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Searched defs:alignPtr (Results 1 – 18 of 18) sorted by relevance

/dports/biology/clustalw/clustalw-2.1/src/tree/
H A DTreeInterface.cpp61 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 …]
H A DClusterTreeOutput.cpp46 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()
H A DClusterTree.cpp41 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()
H A DUnRootedClusterTree.cpp29 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()
H A DTree.cpp109 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()
/dports/biology/clustalw/clustalw-2.1/src/tree/UPGMA/
H A DRootedTreeOutput.cpp21 … 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()
H A DRootedClusterTree.cpp17 …usterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, in treeFromDistMatrix()
106 void RootedClusterTree::treeFromAlignment(TreeNames* treeNames, Alignment *alignPtr) in treeFromAlignment()
/dports/biology/clustalw/clustalw-2.1/src/fileInput/
H A DFileReader.cpp70 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()
/dports/biology/clustalw/clustalw-2.1/src/alignment/
H A DAlignmentOutput.cpp76 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()
/dports/graphics/opencv/opencv-4.5.3/3rdparty/carotene/src/
H A Dcommon.hpp90 template<typename T> inline T* alignPtr(T* ptr, size_t n=sizeof(T)) in alignPtr() function
/dports/lang/ghc/ghc-8.10.7/libraries/base/GHC/
H A DPtr.hs77 alignPtr addr@(Ptr a) (I# i) function
/dports/devel/ignition-common/ignitionrobotics-ign-common-a5c4d5a35bb8/src/
H A DPluginLoader.cc239 void *alignPtr = dlsym(_dlHandle, alignSymbol.c_str()); in LoadPlugins() local
/dports/emulators/mess/mame-mame0226/3rdparty/bx/include/bx/inline/
H A Dallocator.inl32 inline void* alignPtr(void* _ptr, size_t _extra, size_t _align) function
/dports/emulators/mame/mame-mame0226/3rdparty/bx/include/bx/inline/
H A Dallocator.inl32 inline void* alignPtr(void* _ptr, size_t _extra, size_t _align) function
/dports/biology/clustalw/clustalw-2.1/src/pairwise/
H A DFullPairwiseAlign.cpp34 void FullPairwiseAlign::pairwiseAlign(Alignment *alignPtr, DistMatrix *distMat, int iStart, int iEn… in pairwiseAlign()
H A DFastPairwiseAlign.cpp20 void FastPairwiseAlign::pairwiseAlign(Alignment *alignPtr, DistMatrix *distMat, int iStart, in pairwiseAlign()
/dports/graphics/opencv/opencv-4.5.3/modules/core/include/opencv2/core/
H A Dutility.hpp457 template<typename _Tp> static inline _Tp* alignPtr(_Tp* ptr, int n=(int)sizeof(_Tp)) in alignPtr() function
/dports/lang/ficl/ficl-4.1.0/
H A Dcompatibility.c93 FICL_PLATFORM_EXTERN void *alignPtr(void *ptr) { return ficlAlignPointer(ptr); } in alignPtr() function