/dports/biology/mothur/mothur-1.46.1/TestMothur/testcontainers/ |
H A D | testsequence.cpp | 28 EXPECT_EQ(seq.getAligned(), "ATGCGTCATC"); in TEST() 33 EXPECT_EQ(seq1.getAligned(), ""); in TEST() 44 EXPECT_EQ("A--TGC-G-TCA--TC", seq.getAligned()); in TEST() 71 EXPECT_EQ("ATGCG", seq3.getAligned()); in TEST() 74 EXPECT_EQ("ATGCG", seq4.getAligned()); in TEST() 77 EXPECT_EQ("..GCG", seq4.getAligned()); in TEST() 80 EXPECT_EQ("..G..", seq4.getAligned()); in TEST() 84 EXPECT_EQ("..GCG", seq.getAligned()); in TEST() 88 EXPECT_EQ("AT...", seq.getAligned()); in TEST() 92 EXPECT_EQ(".....", seq.getAligned()); in TEST() [all …]
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/dports/biology/mothur/mothur-1.46.1/source/chimera/ |
H A D | mothurchimera.cpp | 19 vector<int> gaps; gaps.resize(seqs[0]->getAligned().length(), 0); in createFilter() 20 vector<int> a; a.resize(seqs[0]->getAligned().length(), 0); in createFilter() 21 vector<int> t; t.resize(seqs[0]->getAligned().length(), 0); in createFilter() 22 vector<int> g; g.resize(seqs[0]->getAligned().length(), 0); in createFilter() 23 vector<int> c; c.resize(seqs[0]->getAligned().length(), 0); in createFilter() 25 filterString = (string(seqs[0]->getAligned().length(), '1')); in createFilter() 32 string seqAligned = seqs[i]->getAligned(); in createFilter() 48 for(int i = 0;i < seqs[0]->getAligned().length(); i++){ in createFilter() 70 string seqAligned = seq->getAligned(); in runFilter() 124 filterString = (string(container[0]->getAligned().length(), '1')); in readSeqs() [all …]
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H A D | maligner.cpp | 72 if (query.getAligned() == "") { return "no"; } in chimeraMaligner() 98 string queryInRange = query.getAligned(); in chimeraMaligner() 128 string queryInRegion = query.getAligned(); in chimeraMaligner() 152 string queryAligned = query.getAligned(); in minCoverageFilter() 156 string refAligned = ref[i].getAligned(); in minCoverageFilter() 216 string seqAligned = seqs[i].getAligned(); in verticalFilter() 234 string seqAligned = seqs[i].getAligned(); in verticalFilter() 308 int numCols = query.getAligned().length(); in fillScoreMatrix() 312 string queryAligned = query.getAligned(); in fillScoreMatrix() 314 string subjectAligned = seqs[i].getAligned(); in fillScoreMatrix() [all …]
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H A D | decalc.cpp | 51 string q = seq->getAligned(); in runMask() 73 string q = query->getAligned(); in trimSeqs() 74 string s = subject->getAligned(); in trimSeqs() 119 if (query->getAligned().length() != subject->getAligned().length()) { in calcObserved() 261 char value = seqs[j]->getAligned()[i]; in calcFreq() 487 string queryAligned = querySeq.getAligned(); in findClosest() 670 int rearPos = query.getAligned().length(); in trimSeqs() 692 string aligned = query.getAligned(); in trimSeqs() 726 aligned = query.getAligned(); in trimSeqs() 752 string newAligned = query.getAligned(); in trimSeqs() [all …]
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H A D | slayer.cpp | 41 …snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].pare… in getResults() 42 …nps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].pare… in getResults() 107 string query = q.getAligned(); in runBellerophon() 108 string parentA = pA.getAligned(); in runBellerophon() 109 string parentB = pB.getAligned(); in runBellerophon() 433 string seqAligned = q.getAligned(); in verticalFilter() 439 seqAligned = pA.getAligned(); in verticalFilter() 445 seqAligned = pB.getAligned(); in verticalFilter() 465 seqAligned = q.getAligned(); in verticalFilter() 484 seqAligned = pA.getAligned(); in verticalFilter() [all …]
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H A D | ccode.cpp | 254 int rearPos = query->getAligned().length(); in trimSequences() 260 string aligned = closest[i].seq->getAligned(); in trimSequences() 276 string aligned = query->getAligned(); in trimSequences() 294 string aligned = closest[i].seq->getAligned(); in trimSequences() 310 aligned = query->getAligned(); in trimSequences() 456 string seqA = seqs[i].seq->getAligned().substr(it->first, length); in removeBadReferenceSeqs() 461 string seqB = seqs[j].seq->getAligned().substr(it->first, length); in removeBadReferenceSeqs() 575 string refI = ref[i].seq->getAligned(); in getAverageRef() 580 string refJ = ref[j].seq->getAligned(); in getAverageRef() 655 string refQuery = query->getAligned(); in getAverageQuery() [all …]
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/dports/biology/mothur/mothur-1.46.1/source/datastructures/ |
H A D | sequencedb.cpp | 44 if (length == 0) { length = newSequence.getAligned().length(); } in SequenceDB() 45 if (length != newSequence.getAligned().length()) { samelength = false; } in SequenceDB() 82 if (length == 0) { length = newSequence.getAligned().length(); } in SequenceDB() 83 if (length != newSequence.getAligned().length()) { samelength = false; } in SequenceDB() 110 if (length == 0) { length = seqI.getAligned().length(); } in SequenceDB() 111 if (length != seqI.getAligned().length()) { samelength = false; } in SequenceDB() 141 if (length == 0) { length = newSequence.getAligned().length(); } in SequenceDB() 142 if (length != newSequence.getAligned().length()) { samelength = false; } in SequenceDB() 180 if (length == 0) { length = newSequence.getAligned().length(); } in push_back() 181 if (length != newSequence.getAligned().length()) { samelength = false; } in push_back()
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H A D | proteindb.cpp | 33 if (length == 0) { length = newProteinSequence.getAligned().size(); } in ProteinDB() 34 if (length != newProteinSequence.getAligned().size()) { samelength = false; } in ProteinDB() 59 if (length == 0) { length = newProteinSequence.getAligned().size(); } in push_back() 60 if (length != newProteinSequence.getAligned().size()) { samelength = false; } in push_back()
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H A D | distancedb.cpp | 33 if (!isAligned(seq.getAligned())) { in addSequence() 39 if (templateSeqsLength == 0) { templateSeqsLength = seq.getAligned().length(); } in addSequence() 55 string sequence = query->getAligned(); in findClosestSequences()
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/dports/biology/mothur/mothur-1.46.1/source/commands/ |
H A D | deconvolutecommand.cpp | 210 itStrings = sequenceStrings.find(seq.getAligned()); in execute() 222 …format == "name") { sequenceStrings[seq.getAligned()] = itNames->second; nameFileOrder.push_back(… in execute() 223 …es(itNames->second)); sequenceStrings[seq.getAligned()] = seq.getName(); nameFileOrder.push_back(s… in execute() 230 … sequenceStrings[seq.getAligned()] = expandedName; nameFileOrder.push_back(seq.getAligned()); in execute() 233 … sequenceStrings[seq.getAligned()] = seq.getName(); nameFileOrder.push_back(seq.getAligned()); in execute() 236 … (format == "name") { sequenceStrings[seq.getAligned()] = seq.getName(); nameFileOrder.push_back(s… in execute() 237 …_back(seq.getName()); sequenceStrings[seq.getAligned()] = seq.getName(); nameFileOrder.push_back(s… in execute() 246 … if (format == "name") { sequenceStrings[seq.getAligned()] += "," + itNames->second; } in execute() 254 sequenceStrings[seq.getAligned()] += "," + expandedName; in execute() 262 … if (format == "name") { sequenceStrings[seq.getAligned()] += "," + seq.getName(); } in execute()
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H A D | pcrseqscommand.cpp | 446 length = ecoli.getAligned().length(); in pcrData() 559 string alignedString = seq.getAligned(); in trimStartEnd() 583 string seqString = seq.getAligned().substr(params->start); in trimStartEnd() 604 Sequence savedSeq(seq.getName(), seq.getAligned()); in trimPrimers() 607 bool aligned = isAligned(savedSeq.getAligned(), mapAligned); in trimPrimers() 644 isAligned(savedSeq.getAligned(), mapAligned); in trimPrimers() 701 seq.setAligned(savedSeq.getAligned()); in trimPrimers() 737 lengths.insert(currSeq.getAligned().length()); in driverPcr() 769 else if (currSeq.getAligned().length() != params->length) { in driverPcr() 1010 string aligned = forwardPad + seq.getAligned() + reversePad; in adjustDots() [all …]
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/dports/biology/mothur/mothur-1.46.1/TestMothur/ |
H A D | testtrimoligos.cpp | 598 string temp = F003D150.getAligned(); in TEST() 612 string primerKeptKeepDots = F003D150_2.getAligned(); in TEST() 631 primerRemovedKeepDots = F003D150_1.getAligned(); in TEST() 635 primerKeptKeepDots = F003D150_2.getAligned(); in TEST() 653 primerRemovedKeepDots = F003D150_1.getAligned(); in TEST() 657 primerKeptKeepDots = F003D150_2.getAligned(); in TEST() 697 string temp = F003D150.getAligned(); in TEST() 726 temp = F003D150.getAligned(); in TEST() 735 primerRemovedKeepDots = F003D150_1.getAligned(); in TEST() 739 primerKeptKeepDots = F003D150_2.getAligned(); in TEST() [all …]
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/dports/www/firefox-esr/firefox-91.8.0/dom/media/webaudio/ |
H A D | AlignedTArray.h | 31 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 33 return getAligned(base_type::Elements()); in Elements() 60 static U* getAligned(U* p) { in getAligned() function 81 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 83 return getAligned(base_type::Elements()); in Elements() 110 static U* getAligned(U* p) { in getAligned() function
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/dports/lang/spidermonkey78/firefox-78.9.0/dom/media/webaudio/ |
H A D | AlignedTArray.h | 31 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 33 return getAligned(base_type::Elements()); in Elements() 60 static U* getAligned(U* p) { in getAligned() function 81 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 83 return getAligned(base_type::Elements()); in Elements() 110 static U* getAligned(U* p) { in getAligned() function
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/dports/www/firefox/firefox-99.0/dom/media/webaudio/ |
H A D | AlignedTArray.h | 31 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 33 return getAligned(base_type::Elements()); in Elements() 60 static U* getAligned(U* p) { in getAligned() function 81 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 83 return getAligned(base_type::Elements()); in Elements() 110 static U* getAligned(U* p) { in getAligned() function
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/dports/mail/thunderbird/thunderbird-91.8.0/dom/media/webaudio/ |
H A D | AlignedTArray.h | 31 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 33 return getAligned(base_type::Elements()); in Elements() 60 static U* getAligned(U* p) { in getAligned() function 81 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 83 return getAligned(base_type::Elements()); in Elements() 110 static U* getAligned(U* p) { in getAligned() function
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/dports/lang/spidermonkey60/firefox-60.9.0/dom/media/webaudio/ |
H A D | AlignedTArray.h | 31 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 33 return getAligned(base_type::Elements()); in Elements() 61 static U* getAligned(U* p) { in getAligned() function 82 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 84 return getAligned(base_type::Elements()); in Elements() 112 static U* getAligned(U* p) { in getAligned() function
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/dports/www/firefox-legacy/firefox-52.8.0esr/dom/media/webaudio/ |
H A D | AlignedTArray.h | 30 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 31 const elem_type* Elements() const { return getAligned(base_type::Elements()); } in Elements() 61 static U* getAligned(U* p) in getAligned() function 83 elem_type* Elements() { return getAligned(base_type::Elements()); } in Elements() 84 const elem_type* Elements() const { return getAligned(base_type::Elements()); } in Elements() 114 static U* getAligned(U* p) in getAligned() function
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/dports/biology/mothur/mothur-1.46.1/source/calculators/ |
H A D | eachgapdist.cpp | 15 string seqA = A.getAligned(); in calcDist() 16 string seqB = B.getAligned(); in calcDist() 62 classifierOTU seq(A.getAligned()); in calcDist()
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H A D | eachgapignore.cpp | 15 string seqA = A.getAligned(); in calcDist() 16 string seqB = B.getAligned(); in calcDist() 65 classifierOTU seq(A.getAligned()); in calcDist()
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H A D | kimura.cpp | 16 vector<AminoAcid> seqA = A.getAligned(); in calcDist() 17 vector<AminoAcid> seqB = B.getAligned(); in calcDist()
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H A D | onegapignore.cpp | 15 string seqA = A.getAligned(); in calcDist() 16 string seqB = B.getAligned(); in calcDist() 81 classifierOTU seq(A.getAligned()); in calcDist()
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H A D | onegapdist.cpp | 19 string seqA = A.getAligned(); in calcDist() 20 string seqB = B.getAligned(); in calcDist() 84 classifierOTU seq(A.getAligned()); in calcDist()
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H A D | ignoregaps.cpp | 19 string seqA = A.getAligned(); in calcDist() 20 string seqB = B.getAligned(); in calcDist() 80 classifierOTU seq(A.getAligned()); in calcDist()
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/dports/net/cjdns/cjdns-cjdns-v21.1/memory/ |
H A D | BufferAllocator.c | 57 #define getAligned(pointer, alignedOn) \ macro 64 char* pointer = getAligned(context->pointer, ALIGNMENT); in allocatorMalloc()
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