| /dports/biology/jalview/jalview/test/jalview/analysis/scoremodels/ |
| H A D | ScoreMatrixTest.java | 45 assertEquals(sm.getMatrixIndex('c'), 2); in testConstructor()
46 assertEquals(sm.getMatrixIndex(' '), -1); in testConstructor()
167 assertEquals(sm.getMatrixIndex('A'), 0); in testGetMatrixIndex()
168 assertEquals(sm.getMatrixIndex('R'), 1); in testGetMatrixIndex()
169 assertEquals(sm.getMatrixIndex('r'), 1); in testGetMatrixIndex()
170 assertEquals(sm.getMatrixIndex('N'), 2); in testGetMatrixIndex()
171 assertEquals(sm.getMatrixIndex('D'), 3); in testGetMatrixIndex()
172 assertEquals(sm.getMatrixIndex('X'), 22); in testGetMatrixIndex()
173 assertEquals(sm.getMatrixIndex('x'), 22); in testGetMatrixIndex()
174 assertEquals(sm.getMatrixIndex('-'), -1); in testGetMatrixIndex()
[all …]
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| /dports/biology/emboss/EMBOSS-6.6.0/jemboss/org/emboss/jemboss/editor/ |
| H A D | Consensus.java | 164 m1 = mat.getMatrixIndex(s1); in calculateCons()
171 m2 = mat.getMatrixIndex(s2); in calculateCons()
200 m1 = mat.getMatrixIndex(s1); in calculateCons()
220 m2 = mat.getMatrixIndex(s2); in calculateCons()
234 m1 = mat.getMatrixIndex(s1); in calculateCons()
246 m1 = mat.getMatrixIndex(s1); in calculateCons()
262 m1 = mat.getMatrixIndex(s1); in calculateCons()
277 m1 = mat.getMatrixIndex(s1); in calculateCons()
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| H A D | PlotConsensus.java | 179 m1 = mat.getMatrixIndex(s1); in createPlot()
183 m2 = mat.getMatrixIndex(s2); in createPlot()
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| H A D | Matrix.java | 309 public int getMatrixIndex(String s) in getMatrixIndex() method in Matrix
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| H A D | GraphicSequenceCollection.java | 457 int m1 = mat.getMatrixIndex(s); in getColor()
472 int m2 = mat.getMatrixIndex(seq.getResidue(pos)); in getColor()
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| /dports/science/plumed/plumed2-2.7.2/src/ves/ |
| H A D | CoeffsMatrix.cpp | 200 size_t CoeffsMatrix::getMatrixIndex(const size_t index1, const size_t index2) const { in getMatrixIndex() function in PLMD::ves::CoeffsMatrix
234 return data[getMatrixIndex(index1,index2)]; in getValue()
244 data[getMatrixIndex(index1,index2)]=value; in setValue()
254 return data[getMatrixIndex(index1,index2)]; in operator ()()
259 return data[getMatrixIndex(index1,index2)]; in operator ()()
264 return data[getMatrixIndex(getIndex(indices1),getIndex(indices2))]; in operator ()()
269 return data[getMatrixIndex(getIndex(indices1),getIndex(indices2))]; in operator ()()
295 data[getMatrixIndex(index1,index2)]+=value; in addToValue()
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| H A D | CoeffsMatrix.h | 117 size_t getMatrixIndex(const size_t, const size_t) const;
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| H A D | VesBias.h | 308 …nst unsigned int coeffs_id) const {return hessian_pntrs_[coeffs_id]->getMatrixIndex(index1,index2)… in getHessianIndex()
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| /dports/biology/jalview/jalview/src/jalview/analysis/scoremodels/ |
| H A D | ScoreMatrix.java | 312 public int getMatrixIndex(char c) in getMatrixIndex() method in ScoreMatrix
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| /dports/graphics/opencollada/OpenCOLLADA-1.6.68/COLLADAMax/include/ |
| H A D | COLLADAMaxAnimationExporter.h | 179 int getMatrixIndex() const in getMatrixIndex() function
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| /dports/graphics/opencollada/OpenCOLLADA-1.6.68/COLLADAMax/src/ |
| H A D | COLLADAMaxAnimationExporter.cpp | 991 if ( animation.getMatrixIndex() < 0) in getBaseId()
998 baseId += "_" + COLLADASW::Utils::toString(animation.getMatrixIndex()) + "_"; in getBaseId()
1014 if ( animation.getMatrixIndex() < 0) in getTarget()
1021 target += "(" + COLLADASW::Utils::toString(animation.getMatrixIndex()) + ")"; in getTarget()
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| /dports/biology/jalview/jalview/src/jalview/analysis/ |
| H A D | Conservation.java | 229 sqnum[j] = sm.getMatrixIndex(residue); in calcSeqNum()
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| H A D | AlignSeq.java | 778 encoded[i] = scoreMatrix.getMatrixIndex(c); in indexEncode()
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