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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/
H A DroadMap.c101 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 …]
H A Dsplay.c42 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()
H A DsplayTable.c377 *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 …]
/dports/biology/velvet/velvet_1.2.10/src/
H A DroadMap.c101 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 …]
H A DsplayTable.c480 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 …]
H A Dsplay.c42 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()
/dports/devel/fbthrift/fbthrift-2021.12.27.00/thrift/lib/go/thrift/
H A Dserial_channel.go29 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 …]
H A Dclientconn_test.go45 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},
H A Dclientconn.go29 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 {
H A Dprocessor.go51 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 {
/dports/biology/py-crossmap/CrossMap-0.5.4/lib/cmmodule/
H A Dfasta.py68 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:
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/
H A Dsplay.c37 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 …]
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/
H A DSimilarityPlot.bf57 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);
/dports/biology/viennarna/ViennaRNA-2.4.18/src/RNAforester/src/
H A Dparser.cpp14 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/
H A DcuSequence.cpp860 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 …]
/dports/net/storj/storj-1.45.3/vendor/github.com/apache/thrift/lib/csharp/src/Protocol/
H A DTMessage.cs34 private int seqID; field
41 this.seqID = seqid; in TMessage()
58 get { return seqID; }
59 set { seqID = value; }
/dports/www/fabio/fabio-1.5.14/vendor/github.com/apache/thrift/thrift-da1169d75b15/lib/csharp/src/Protocol/
H A DTMessage.cs34 private int seqID; field
41 this.seqID = seqid; in TMessage()
58 get { return seqID; }
59 set { seqID = value; }
/dports/misc/concourse/concourse-6.7.2/vendor/github.com/apache/thrift/lib/csharp/src/Protocol/
H A DTMessage.cs34 private int seqID; field
41 this.seqID = seqid; in TMessage()
58 get { return seqID; }
59 set { seqID = value; }
/dports/biology/iqtree/IQ-TREE-2.0.6/tree/
H A Dquartet.cpp776 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 …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/rna_io/
H A Dstockholm_read_write.h204 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
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/rna_io/
H A Dstockholm_read_write.h204 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
/dports/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO/
H A DBCCachedSequenceFile.h61 - (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;
/dports/graphics/openjpeg15/openjpeg-version.1.5.2/applications/jpip/libopenjpip/
H A Djp2k_encoder.c426 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 …]
/dports/graphics/openjpeg/openjpeg-2.4.0/src/lib/openjpip/
H A Djp2k_encoder.c487 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 …]
/dports/biology/iqtree/IQ-TREE-2.0.6/alignment/
H A Dmaalignment.cpp149 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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