Home
last modified time | relevance | path

Searched refs:alignmentIndex (Results 1 – 21 of 21) sorted by relevance

/dports/biology/jalview/jalview/src/jalview/datamodel/
H A DHiddenSequences.java160 if (alignmentIndex < 0 || hiddenSequences[alignmentIndex] != null) in hideSequence()
166 hiddenSequences[alignmentIndex] = sequence; in hideSequence()
219 int end = adjustForHiddenSeqs(alignmentIndex); in showSequence()
238 asequences.add(alignmentIndex, seq); in showSequence()
267 return alignmentIndex; in findIndexWithoutHiddenSeqs()
272 if (hiddenSequences.length <= alignmentIndex) in findIndexWithoutHiddenSeqs()
282 while (index <= alignmentIndex) in findIndexWithoutHiddenSeqs()
291 return (alignmentIndex - hiddenSeqs + diff); in findIndexWithoutHiddenSeqs()
339 return alignmentIndex; in adjustForHiddenSeqs()
347 alignmentIndex++; in adjustForHiddenSeqs()
[all …]
H A DAlignmentI.java97 boolean isHidden(int alignmentIndex); in isHidden() argument
H A DAlignment.java806 public boolean isHidden(int alignmentIndex) in isHidden() argument
808 return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null); in isHidden()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/bma_refine/
H A DColumnScorer.cpp56 void ColumnScorer::ColumnScores(const BMA& bma, unsigned int alignmentIndex, vector< double >& colu… in ColumnScores() argument
58 columnScores.push_back(ColumnScore(bma, alignmentIndex)); in ColumnScores()
90 BMAUtils::GetPSSMScoresForColumn(bma, alignmentIndex, scores); in GetAndCopyPSSMScoresForColumn()
113 GetAndCopyPSSMScoresForColumn(bma, alignmentIndex, scores, rowScores); in ColumnScore()
132 GetAndCopyPSSMScoresForColumn(bma, alignmentIndex, scores, rowScores); in ColumnScore()
153 GetAndCopyPSSMScoresForColumn(bma, alignmentIndex, scores, rowScores); in ColumnScore()
184 GetAndCopyPSSMScoresForColumn(bma, alignmentIndex, scores, rowScores); in ColumnScore()
250 …bool inPssm, isAligned = BMAUtils::IsColumnOfType(bma, alignmentIndex, align_refine::eAlignedResid… in ColumnScore()
254 GetAndCopyPSSMScoresForColumn(bma, alignmentIndex, scores, rowScores); in ColumnScore()
257 BMAUtils::GetResiduesForColumn(bma, alignmentIndex, residues); in ColumnScore()
[all …]
H A DBMAUtils.cpp63 if (alignmentIndex < pos + (*blit)->m_width) { in BEGIN_SCOPE()
177 unsigned int seqIndex = 0, alignmentIndex = 0; in MapAlignmentIndexToSeqIndex() local
201 aI2sI[alignmentIndex] = seqIndex; in MapAlignmentIndexToSeqIndex()
207 ++alignmentIndex; in MapAlignmentIndexToSeqIndex()
405 unsigned int alignmentIndex, aWidth; in PrintPSSMByColumn() local
418 for (alignmentIndex = 0; alignmentIndex < aWidth; ++alignmentIndex) { in PrintPSSMByColumn()
459 if (column < alignmentIndex + (*b)->m_width) { in PrintPSSMForColumn()
461 blockIndex = column - alignmentIndex; in PrintPSSMForColumn()
464 alignmentIndex += (*b)->m_width; in PrintPSSMForColumn()
541 unsigned int alignmentIndex = 0; in IsColumnOfType() local
[all …]
H A DBlockEditor.cpp136 bool CBlockedAlignmentEditor::GetCharacterForColumn(unsigned alignmentIndex, unsigned row, char* re… in GetCharacterForColumn() argument
149 if (alignmentIndex < pos + (*blit)->m_width) { in GetCharacterForColumn()
151 result = m_bma->GetCharacterAt(alignmentIndex, row, just, residue); in GetCharacterForColumn()
374 unsigned CBlockedAlignmentEditor::GetSeqIndexForColumn(unsigned alignmentIndex, unsigned row) const… in GetSeqIndexForColumn() argument
386 if (alignmentIndex < pos + (*blit)->m_width) { in GetSeqIndexForColumn()
387 … result = GetSeqIndexForColumn(alignmentIndex - pos, row, (*blit).GetPointer(), blockNum); in GetSeqIndexForColumn()
396 bool CBlockedAlignmentEditor::IsResidueAtIndexOnAllRows(unsigned alignmentIndex) const { in IsResidueAtIndexOnAllRows()
410 if (alignmentIndex < pos + (*blit)->m_width) { in IsResidueAtIndexOnAllRows()
414 …if (GetSeqIndexForColumn(alignmentIndex - pos, i, (*blit).GetPointer(), blockNum) == BMA::eUndefin… in IsResidueAtIndexOnAllRows()
H A DBlockBoundaryAlgorithm.cpp79 bool SimpleBoundaryExtender::PassAllTests(const BMA& bma, unsigned int alignmentIndex) const { in PassAllTests()
87 columnScore = m_columnScorers[j]->ColumnScore(bma, alignmentIndex, &rowScoreCache); in PassAllTests()
89 …TRACE_MESSAGE_CL(" (aindex, score, thold, scorer) = (" << alignmentIndex+1 << ", " << col… in PassAllTests()
154 bool SimpleBoundaryShrinker::PassAllTests(const BMA& bma, unsigned int alignmentIndex) const { in PassAllTests()
162 columnScore = m_columnScorers[j]->ColumnScore(bma, alignmentIndex, &rowScoreCache); in PassAllTests()
164 …TRACE_MESSAGE_CL(" (aindex, score, thold, scorer) = (" << alignmentIndex+1 << ", " << col… in PassAllTests()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/structure/bma_refine/
H A DColumnScorer.hpp75 …virtual double ColumnScore(const BMA& bma, unsigned int alignmentIndex, vector< double >* rowScore…
81 …virtual void ColumnScores(const BMA& bma, unsigned int alignmentIndex, vector< double >& columnSco…
106 …void GetAndCopyPSSMScoresForColumn(const BMA& bma, unsigned int alignmentIndex, vector< int >& sco…
123 …virtual double ColumnScore(const BMA& bma, unsigned int alignmentIndex, vector< double >* rowScore…
137 …virtual double ColumnScore(const BMA& bma, unsigned int alignmentIndex, vector< double >* rowScore…
146 …virtual double ColumnScore(const BMA& bma, unsigned int alignmentIndex, vector< double >* rowScore…
192 …virtual double ColumnScore(const BMA& bma, unsigned int alignmentIndex, vector< double >* rowScore…
208 …virtual double ColumnScore(const BMA& bma, unsigned int alignmentIndex, vector< double >* rowScore…
219 …virtual double ColumnScore(const BMA& bma, unsigned int alignmentIndex, vector< double >* rowScore…
220 …virtual void ColumnScores(const BMA& bma, unsigned int alignmentIndex, vector< double >& columnSco…
H A DBMAUtils.hpp69 …static bool GetCharacterAndIndexForColumn(const BMA& bma, unsigned alignmentIndex, unsigned row, c…
70 …static bool GetCharacterForColumn(const BMA& bma, unsigned alignmentIndex, unsigned row, char* res…
78 …static void GetResiduesForColumn(const BMA& bma, unsigned alignmentIndex, vector< char >& residues…
84 …static void GetPSSMScoresForColumn(const BMA& bma, unsigned alignmentIndex, vector< int >& scores,…
H A DBlockEditor.hpp87 bool IsResidueAtIndexOnAllRows(unsigned alignmentIndex) const;
88 unsigned GetSeqIndexForColumn(unsigned alignmentIndex, unsigned row) const;
89 bool GetCharacterForColumn(unsigned alignmentIndex, unsigned row, char* residue) const;
H A DBlockBoundaryAlgorithm.hpp141 bool PassAllTests(const BMA& bma, unsigned int alignmentIndex) const;
166 bool PassAllTests(const BMA& bma, unsigned int alignmentIndex) const;
/dports/www/firefox-esr/firefox-91.8.0/mobile/android/geckoview/src/thirdparty/java/org/mozilla/thirdparty/com/google/android/exoplayer2/text/ssa/
H A DSsaStyle.java108 styleValues[format.nameIndex].trim(), parseAlignment(styleValues[format.alignmentIndex])); in fromStyleLine()
156 public final int alignmentIndex; field in SsaStyle.Format
159 private Format(int nameIndex, int alignmentIndex, int length) { in Format() argument
161 this.alignmentIndex = alignmentIndex; in Format()
173 int alignmentIndex = C.INDEX_UNSET; in fromFormatLine() local
182 alignmentIndex = i; in fromFormatLine()
186 return nameIndex != C.INDEX_UNSET ? new Format(nameIndex, alignmentIndex, keys.length) : null; in fromFormatLine()
/dports/www/firefox/firefox-99.0/mobile/android/exoplayer2/src/main/java/org/mozilla/thirdparty/com/google/android/exoplayer2/text/ssa/
H A DSsaStyle.java108 styleValues[format.nameIndex].trim(), parseAlignment(styleValues[format.alignmentIndex])); in fromStyleLine()
156 public final int alignmentIndex; field in SsaStyle.Format
159 private Format(int nameIndex, int alignmentIndex, int length) { in Format() argument
161 this.alignmentIndex = alignmentIndex; in Format()
173 int alignmentIndex = C.INDEX_UNSET; in fromFormatLine() local
182 alignmentIndex = i; in fromFormatLine()
186 return nameIndex != C.INDEX_UNSET ? new Format(nameIndex, alignmentIndex, keys.length) : null; in fromFormatLine()
/dports/mail/thunderbird/thunderbird-91.8.0/mobile/android/geckoview/src/thirdparty/java/org/mozilla/thirdparty/com/google/android/exoplayer2/text/ssa/
H A DSsaStyle.java108 styleValues[format.nameIndex].trim(), parseAlignment(styleValues[format.alignmentIndex])); in fromStyleLine()
156 public final int alignmentIndex; field in SsaStyle.Format
159 private Format(int nameIndex, int alignmentIndex, int length) { in Format() argument
161 this.alignmentIndex = alignmentIndex; in Format()
173 int alignmentIndex = C.INDEX_UNSET; in fromFormatLine() local
182 alignmentIndex = i; in fromFormatLine()
186 return nameIndex != C.INDEX_UNSET ? new Format(nameIndex, alignmentIndex, keys.length) : null; in fromFormatLine()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/
H A Dblock_multiple_alignment.hpp175 …void GetAlignedBlockPosition(unsigned int alignmentIndex, int *blockColumn, int *blockWidth) const;
185 bool SplitBlock(unsigned int alignmentIndex);
196 bool DeleteBlock(unsigned int alignmentIndex);
206 …bool ZipAlignResidue(unsigned int row, unsigned int alignmentIndex, bool moveRight, eUnalignedJust…
209 …bool OptimizeBlock(unsigned int row, unsigned int alignmentIndex, eUnalignedJustification justific…
300 …int GetAlignedBlockNumber(unsigned int alignmentIndex) const { return blockMap[alignmentIndex].ali… in GetAlignedBlockNumber()
303 int GetLoopLength(unsigned int row, unsigned int alignmentIndex);
307 double GetRelativeAlignmentFraction(unsigned int alignmentIndex) const;
H A Dblock_multiple_alignment.cpp649 const BlockInfo& info = blockMap[alignmentIndex]; in GetAlignedBlockPosition()
974 if (blockMap[alignmentIndex].block->IsAligned()) { in ZipAlignResidue()
980 …moveRight ? GetBlockAfter(blockMap[alignmentIndex].block) : GetBlockBefore(blockMap[alignmentIndex… in ZipAlignResidue()
986 return ShiftRow(row, alignmentIndex, in ZipAlignResidue()
1103 const BlockInfo& info = blockMap[alignmentIndex]; in SplitBlock()
1242 Block *block = blockMap[alignmentIndex].block; in DeleteBlock()
1726 if (!blockMap[alignmentIndex].block->IsAligned()) in GetRelativeAlignmentFraction()
1756 unsigned int alignmentIndex, blockColumn; in GetAlignmentIndex() local
1760 for (alignmentIndex=0; alignmentIndex<totalWidth; ++alignmentIndex) { in GetAlignmentIndex()
1763 if (block != blockMap[alignmentIndex].block) { in GetAlignmentIndex()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/structure/struct_util/
H A Dsu_block_multiple_alignment.hpp142 unsigned int GetAlignedBlockNumber(unsigned int alignmentIndex) const in GetAlignedBlockNumber()
143 { return m_blockMap[alignmentIndex].alignedBlockNum; } in GetAlignedBlockNumber()
164 void GetAlignedBlockPosition(unsigned int alignmentIndex,
175 bool SplitBlock(unsigned int alignmentIndex);
187 bool DeleteBlock(unsigned int alignmentIndex);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/struct_util/
H A Dsu_block_multiple_alignment.cpp394 void BlockMultipleAlignment::GetAlignedBlockPosition(unsigned int alignmentIndex, in GetAlignedBlockPosition() argument
398 const BlockInfo& info = m_blockMap[alignmentIndex]; in GetAlignedBlockPosition()
745 bool BlockMultipleAlignment::SplitBlock(unsigned int alignmentIndex) in SplitBlock() argument
747 const BlockInfo& info = m_blockMap[alignmentIndex]; in SplitBlock()
888 bool BlockMultipleAlignment::DeleteBlock(unsigned int alignmentIndex) in DeleteBlock() argument
890 Block *block = m_blockMap[alignmentIndex].block; in DeleteBlock()
1313 unsigned int alignmentIndex, blockColumn; in GetAlignmentIndex() local
1317 for (alignmentIndex=0; alignmentIndex<m_totalWidth; ++alignmentIndex) { in GetAlignmentIndex()
1320 if (block != m_blockMap[alignmentIndex].block) { in GetAlignmentIndex()
1321 block = m_blockMap[alignmentIndex].block; in GetAlignmentIndex()
[all …]
/dports/biology/jalview/jalview/src/jalview/api/
H A DAlignViewportI.java385 int adjustForHiddenSeqs(int alignmentIndex); in adjustForHiddenSeqs() argument
/dports/graphics/opencv/opencv-4.5.3/contrib/modules/wechat_qrcode/src/zxing/qrcode/detector/
H A Ddetector.hpp108 Ref<DetectorResult> getResultViaAlignment(int patternIdx, int alignmentIndex,
/dports/biology/jalview/jalview/src/jalview/viewmodel/
H A DAlignmentViewport.java1631 public int adjustForHiddenSeqs(int alignmentIndex) in adjustForHiddenSeqs() argument
1634 .adjustForHiddenSeqs(alignmentIndex); in adjustForHiddenSeqs()