| /dports/biology/mothur/mothur-1.46.1/source/calculators/ |
| H A D | calculator.cpp | 15 int alignLength = seqA.length(); in setStart() local
35 int alignLength = seqA.length(); in setEnd() local
56 int alignLength = seqA.length(); in setStartIgnoreTermGap() local
80 int alignLength = seqA.length(); in setEndIgnoreTermGap() local
104 int alignLength = cols.size(); in setStartsIgnoreTermGap() local
153 int alignLength = cols.size(); in setEndsIgnoreTermGap() local
202 int alignLength = cols.size(); in setStarts() local
256 int alignLength = cols.size(); in setEnds() local
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| H A D | ignoregaps.cpp | 21 int alignLength = (int)seqA.length(); in calcDist() local
84 int alignLength = cols.size(); in calcDist() local
138 int alignLength = cols.size(); in setStarts() local
187 int alignLength = cols.size(); in setEnds() local
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| H A D | eachgapdist.cpp | 18 int alignLength = (int)seqA.length(); in calcDist() local
66 int alignLength = cols.size(); in calcDist() local
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| H A D | eachgapignore.cpp | 18 int alignLength = seqA.length(); in calcDist() local
69 int alignLength = cols.size(); in calcDist() local
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| H A D | onegapdist.cpp | 21 int alignLength = seqA.length(); in calcDist() local
88 int alignLength = cols.size(); in calcDist() local
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| H A D | onegapignore.cpp | 85 int alignLength = cols.size(); in calcDist() local
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| /dports/biology/mothur/mothur-1.46.1/source/ |
| H A D | refchimeratest.h | 43 int alignLength; variable
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| H A D | refchimeratest.cpp | 236 double alignLength = 0.0; in analyzeUnalignedQuery() local
433 int alignLength = qAlign.length(); in getUnalignedDiffs() local
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| H A D | myseqdist.cpp | 85 int alignLength = sequence.length(); in fixSequence() local
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| /dports/java/openjdk11/jdk11u-jdk-11.0.13-8-1/src/java.base/share/classes/java/util/zip/ |
| H A D | CRC32C.java | 217 int alignLength in updateBytes() local
292 int alignLength = (8 - (int) ((address + off) & 0x7)) & 0x7; in updateDirectByteBuffer() local
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| /dports/java/openjdk13/jdk13u-jdk-13.0.10-1-1/src/java.base/share/classes/java/util/zip/ |
| H A D | CRC32C.java | 217 int alignLength in updateBytes() local
292 int alignLength = (8 - (int) ((address + off) & 0x7)) & 0x7; in updateDirectByteBuffer() local
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| /dports/java/openjdk11-jre/jdk11u-jdk-11.0.13-8-1/src/java.base/share/classes/java/util/zip/ |
| H A D | CRC32C.java | 217 int alignLength in updateBytes() local
292 int alignLength = (8 - (int) ((address + off) & 0x7)) & 0x7; in updateDirectByteBuffer() local
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| /dports/java/openjdk16/jdk16u-jdk-16.0.2-7-1/src/java.base/share/classes/java/util/zip/ |
| H A D | CRC32C.java | 222 int alignLength in updateBytes() local
297 int alignLength = (8 - (int) ((address + off) & 0x7)) & 0x7; in updateDirectByteBuffer() local
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| /dports/java/openjdk17/jdk17u-jdk-17.0.1-12-1/src/java.base/share/classes/java/util/zip/ |
| H A D | CRC32C.java | 222 int alignLength in updateBytes() local
297 int alignLength = (8 - (int) ((address + off) & 0x7)) & 0x7; in updateDirectByteBuffer() local
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| /dports/java/openjdk12/openjdk-jdk12u-jdk-12.0.2-10-4/src/java.base/share/classes/java/util/zip/ |
| H A D | CRC32C.java | 217 int alignLength in updateBytes() local
292 int alignLength = (8 - (int) ((address + off) & 0x7)) & 0x7; in updateDirectByteBuffer() local
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| /dports/java/openjdk15/jdk15u-jdk-15.0.6-1-1/src/java.base/share/classes/java/util/zip/ |
| H A D | CRC32C.java | 217 int alignLength in updateBytes() local
292 int alignLength = (8 - (int) ((address + off) & 0x7)) & 0x7; in updateDirectByteBuffer() local
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| /dports/java/openjdk14/jdk14u-jdk-14.0.2-12-1/src/java.base/share/classes/java/util/zip/ |
| H A D | CRC32C.java | 217 int alignLength in updateBytes() local
292 int alignLength = (8 - (int) ((address + off) & 0x7)) & 0x7; in updateDirectByteBuffer() local
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| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | chimeraperseuscommand.h | 44 int processors, alignLength; variable
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/ |
| H A D | ExportHighlightedDialogController.cpp | 60 int alignLength = editor->getAlignmentLen(); in ExportHighligtingDialogController() local
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| H A D | MSASelectSubalignmentDialog.cpp | 135 int alignLength = mobj->getLength(); in init() local
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| /dports/biology/mothur/mothur-1.46.1/source/classifier/ |
| H A D | alignnode.h | 43 int alignLength; variable
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| /dports/biology/mothur/mothur-1.46.1/source/chimera/ |
| H A D | decalc.h | 72 int alignLength; variable
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| H A D | myPerseus.cpp | 193 int alignLength = qAlign.length(); in getDiffs() local
393 int alignLength = 0; in modeledPairwiseAlignSeqs() local
624 int alignLength = leftDiffs[0].size(); in getTrimera() local
830 int alignLength = queryAln.length(); in calcLoonIndex() local
1030 int alignLength = query.length(); in calcBestDistance() local
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| /dports/biology/ncbi-toolkit/ncbi/tools/ |
| H A D | posit.c | 3121 Int4 alignLength; /*number of columns in alignment, to be returned*/ in posPreprocessAlignment() local
3161 …indQuery(posDesc ** alignArray, compactSearchItems * compactSearch, Int4 numSeqs, Int4 alignLength) in findQuery()
3217 …tems *compactSearch, char * fileName, Int4 numSeqs, Int4 numBlocks, Int4 alignLength, Int4 * numCo… in posReadAlignment()
3296 …tems *compactSearch, char * fileName, Int4 numSeqs, Int4 numBlocks, Int4 alignLength, Int4 * numCo… in posProcessAlignment()
3377 Int4 numSeqs, numBlocks, alignLength; /*number of sequences, number of pieces in BposComputation() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/ |
| H A D | AssemblyBasedSVDiscoveryTestDataProviderForBreakEndVariants.java | 124 … final int mapQ, final int alignLength, in addStandardAttributes()
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