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Searched refs:getAligned (Results 1 – 25 of 108) sorted by relevance

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/dports/biology/mothur/mothur-1.46.1/TestMothur/testcontainers/
H A Dtestsequence.cpp28 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()
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/dports/biology/mothur/mothur-1.46.1/source/chimera/
H A Dmothurchimera.cpp19 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()
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H A Dmaligner.cpp72 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()
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H A Ddecalc.cpp51 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()
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H A Dslayer.cpp41 …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()
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H A Dccode.cpp254 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()
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/dports/biology/mothur/mothur-1.46.1/source/datastructures/
H A Dsequencedb.cpp44 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()
H A Dproteindb.cpp33 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()
H A Ddistancedb.cpp33 if (!isAligned(seq.getAligned())) { in addSequence()
39 if (templateSeqsLength == 0) { templateSeqsLength = seq.getAligned().length(); } in addSequence()
55 string sequence = query->getAligned(); in findClosestSequences()
/dports/biology/mothur/mothur-1.46.1/source/commands/
H A Ddeconvolutecommand.cpp210 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()
H A Dpcrseqscommand.cpp446 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()
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/dports/biology/mothur/mothur-1.46.1/TestMothur/
H A Dtesttrimoligos.cpp598 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()
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/dports/www/firefox-esr/firefox-91.8.0/dom/media/webaudio/
H A DAlignedTArray.h31 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
/dports/lang/spidermonkey78/firefox-78.9.0/dom/media/webaudio/
H A DAlignedTArray.h31 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
/dports/www/firefox/firefox-99.0/dom/media/webaudio/
H A DAlignedTArray.h31 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
/dports/mail/thunderbird/thunderbird-91.8.0/dom/media/webaudio/
H A DAlignedTArray.h31 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
/dports/lang/spidermonkey60/firefox-60.9.0/dom/media/webaudio/
H A DAlignedTArray.h31 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
/dports/www/firefox-legacy/firefox-52.8.0esr/dom/media/webaudio/
H A DAlignedTArray.h30 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
/dports/biology/mothur/mothur-1.46.1/source/calculators/
H A Deachgapdist.cpp15 string seqA = A.getAligned(); in calcDist()
16 string seqB = B.getAligned(); in calcDist()
62 classifierOTU seq(A.getAligned()); in calcDist()
H A Deachgapignore.cpp15 string seqA = A.getAligned(); in calcDist()
16 string seqB = B.getAligned(); in calcDist()
65 classifierOTU seq(A.getAligned()); in calcDist()
H A Dkimura.cpp16 vector<AminoAcid> seqA = A.getAligned(); in calcDist()
17 vector<AminoAcid> seqB = B.getAligned(); in calcDist()
H A Donegapignore.cpp15 string seqA = A.getAligned(); in calcDist()
16 string seqB = B.getAligned(); in calcDist()
81 classifierOTU seq(A.getAligned()); in calcDist()
H A Donegapdist.cpp19 string seqA = A.getAligned(); in calcDist()
20 string seqB = B.getAligned(); in calcDist()
84 classifierOTU seq(A.getAligned()); in calcDist()
H A Dignoregaps.cpp19 string seqA = A.getAligned(); in calcDist()
20 string seqB = B.getAligned(); in calcDist()
80 classifierOTU seq(A.getAligned()); in calcDist()
/dports/net/cjdns/cjdns-cjdns-v21.1/memory/
H A DBufferAllocator.c57 #define getAligned(pointer, alignedOn) \ macro
64 char* pointer = getAligned(context->pointer, ALIGNMENT); in allocatorMalloc()

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