/dports/biology/clustalw/clustalw-2.1/src/tree/ |
H A D | TreeInterface.cpp | 61 Alignment *alignPtr, int seq1, int nSeqs, in getWeightsFromDistMat() 80 TreeInterface::getWeightsForProfileAlign(Alignment* alignPtr, DistMatrix* distMat, in getWeightsForProfileAlign() 104 TreeInterface::getWeightsAndStepsFromTree(Alignment* alignPtr, in getWeightsAndStepsFromTree() 120 TreeInterface::getWeightsFromGuideTree(Alignment* alignPtr, DistMatrix* distMat, in getWeightsFromGuideTree() 136 TreeInterface::generateTreeFromDistMat(DistMatrix* distMat, Alignment *alignPtr, in generateTreeFromDistMat() 156 TreeInterface::treeFromAlignment(TreeNames* treeNames, Alignment *alignPtr) in treeFromAlignment() 171 TreeInterface::bootstrapTree(TreeNames* treeNames, Alignment *alignPtr) in bootstrapTree() 257 TreeInterface::readTreeAndCalcWeightsNJ(Tree* groupTree, Alignment* alignPtr, in readTreeAndCalcWeightsNJ() 440 TreeInterface::getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, in getWeightsAndStepsFromTreeNJ() 525 Alignment *alignPtr, int seq1, int nSeqs, in getWeightsFromDistMatUPGMA() [all …]
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H A D | ClusterTreeOutput.cpp | 46 Alignment *alignPtr, DistMatrix* distMat, vector<int>* bootTotals) in printPhylipTree() 107 int startRow, int flag, Alignment *alignPtr, vector<int>* bootTotals) in twoWaySplit() 228 Alignment *alignPtr, DistMatrix* distMat, vector<int>* bootTotals) in printNexusTree() 306 int startRow, int flag, Alignment *alignPtr, vector<int>* bootTotals) in twoWaySplitNexus()
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H A D | ClusterTree.cpp | 41 clustalw::Alignment *alignPtr) in distanceMatrixOutput() 101 void ClusterTree::treeGapDelete(clustalw::Alignment *alignPtr) in treeGapDelete() 132 int ClusterTree::dnaDistanceMatrix(ofstream* treeFile, clustalw::Alignment *alignPtr) in dnaDistanceMatrix() 384 int ClusterTree::protDistanceMatrix(ofstream* treeFile, clustalw::Alignment *alignPtr) in protDistanceMatrix() 568 void ClusterTree::calcPercIdentity(ofstream* pfile, clustalw::Alignment *alignPtr) in calcPercIdentity() 850 clustalw::Alignment* alignPtr) in calcQuickDistMatForAll() 889 ofstream* nexusFile, clustalw::Alignment* alignPtr, in calcQuickDistMatForSubSet()
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H A D | UnRootedClusterTree.cpp | 29 void UnRootedClusterTree::treeFromAlignment(TreeNames* treeNames, Alignment *alignPtr) in treeFromAlignment() 171 Alignment *alignPtr, int seq1, int nSeqs, in treeFromDistMatrix() 277 void UnRootedClusterTree::bootstrapTree(TreeNames* treeNames, Alignment *alignPtr) in bootstrapTree()
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H A D | Tree.cpp | 109 int Tree::readTree(clustalw::Alignment* alignPtr, const string& treeFileName, int firstSeq, int las… in readTree() 332 int Tree::calcSimilarities(clustalw::Alignment* alignPtr, clustalw::DistMatrix* distMat) in calcSimilarities()
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/dports/biology/clustalw/clustalw-2.1/src/tree/UPGMA/ |
H A D | RootedTreeOutput.cpp | 21 … RootedTreeOutput::printPhylipTree(RootedGuideTree* tree, ofstream* ptrToFile, Alignment *alignPtr, in printPhylipTree() 54 Alignment *alignPtr, DistMatrix* distMat) in printNexusTree() 95 void RootedTreeOutput::phylipTraverse(ofstream* ptrToFile, Alignment *alignPtr, Node* t) in phylipTraverse() 125 void RootedTreeOutput::nexusTraverse(ofstream* ptrToFile, Alignment *alignPtr, Node* t) in nexusTraverse()
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H A D | RootedClusterTree.cpp | 17 …usterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, in treeFromDistMatrix() 106 void RootedClusterTree::treeFromAlignment(TreeNames* treeNames, Alignment *alignPtr) in treeFromAlignment()
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/dports/biology/clustalw/clustalw-2.1/src/fileInput/ |
H A D | FileReader.cpp | 70 int FileReader::seqInput(Alignment *alignPtr, bool append, string *offendingSeq) in seqInput() 142 int FileReader::readSeqs(Alignment *alignPtr, int firstSeq, string *offendingSeq) in readSeqs() 316 int FileReader::profileInput(Alignment *alignPtr) in profileInput()
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/dports/biology/clustalw/clustalw-2.1/src/alignment/ |
H A D | AlignmentOutput.cpp | 76 void AlignmentOutput::createAlignmentOutput(Alignment* alignPtr, int firstSeq, int lastSeq) in createAlignmentOutput() 580 void AlignmentOutput::fastaOut(Alignment* alignPtr, outputRegion partToOutput) in fastaOut() 692 void AlignmentOutput::gcgOut(Alignment* alignPtr, outputRegion partToOutput) in gcgOut() 883 void AlignmentOutput::phylipOut(Alignment* alignPtr, outputRegion partToOutput) in phylipOut() 1042 void AlignmentOutput::nexusOut(Alignment* alignPtr, outputRegion partToOutput) in nexusOut() 1174 void AlignmentOutput::gdeOut(Alignment* alignPtr, outputRegion partToOutput) in gdeOut() 1460 void AlignmentOutput::nbrfOut(Alignment* alignPtr, outputRegion partToOutput) in nbrfOut() 1579 void AlignmentOutput::clustalOut(Alignment* alignPtr, outputRegion partToOutput) in clustalOut() 2226 void AlignmentOutput::findRangeValues(Alignment* alignPtr, rangeNum *rnum, int firstRes, in findRangeValues()
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/dports/graphics/opencv/opencv-4.5.3/3rdparty/carotene/src/ |
H A D | common.hpp | 90 template<typename T> inline T* alignPtr(T* ptr, size_t n=sizeof(T)) in alignPtr() function
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/dports/lang/ghc/ghc-8.10.7/libraries/base/GHC/ |
H A D | Ptr.hs | 77 alignPtr addr@(Ptr a) (I# i) function
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/dports/devel/ignition-common/ignitionrobotics-ign-common-a5c4d5a35bb8/src/ |
H A D | PluginLoader.cc | 239 void *alignPtr = dlsym(_dlHandle, alignSymbol.c_str()); in LoadPlugins() local
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/dports/emulators/mess/mame-mame0226/3rdparty/bx/include/bx/inline/ |
H A D | allocator.inl | 32 inline void* alignPtr(void* _ptr, size_t _extra, size_t _align) function
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/dports/emulators/mame/mame-mame0226/3rdparty/bx/include/bx/inline/ |
H A D | allocator.inl | 32 inline void* alignPtr(void* _ptr, size_t _extra, size_t _align) function
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/dports/biology/clustalw/clustalw-2.1/src/pairwise/ |
H A D | FullPairwiseAlign.cpp | 34 void FullPairwiseAlign::pairwiseAlign(Alignment *alignPtr, DistMatrix *distMat, int iStart, int iEn… in pairwiseAlign()
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H A D | FastPairwiseAlign.cpp | 20 void FastPairwiseAlign::pairwiseAlign(Alignment *alignPtr, DistMatrix *distMat, int iStart, in pairwiseAlign()
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/dports/graphics/opencv/opencv-4.5.3/modules/core/include/opencv2/core/ |
H A D | utility.hpp | 457 template<typename _Tp> static inline _Tp* alignPtr(_Tp* ptr, int n=(int)sizeof(_Tp)) in alignPtr() function
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/dports/lang/ficl/ficl-4.1.0/ |
H A D | compatibility.c | 93 FICL_PLATFORM_EXTERN void *alignPtr(void *ptr) { return ficlAlignPointer(ptr); } in alignPtr() function
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