| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/sequence/ |
| H A D | Strand.java | 74 public Bases getBases () { in getBases() method in Strand
83 return getBases ().toString (); in getStrandBases()
115 return getBases ().getLength (); in getSequenceLength()
647 return getBases ().getACount (); in getACount()
649 return getBases ().getTCount (); in getACount()
658 return getBases ().getTCount (); in getTCount()
660 return getBases ().getACount (); in getTCount()
669 return getBases ().getGCount (); in getGCount()
671 return getBases ().getCCount (); in getGCount()
680 return getBases ().getCCount (); in getCCount()
[all …]
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| H A D | Marker.java | 55 strand.getBases ().addSequenceChangeListener (markerinternal, in Marker()
194 getStrand ().getBases ().removeSequenceChangeListener (markerinternal); in finalize()
296 final Bases bases = getStrand ().getBases (); in sequenceChanged()
341 if(!(strand.getBases().getSequence() instanceof PartialSequence)) in checkPosition()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/circular/ |
| H A D | GCGraph.java | 41 if(end<=getBases().getLength()) in calculateValue()
43 getBases().getSequence().getCharSubSequence(start, end); in calculateValue()
46 final Sequence s = getBases().getSequence(); in calculateValue()
47 char[] seq1 = s.getCharSubSequence(start, getBases().getLength()); in calculateValue()
48 char[] seq2 = s.getCharSubSequence(1, getWindowSize()-(getBases().getLength()-start)); in calculateValue()
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| H A D | GCSkewGraph.java | 41 if(end<=getBases().getLength()) in calculateValue()
43 getBases().getSequence().getCharSubSequence(start, end); in calculateValue()
46 final Sequence s = getBases().getSequence(); in calculateValue()
47 char[] seq1 = s.getCharSubSequence(start, getBases().getLength()); in calculateValue()
48 char[] seq2 = s.getCharSubSequence(1, getWindowSize()-(getBases().getLength()-start)); in calculateValue()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/uk/ac/sanger/artemis/components/variant/ |
| H A D | WriteVariantSitesTest.java | 43 entryGroup.getSequenceEntry().getBases().getLength(), in testSNPSites()
45 entryGroup.getSequenceEntry().getBases()); in testSNPSites()
72 entryGroup.getSequenceEntry().getBases().getLength(), in testInsertionSites()
74 entryGroup.getSequenceEntry().getBases()); in testInsertionSites()
101 entryGroup.getSequenceEntry().getBases().getLength(), in testMultiAlleleSites()
103 entryGroup.getSequenceEntry().getBases()); in testMultiAlleleSites()
131 entryGroup.getSequenceEntry().getBases().getLength(), in testDeletionSites()
133 entryGroup.getSequenceEntry().getBases()); in testDeletionSites()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/ |
| H A D | ReferenceContext.java | 194 public byte[] getBases() { in getBases() method in ReferenceContext
203 return cachedSequence.getBases(); in getBases()
214 public byte[] getBases(final SimpleInterval window) { in getBases() method in ReferenceContext
226 return dataSource.queryAndPrefetch(trimmedWindow).getBases(); in getBases()
237 public byte[] getBases(final int windowLeadingBases, final int windowTrailingBases) { in getBases() method in ReferenceContext
249 return dataSource.queryAndPrefetch(trimmedWindow).getBases(); in getBases()
256 final byte[] bases = getBases(); in getForwardBases()
411 return getBases()[interval.getStart() - window.getStart()]; in getBase()
431 return new String(getBases(newWindow)); in getKmerAround()
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| /dports/games/openxcom/OpenXcom-1.0/src/Basescape/ |
| H A D | BasescapeState.cpp | 116 _mini->setBases(_game->getSavedGame()->getBases()); in BasescapeState()
183 …tor<Base*>::iterator i = _game->getSavedGame()->getBases()->begin(); i != _game->getSavedGame()->g… in ~BasescapeState()
222 _btnNewBase->setVisible(_game->getSavedGame()->getBases()->size() < MiniBaseView::MAX_BASES); in init()
231 if (!_game->getSavedGame()->getBases()->empty()) in setBase()
235 for (size_t i = 0; i < _game->getSavedGame()->getBases()->size(); ++i) in setBase()
237 if (_game->getSavedGame()->getBases()->at(i) == base) in setBase()
249 _base = _game->getSavedGame()->getBases()->front(); in setBase()
489 if (base < _game->getSavedGame()->getBases()->size()) in miniClick()
491 _base = _game->getSavedGame()->getBases()->at(base); in miniClick()
513 for (size_t i = 0; i < _game->getSavedGame()->getBases()->size(); ++i) in handleKeyPress()
[all …]
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| H A D | DismantleFacilityState.cpp | 127 …tor<Base*>::iterator i = _game->getSavedGame()->getBases()->begin(); i != _game->getSavedGame()->g… in btnOkClick()
131 _game->getSavedGame()->getBases()->erase(i); in btnOkClick()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/haplotype/ |
| H A D | Haplotype.java | 26 Comparator.comparingInt((Haplotype hap) -> hap.getBases().length)
100 …ewBases = AlignmentUtils.getBasesCoveringRefInterval(newStart, newStop, getBases(), 0, getCigar()); in trim()
133 return h instanceof Haplotype && Arrays.equals(getBases(), ((Haplotype) h).getBases()); in equals()
138 return Arrays.hashCode(getBases()); in hashCode()
224 final byte[] myBases = getBases(); in insertAllele()
233 …newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, altAllele.getBases()); // the alt allele … in insertAllele()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/reference/ |
| H A D | ReferenceBases.java | 46 if (!Arrays.equals(getBases(), that.getBases())) return false; in equals()
53 int result = Arrays.hashCode(getBases()); in hashCode()
58 public byte[] getBases() { in getBases() method in ReferenceBases
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/ |
| H A D | ReadThreadingAssemblerUnitTest.java | 108 …l byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getEnd()).getBases(); in testAssembleRef()
127 …l byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getEnd()).getBases(); in testAssembleRefAndSNP()
129 … final Allele altBase = Allele.create((byte) (refBase.getBases()[0] == 'A' ? 'C' : 'A'), false); in testAssembleRefAndSNP()
136 …l byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getEnd()).getBases(); in testAssembleRefAndDeletion()
139 final Allele altBase = Allele.create(refBase.getBases()[0], false); in testAssembleRefAndDeletion()
147 …l byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getEnd()).getBases(); in testAssembleRefAndInsertion()
183 c.add(new CigarElement(refHaplotype.getBases().length, CigarOperator.M)); in assemble()
205 final String ref = new String(seq.getSubsequenceAt(contig, start, end).getBases()); in makeSimpleAssemblyTestData()
292 final String seq = new String(path.getBases()); in assertSingleBubble()
403 …inal byte[] refPath = paths.get(0).getBases().length == ref.length() ? paths.get(0).getBases() : p… in testSingleIndelAsDoubleIndel3Reads()
[all …]
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | ArtificialReadUtils.java | 665 … String cigarString = (offsetIntoRead + 1) + "M" + (insertionAllele.getBases().length - 1) + "I"; in createSplicedInsertionPileupElement()
675 final byte[] bases = gatkRead.getBases(); in createSplicedInsertionPileupElement()
676 final int newReadLength = lengthOfRead + insertionAllele.getBases().length - 1; in createSplicedInsertionPileupElement()
678 …te[] basesToInsert = ArrayUtils.subarray(insertionAllele.getBases(), 1, insertionAllele.getBases()… in createSplicedInsertionPileupElement()
682 destBases[offsetIntoRead] = insertionAllele.getBases()[0]; in createSplicedInsertionPileupElement()
710 final int numberOfSpecifiedBasesToDelete = referenceAllele.getBases().length - 1; in createSplicedDeletionPileupElement()
730 final byte[] bases = gatkRead.getBases(); in createSplicedDeletionPileupElement()
733 bases[offsetIntoRead] = referenceAllele.getBases()[0]; in createSplicedDeletionPileupElement()
761 final byte[] newBases = gatkRead.getBases(); in createNonIndelPileupElement()
762 final int upperBound = Math.min(offsetIntoRead + newAllele.getBases().length, lengthOfRead); in createNonIndelPileupElement()
[all …]
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/plot/ |
| H A D | GCSDWindowAlgorithm.java | 107 getStrand ().getBases ().getAverageGCPercent (); in getValues()
123 final int sequence_length = getStrand ().getBases ().getLength (); in calculateSD()
125 final String bases = getStrand ().getBases ().toString (); in calculateSD()
251 return new Float (getStrand ().getBases ().getAverageGCPercent ()); in getAverage()
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| H A D | BaseAlgorithm.java | 60 this.bases = strand.getBases(); in BaseAlgorithm()
74 public Bases getBases () { in getBases() method in BaseAlgorithm
83 return getBases ().getForwardStrand (); in getStrand()
85 return getBases ().getReverseStrand (); in getStrand()
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| H A D | EntropyAlgorithm.java | 70 getStrand().getBases().getComplementPosition(start); in getValues()
72 getStrand().getBases().getComplementPosition(end); in getValues()
221 return new Float(getStrand().getBases().getAverageGCPercent()); in getAverage()
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| H A D | GCFrameAlgorithm.java | 77 getStrand().getBases().getComplementPosition(start); in getValues()
79 getStrand().getBases().getComplementPosition(end); in getValues()
252 return new Float(getStrand().getBases().getAverageGCPercent()); in getAverage()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/transformers/ |
| H A D | IUPACReadTransformer.java | 32 … final byte[] maybeTransformed = BaseUtils.convertIUPACtoN(read.getBases(), strictMode, false); in apply()
33 if (!Arrays.equals(read.getBases(), maybeTransformed)) { in apply()
35 + IntStream.range(0, read.getBases().length).map(idx -> read.getBase(idx)) in apply()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/fasta/ |
| H A D | CachingIndexedFastaSequenceFile.java | 320 if ( ! preserveCase ) StringUtil.toUpperCase(result.getBases()); in getSubsequenceAt()
321 if ( ! preserveIUPAC ) BaseUtils.convertIUPACtoN(result.getBases(), true, start < 1); in getSubsequenceAt()
339 if ( ! preserveCase ) StringUtil.toUpperCase(cache.seq.getBases()); in getSubsequenceAt()
340 … if ( ! preserveIUPAC ) BaseUtils.convertIUPACtoN(cache.seq.getBases(), true, cache.start == 0); in getSubsequenceAt()
350 …seq.getName(), cache.seq.getContigIndex(), Arrays.copyOfRange(cache.seq.getBases(), cacheOffsetSta… in getSubsequenceAt()
353 …tart, cache.stop, start, stop, cacheOffsetStart, cacheOffsetStop, cache.seq.getBases().length), e); in getSubsequenceAt()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/ |
| H A D | SubsettedLikelihoodMatrix.java | 43 …inal Allele a, final Allele b) { return a.getBases() == b.getBases() || Arrays.equals(a.getBases()… in basesMatch()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/ |
| H A D | ComparatorGlue.java | 63 getSubjectEntryGroup ().getBases ().getForwardStrand (); in ComparatorGlue()
65 getQueryEntryGroup ().getBases ().getForwardStrand (); in ComparatorGlue()
463 return getSubjectEntryGroup ().getBases ().getForwardStrand (); in getSubjectForwardStrand()
470 return getQueryEntryGroup ().getBases ().getForwardStrand (); in getQueryForwardStrand()
477 return getSubjectEntryGroup ().getBases ().getReverseStrand (); in getSubjectReverseStrand()
484 return getQueryEntryGroup ().getBases ().getReverseStrand (); in getQueryReverseStrand()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/fasta/ |
| H A D | CachingIndexedFastaSequenceFileUnitTest.java | 88 Assert.assertEquals(cachedVal.getBases(), uncachedVal.getBases()); in testSequential()
132 Assert.assertEquals(cachedVal.getBases(), uncachedVal.getBases()); in testCachingIndexedFastaReaderTwoStage()
181 return new String(reader.getSequence(contig).getBases()); in fetchBaseString()
183 return new String(reader.getSubsequenceAt(contig, start, stop).getBases()); in fetchBaseString()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/ |
| H A D | SimpleEntryGroup.java | 93 getBases().addSequenceChangeListener(getActionController(), in SimpleEntryGroup()
353 return getBases().getLength(); in getSequenceLength()
360 public Bases getBases() in getBases() method in SimpleEntryGroup
376 getBases().reverseComplement(); in reverseComplement()
629 final Bases first_entry_bases = first_entry.getBases(); in addElement()
738 new_entry = new Entry(getBases(), new_doc_entry); in createEntry()
747 new_entry = Entry.newEntry(getBases()); in createEntry()
1015 final Bases new_bases = getBases().truncate(constraint); in truncate()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/ |
| H A D | SVContextUnitTest.java | 116 …Assert.assertEquals(refHaplotype.getBases(), reference.getReferenceBases(expectedInterval).getBase… in testComposeReferenceHaplotype()
141 … new SimpleInterval(vc.getContig(), vc.getStart() + 1 - paddingSize, vc.getStart())).getBases(), in testComposeAlternativeHaplotype()
143 …es(new SimpleInterval(vc.getContig(), vc.getStart() + 1, vc.getStart() + paddingSize)).getBases()); in testComposeAlternativeHaplotype()
147 … new SimpleInterval(vc.getContig(), vc.getStart() + 1 - paddingSize, vc.getStart())).getBases(), in testComposeAlternativeHaplotype()
149 …lVariantLength() + 1, vc.getStart() + svc.getStructuralVariantLength() + paddingSize)).getBases()); in testComposeAlternativeHaplotype()
153 …sertEquals(altHaplotype.getBases(), expectedBases, svc.getStructuralVariantType().name() + " " + n… in testComposeAlternativeHaplotype()
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| /dports/biology/fastp/fastp-0.23.2/src/ |
| H A D | jsonreporter.cpp | 39 long pre_total_bases = preStats1->getBases(); in report()
41 pre_total_bases += preStats2->getBases(); in report()
59 long post_total_bases = postStats1->getBases(); in report()
61 post_total_bases += postStats2->getBases(); in report()
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| /dports/games/openxcom/OpenXcom-1.0/src/Geoscape/ |
| H A D | BaseDestroyedState.cpp | 123 …tor<Base*>::iterator i = _game->getSavedGame()->getBases()->begin(); i != _game->getSavedGame()->g… in btnOkClick()
128 _game->getSavedGame()->getBases()->erase(i); in btnOkClick()
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