905 else if (seqID->IsGibbmt()) { in GetAccessionAndDatabaseSource() 908 else if (seqID->IsGiim()) { in GetAccessionAndDatabaseSource() 909 if (seqID->GetGiim().CanGetDb()) { in GetAccessionAndDatabaseSource() [all …]
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/dports/net/storj/storj-1.45.3/vendor/github.com/apache/thrift/lib/csharp/src/Protocol/ |
H A D | TMessage.cs | 34 private int seqID; field 41 this.seqID = seqid; in TMessage() 58 get { return seqID; } 59 set { seqID = value; }
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/dports/www/fabio/fabio-1.5.14/vendor/github.com/apache/thrift/thrift-da1169d75b15/lib/csharp/src/Protocol/ |
H A D | TMessage.cs | 34 private int seqID; field 41 this.seqID = seqid; in TMessage() 58 get { return seqID; } 59 set { seqID = value; }
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/dports/misc/concourse/concourse-6.7.2/vendor/github.com/apache/thrift/lib/csharp/src/Protocol/ |
H A D | TMessage.cs | 34 private int seqID; field 41 this.seqID = seqid; in TMessage() 58 get { return seqID; } 59 set { seqID = value; }
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/dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
H A D | quartet.cpp | 776 lmap_quartet_info[qid].seqID[0] = LMGroups.GroupA[i0]; in computeQuartetLikelihoods() 777 lmap_quartet_info[qid].seqID[1] = LMGroups.GroupA[i1]; in computeQuartetLikelihoods() 864 } while (lmap_quartet_info[qid].seqID[1] == lmap_quartet_info[qid].seqID[0]); in computeQuartetLikelihoods() 875 …ap_quartet_info[qid].seqID[2] == lmap_quartet_info[qid].seqID[0] || lmap_quartet_info[qid].seqID[2… in computeQuartetLikelihoods() 886 …ap_quartet_info[qid].seqID[3] == lmap_quartet_info[qid].seqID[0] || lmap_quartet_info[qid].seqID[3… in computeQuartetLikelihoods() 887 || lmap_quartet_info[qid].seqID[3] == lmap_quartet_info[qid].seqID[2]); in computeQuartetLikelihoods() 902 seq_id.insert(seq_id.begin(), lmap_quartet_info[qid].seqID, lmap_quartet_info[qid].seqID+4); in computeQuartetLikelihoods() 1478 out << "(" << lmap_quartet_info[qid].seqID[0]+1 << "," in doLikelihoodMapping() 1479 << lmap_quartet_info[qid].seqID[1]+1 << "," in doLikelihoodMapping() 1480 << lmap_quartet_info[qid].seqID[2]+1 << "," in doLikelihoodMapping() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/rna_io/ |
H A D | stockholm_read_write.h | 204 while (idx < length(record.seqID) && record.seqID[idx] != buffer) 208 TSizeRna5String const offset = idx == length(record.seqID) ? 0u : length(sequence[idx]); 211 appendValue(record.seqID, buffer); 307 SEQAN_ASSERT_EQ(length(record.seqID), length(rows(record.align))); 309 forEach(record.seqID, [&](CharString const & sID) 314 for (typename Size<StringSet<CharString> >::Type idx = 0; idx < length(record.seqID); ++idx) 316 CharString str = record.seqID[idx]; // write id
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/rna_io/ |
H A D | stockholm_read_write.h | 204 while (idx < length(record.seqID) && record.seqID[idx] != buffer) 208 TSizeRna5String const offset = idx == length(record.seqID) ? 0u : length(sequence[idx]); 211 appendValue(record.seqID, buffer); 307 SEQAN_ASSERT_EQ(length(record.seqID), length(rows(record.align))); 309 forEach(record.seqID, [&](CharString const & sID) 314 for (typename Size<StringSet<CharString> >::Type idx = 0; idx < length(record.seqID); ++idx) 316 CharString str = record.seqID[idx]; // write id
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/dports/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO/ |
H A D | BCCachedSequenceFile.h | 61 - (NSDictionary *)infoForSequence:(NSString *)seqID; 64 - (char)symbolAtPosition:(unsigned long long)aPos forSequence:(NSString *)seqID; 68 …)aBuffer atPosition:(unsigned long long)aPos ofLength:(unsigned)aLen forSequence:(NSString *)seqID;
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/dports/graphics/openjpeg15/openjpeg-version.1.5.2/applications/jpip/libopenjpip/ |
H A D | jp2k_encoder.c | 426 Byte8_t seqID; in recons_RPCLbitstream() local 435 for( p=0; p<numOfprcts; p++, seqID++) in recons_RPCLbitstream() 448 Byte8_t seqID; in recons_PCRLbitstream() local 467 seqID = comp_seqID( tileID, SIZ, COD, r, p); in recons_PCRLbitstream() 480 Byte8_t seqID; in recons_CPRLbitstream() local 499 seqID = comp_seqID( tileID, SIZ, COD, r, p); in recons_CPRLbitstream() 522 Byte8_t seqID, precID, binOffset; in recons_packet() local 593 Byte8_t seqID = 0; in comp_seqID() local 597 seqID += comp_numOfprcts( tileID, SIZ, COD, rr); in comp_seqID() 599 seqID += p; in comp_seqID() [all …]
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/dports/graphics/openjpeg/openjpeg-2.4.0/src/lib/openjpip/ |
H A D | jp2k_encoder.c | 487 Byte8_t seqID; in recons_RPCLbitstream() local 497 for (p = 0; p < numOfprcts; p++, seqID++) in recons_RPCLbitstream() 513 Byte8_t seqID; in recons_PCRLbitstream() local 533 seqID = comp_seqID(tileID, SIZ, COD, r, p); in recons_PCRLbitstream() 548 Byte8_t seqID; in recons_CPRLbitstream() local 568 seqID = comp_seqID(tileID, SIZ, COD, r, p); in recons_CPRLbitstream() 598 Byte8_t seqID, precID, binOffset; in recons_packet() local 603 seqID = comp_seqID(tileID, SIZ, COD, res_idx, prct_idx); in recons_packet() 678 Byte8_t seqID = 0; in comp_seqID() local 687 seqID += (Byte8_t)p; in comp_seqID() [all …]
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/dports/biology/iqtree/IQ-TREE-2.0.6/alignment/ |
H A D | maalignment.cpp | 149 int seqID; in printPatObsExpFre() local 153 for ( seqID = 0; seqID < seqNum; seqID++ ){ in printPatObsExpFre() 154 out << convertStateBackStr(at(i)[seqID]); in printPatObsExpFre()
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