| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/ |
| H A D | BaseEdge.java | 34 return new BaseEdge(isRef(), getMultiplicity()); in copy()
41 public final int getMultiplicity() { in getMultiplicity() method in BaseEdge
50 return Integer.toString(getMultiplicity()); in getDotLabel()
68 return getMultiplicity(); in getPruningMultiplicity()
100 …<BaseEdge> EDGE_MULTIPLICITY_ORDER = Comparator.comparingInt(BaseEdge::getMultiplicity).reversed();
113 multiplicity += edge.getMultiplicity(); in add()
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| H A D | AdaptiveChainPruner.java | 41 …t errorCount = probableErrorChains.stream().mapToInt(c -> c.getLastEdge().getMultiplicity()).sum(); in chainsToRemove()
42 …es = chains.stream().mapToInt(c -> c.getEdges().stream().mapToInt(E::getMultiplicity).sum()).sum(); in chainsToRemove()
137 …t((Path<V, E> chain) -> chain.getEdges().stream().mapToInt(BaseEdge::getMultiplicity).max().orElse… in getMaxWeightChain()
145 …city = MathUtils.sumIntFunction(graph.outgoingEdgesOf(chain.getFirstVertex()), E::getMultiplicity); in chainLogOdds()
146 …icity = MathUtils.sumIntFunction(graph.incomingEdgesOf(chain.getLastVertex()), E::getMultiplicity); in chainLogOdds()
148 final int leftMultiplicity = chain.getEdges().get(0).getMultiplicity(); in chainLogOdds()
149 final int rightMultiplicity = chain.getLastEdge().getMultiplicity(); in chainLogOdds()
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| H A D | JTBestHaplotype.java | 143 totalOutgoingMultiplicity += edge.getMultiplicity(); in getApplicableNextEdgesBasedOnJunctionTrees()
150 totalOutgoingMultiplicity != 0 && edge.getMultiplicity() != 0) { in getApplicableNextEdgesBasedOnJunctionTrees()
154 if ((edge.isRef() && edge.getMultiplicity() == 1) && in getApplicableNextEdgesBasedOnJunctionTrees()
161 …output.add(new JTBestHaplotype<>(this, chainCopy, edge.getMultiplicity(), totalOutgoingMultiplicit… in getApplicableNextEdgesBasedOnJunctionTrees()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/ |
| H A D | BaseEdgeUnitTest.java | 32 Assert.assertEquals(e.getMultiplicity(), mult); in testBasic()
44 Assert.assertEquals(e.getMultiplicity(), mult + 1); in testBasic()
51 Assert.assertEquals(e.getMultiplicity(), mult + 3); in testBasic()
59 Assert.assertEquals(copy.getMultiplicity(), e.getMultiplicity()); in testBasic()
73 Assert.assertEquals(e1.getMultiplicity(), mult*2); in testAdd()
87 Assert.assertEquals(e1e2.getMultiplicity(), 4); in testAddOr()
92 Assert.assertEquals(e1e2e3.getMultiplicity(), 4); in testAddOr()
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| H A D | MultiSampleEdgeUnitTest.java | 47 Assert.assertEquals(edge.getMultiplicity(), 0); in testMultiplicity()
54 Assert.assertEquals(edge.getMultiplicity(), copy.getMultiplicity()); in testMultiplicity()
64 Assert.assertEquals(edge.getMultiplicity(), total); in testMultiplicity()
74 Assert.assertEquals(edge.getMultiplicity(), total); in testMultiplicity()
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| /dports/lang/maude/maude-2.7.1/src/ACU_Theory/ |
| H A D | ACU_FastMerge.cc | 118 d->multiplicity = s1.getMultiplicity(); in fastMerge()
126 d->multiplicity = s0->multiplicity + s1.getMultiplicity(); in fastMerge()
170 d->multiplicity = s0.getMultiplicity(); in fastMerge()
179 d->multiplicity = s1.getMultiplicity(); in fastMerge()
187 d->multiplicity = s0.getMultiplicity() + s1.getMultiplicity(); in fastMerge()
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| H A D | ACU_TreeMatcher.cc | 45 if (j.getMultiplicity() < multiplicity) in eliminateBoundVariables()
66 if (j.getMultiplicity() < multiplicity) in eliminateGroundAliens()
94 if (j.getMultiplicity() < multiplicity) in eliminateGroundedOutAliens()
134 if (j.getMultiplicity() >= multiplicity) in greedyMatch()
252 int m = i.getMultiplicity(); in makeHighMultiplicityAssignment()
278 m = i.getMultiplicity(); in makeHighMultiplicityAssignment()
402 int m = i.getMultiplicity(); in tryToBindLastVariable()
624 int m = i.getMultiplicity(); in forcedLoneVariableCase()
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| H A D | ACU_TreeDagNode.cc | 60 hashValue = hash(hashValue, i.getDagNode()->getHashValue(), i.getMultiplicity()); in getHashValue()
80 r = i.getMultiplicity() - j.getMultiplicity(); in compareArguments()
221 j->multiplicity = i.getMultiplicity(); in treeToArgVec()
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| H A D | ACU_DagNode.hh | 85 int getMultiplicity(int i) const;
196 ACU_DagNode::getMultiplicity(int i) const in getMultiplicity() function in ACU_DagNode
226 d->multiplicity = i.getMultiplicity(); in fastCopy()
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| /dports/lang/maude/maude-2.7.1/src/ACU_Persistent/ |
| H A D | ACU_FastIter.hh | 44 int getMultiplicity() const;
67 ACU_FastIter::getMultiplicity() const in getMultiplicity() function in ACU_FastIter
69 return top()->getMultiplicity(); in getMultiplicity()
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| H A D | ACU_SlowIter.hh | 44 int getMultiplicity() const;
72 ACU_SlowIter::getMultiplicity() const in getMultiplicity() function in ACU_SlowIter
74 return top()->getMultiplicity(); in getMultiplicity()
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| H A D | ACU_Copy.cc | 47 int t = parent->getMultiplicity(); in copy()
84 parent->getMultiplicity(), in copy()
128 int t = source->getMultiplicity(); in copy()
165 source->getMultiplicity(), in copy()
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| H A D | ACU_RedBlackNode.cc | 62 key->getMultiplicity(), in blackNode()
101 ACU_RedBlackNode* n = new ACU_RedBlackNode(c, getMultiplicity(), left, right, getMaxMult()); in canonicalRebuild()
169 "\tmultiplicity = " << getMultiplicity() << in dump()
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| H A D | ACU_Insert.cc | 53 int newMult = p->getMultiplicity() + multiplicity; in consInsert()
96 multiplicity = parent->getMultiplicity(); in consInsert()
118 multiplicity = parent->getMultiplicity(); in consInsert()
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| H A D | ACU_Pair.hh | 37 int getMultiplicity() const;
72 ACU_Pair::getMultiplicity() const in getMultiplicity() function in ACU_Pair
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| H A D | ACU_Tree.cc | 125 f = symbol->computeMultSortIndex(f, f, root->getMultiplicity() - 1); in computeBaseSort2()
145 root->getMultiplicity()); in computeBaseSort2()
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| /dports/biology/abyss/abyss-2.3.1/Assembly/ |
| H A D | ErodeAlgorithm.h | 75 if (data.getMultiplicity() < opt::erode in erode()
76 || data.getMultiplicity(SENSE) < opt::erodeStrand in erode()
77 || data.getMultiplicity(ANTISENSE) < opt::erodeStrand) { in erode()
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| H A D | VertexData.h | 74 unsigned getMultiplicity(extDirection dir) const in getMultiplicity() function
79 unsigned getMultiplicity() const in getMultiplicity() function
98 assert(getMultiplicity() == multiplicity); in setMultiplicity()
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| H A D | CoverageAlgorithm.h | 22 h.insert(it->second.getMultiplicity()); in coverageHistogram()
124 if (it->second.getMultiplicity() < kc) in applyKmerCoverageThreshold()
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| /dports/biology/abyss/abyss-2.3.1/kmerprint/ |
| H A D | kmerprint.cc | 69 << opt::ofs << data.getMultiplicity() in print()
81 << opt::ofs << data.getMultiplicity(sense) in print()
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| /dports/math/gfan/gfan0.6.2/src/ |
| H A D | tropical_weildivisor.cpp | 96 evaluationVector+=j->getMultiplicity()*ray; in weilDivisor()
98 multiplicity+=j->getMultiplicity()*localG.evaluatePiecewiseLinearFunction(ray); in weilDivisor()
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| H A D | app_isbalanced.cpp | 155 sum=sum+(j->getMultiplicity()*(j->semiGroupGeneratorOfRay())); in main()
160 debug<<j->getMultiplicity()<<(j->semiGroupGeneratorOfRay())<<"\n"; in main()
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| /dports/graphics/quickqanava/QuickQanava-ab88d77ec62175b9fd499a154ffaf92f7bf23989/src/ |
| H A D | qanPortItem.h | 110 …Q_PROPERTY( Multiplicity multiplicity READ getMultiplicity WRITE setMultiplicity NOTIFY multiplici… in Q_PROPERTY()
112 inline Multiplicity getMultiplicity() const noexcept { return _multiplicity; } in Q_PROPERTY()
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| /dports/math/gfanlib/gfan0.6.2/src/ |
| H A D | tropical_weildivisor.cpp | 96 evaluationVector+=j->getMultiplicity()*ray; in weilDivisor()
98 multiplicity+=j->getMultiplicity()*localG.evaluatePiecewiseLinearFunction(ray); in weilDivisor()
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| /dports/devel/umbrello/umbrello-21.12.3/unittests/ |
| H A D | testassociation.cpp | 136 QCOMPARE(a.getMultiplicity(Uml::RoleType::A), QString()); in test_multiplicity()
137 QCOMPARE(a.getMultiplicity(Uml::RoleType::B), QString()); in test_multiplicity()
140 QCOMPARE(a.getMultiplicity(Uml::RoleType::A), QLatin1String("1")); in test_multiplicity()
141 QCOMPARE(a.getMultiplicity(Uml::RoleType::B), QLatin1String("2")); in test_multiplicity()
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