+++ /dev/null
-/**
- * Author: Mark Larkin
- *
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
- */
-/**
- * Changes:
- * Mark 10-5-2007: Bug fix # 42. Added getWeightsForQtLowScore function.
- * Mark 22-5-2007: Made a change to getWeightsForQtLowScore
- * Mark 23-5-2007: Made a change to getWeightsForQtLowScore
- */
-#ifdef HAVE_CONFIG_H
- #include "config.h"
-#endif
-#include "TreeInterface.h"
-#include <sstream>
-#include "UnRootedClusterTree.h"
-#include "Tree.h"
-#include "../multipleAlign/MSA.h"
-#include "../general/userparams.h"
-#include "../general/debuglogObject.h"
-#include "UPGMA/RootedGuideTree.h"
-#include "UPGMA/RootedClusterTree.h"
-namespace clustalw
-{
-
-/**
- * This will be called by align!
- *
- */
-auto_ptr<AlignmentSteps>
-TreeInterface::getWeightsAndStepsFromDistMat(vector<int>* seqWeights, DistMatrix* distMat,
- Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success)
-{
- #if DEBUGFULL
- if(logObject && DEBUGLOG)
- {
- logObject->logMsg("In getWeightsAndStepsFromDistMat\n");
- }
- #endif
- if(userParameters->getClusterAlgorithm() == UPGMA)
- {
- return getWeightsAndStepsFromDistMatUPGMA(seqWeights, distMat, alignPtr,
- seq1, nSeqs, phylipName, success);
- }
- else
- {
- return getWeightsAndStepsFromDistMatNJ(seqWeights, distMat, alignPtr,
- seq1, nSeqs, phylipName, success);
- }
-}
-
-
-/**
- * This will be called by sequencesAlignToProfile. This function will put the distMat into
- * a similarity matrix.
- */
-void
-TreeInterface::getWeightsFromDistMat(vector<int>* seqWeights, DistMatrix* distMat,
- Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success)
-{
- if(userParameters->getClusterAlgorithm() == UPGMA)
- {
- getWeightsFromDistMatUPGMA(seqWeights, distMat, alignPtr, seq1, nSeqs, phylipName,
- success);
- }
- else
- {
- getWeightsFromDistMatNJ(seqWeights, distMat, alignPtr, seq1, nSeqs, phylipName,
- success);
- }
-}
-
-/**
- * This function will be called by profileAlign
- */
-void
-TreeInterface::getWeightsForProfileAlign(Alignment* alignPtr, DistMatrix* distMat,
- string* p1TreeName, vector<int>* p1Weights, string* p2TreeName,
- vector<int>* p2Weights, int numSeqs, int profile1NumSeqs, bool useTree1,
- bool useTree2, bool* success)
-{
- if(userParameters->getClusterAlgorithm() == UPGMA)
- {
- getWeightsForProfileAlignUPGMA(alignPtr, distMat, p1TreeName, p1Weights, p2TreeName,
- p2Weights, numSeqs, profile1NumSeqs, useTree1, useTree2,
- success);
- }
- else
- {
- getWeightsForProfileAlignNJ(alignPtr, distMat, p1TreeName, p1Weights, p2TreeName,
- p2Weights, numSeqs, profile1NumSeqs, useTree1, useTree2,
- success);
- }
-}
-
-/**
- * This function will be called by doAlignUseOldGuideTree
- *
- */
-auto_ptr<AlignmentSteps>
-TreeInterface::getWeightsAndStepsFromTree(Alignment* alignPtr,
- DistMatrix* distMat, string* treeName,
- vector<int>* seqWeights, int fSeq,
- int numSeqs, bool* success)
-{
- /**
- * This will only use the NJ. It will not use UPGMA
- */
- return getWeightsAndStepsFromTreeNJ(alignPtr, distMat, treeName, seqWeights,
- fSeq, numSeqs, success);
-}
-
-/**
- * Called by sequencesAlignToProfile
- */
-int
-TreeInterface::getWeightsFromGuideTree(Alignment* alignPtr, DistMatrix* distMat,
- string* treeName, vector<int>* seqWeights, int fSeq,
- int nSeqs, bool* success)
-{
- /**
- * This will only use the NJ. It will not use UPGMA
- */
- return getWeightsFromGuideTreeNJ(alignPtr, distMat, treeName, seqWeights, fSeq, nSeqs,
- success);
-}
-
-/**
- * This will be called by doGuideTreeOnly. This does not put the distMat into similarity.
- *
- */
-void
-TreeInterface::generateTreeFromDistMat(DistMatrix* distMat, Alignment *alignPtr,
- int seq1, int nSeqs,
- string* phylipName, bool* success)
-{
- /**
- * This function does not put distMat into similarities
- */
- if(userParameters->getClusterAlgorithm() == UPGMA)
- {
- RootedGuideTree guideTree;
- generateTreeFromDistMatUPGMA(&guideTree, distMat, alignPtr, seq1, nSeqs,
- phylipName, success);
- }
- else
- {
- generateTreeFromDistMatNJ(distMat, alignPtr, seq1, nSeqs, phylipName, success);
- }
-}
-
-void
-TreeInterface::treeFromAlignment(TreeNames* treeNames, Alignment *alignPtr)
-{
- if(userParameters->getClusterAlgorithm() == UPGMA)
- {
- RootedClusterTree clusterTree;
- clusterTree.treeFromAlignment(treeNames, alignPtr);
- }
- else
- {
- UnRootedClusterTree clusterTree;
- clusterTree.treeFromAlignment(treeNames, alignPtr);
- }
-}
-
-void
-TreeInterface::bootstrapTree(TreeNames* treeNames, Alignment *alignPtr)
-{
- /**
- * NOTE We only do bootstrapping on the NJ tree.
- */
- UnRootedClusterTree clusterTree;
- clusterTree.bootstrapTree(treeNames, alignPtr);
-}
-
-
-/**
- * Private functions!!!!
- *
- */
-
-
-/** *******************
- *
- * Neighbour joining functions
- */
-/**
- * Note: After this function has been called the distance matrix will all be in similarities.
- *
- */
-auto_ptr<AlignmentSteps>
-TreeInterface::getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights, DistMatrix* distMat,
- Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success)
-{
- auto_ptr<AlignmentSteps> progSteps;
- generateTreeFromDistMatNJ(distMat, alignPtr, seq1, nSeqs, phylipName, success);
-
- progSteps = getWeightsAndStepsUseOldGuideTreeNJ(distMat, alignPtr, phylipName,
- seqWeights, seq1, nSeqs, success);
- return progSteps;
-}
-
-auto_ptr<AlignmentSteps>
-TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, Alignment *alignPtr,
- string* treeName, vector<int>* seqWeights,
- int fSeq, int nSeqs, bool* success)
-{
- Tree groupTree;
- auto_ptr<AlignmentSteps> progSteps;
-
- if(nSeqs == 1)
- {
- utilityObject->info("Only 1 sequence, cannot do multiple alignment\n");
- *success = false;
- return progSteps;
- }
-
- int status = 0;
-
- status = readTreeAndCalcWeightsNJ(&groupTree, alignPtr, distMat, treeName,
- seqWeights, fSeq, nSeqs);
-
- if(status == 0)
- {
- *success = false;
- return progSteps;
- }
-
- progSteps = groupTree.createSets(0, nSeqs);
- int _numSteps = progSteps->getNumSteps();
-
- utilityObject->info("There are %d groups", _numSteps);
- // clear the memory used for the phylogenetic tree
-
- if (nSeqs >= 2)
- {
- groupTree.clearTree(NULL);
- }
-
- *success = true;
- return progSteps;
-}
-
-
-
-/**
- * The function readTreeAndCalcWeightsNJ is used to read in the tree given the treeName.
- * It then calls the appropriate functions to calc the seqWeights and make sure the matrix
- * is in similarity mode.
- */
-int
-TreeInterface::readTreeAndCalcWeightsNJ(Tree* groupTree, Alignment* alignPtr,
- DistMatrix* distMat, string* treeName,
- vector<int>* seqWeights, int fSeq, int nSeqs)
-{
- int status = 0;
- if (nSeqs >= 2)
- {
- status = groupTree->readTree(alignPtr, treeName->c_str(), fSeq - 1, nSeqs);
- if (status == 0)
- {
- return status;
- }
- }
-
- groupTree->calcSeqWeights(fSeq - 1, nSeqs, seqWeights);
-
- status = groupTree->calcSimilarities(alignPtr, distMat);
-
- return status;
-}
-
-int
-TreeInterface::getWeightsFromGuideTreeNJ(Alignment* alignPtr, DistMatrix* distMat,
- string* treeName, vector<int>* seqWeights, int fSeq, int nSeqs,
- bool* success)
-{
- Tree groupTree;
- int status = readTreeAndCalcWeightsNJ(&groupTree, alignPtr, distMat, treeName,
- seqWeights, fSeq, nSeqs);
- if(status == 0)
- {
- *success = false;
- }
- else
- {
- *success = true;
- }
- return status;
-}
-
-void
-TreeInterface::getWeightsFromDistMatNJ(vector<int>* seqWeights, DistMatrix* distMat,
- Alignment *alignPtr, int seq1, int _nSeqs,
- string* phylipName, bool* success)
-{
- string copyOfPhylipName = string(*phylipName);
- int nSeqs = _nSeqs;
- int status = 0;
-
- generateTreeFromDistMatNJ(distMat, alignPtr, seq1, nSeqs, phylipName, success);
-
- Tree groupTree;
- status = readTreeAndCalcWeightsNJ(&groupTree, alignPtr, distMat, phylipName,
- seqWeights, seq1, nSeqs);
- if(status == 0)
- {
- *success = false;
- }
- else
- {
- *success = true;
- }
-}
-
-void
-TreeInterface::getWeightsForProfileAlignNJ(Alignment* alignPtr, DistMatrix* distMat,
- string* p1TreeName, vector<int>* p1Weights, string* p2TreeName,
- vector<int>* p2Weights, int numSeqs, int profile1NumSeqs, bool useTree1,
- bool useTree2, bool* success)
-{
- if(!useTree1)
- {
- if (profile1NumSeqs >= 2)
- {
- generateTreeFromDistMatNJ(distMat, alignPtr, 1, profile1NumSeqs, p1TreeName,
- success);
- }
- }
-
- if(!useTree2)
- {
- if(numSeqs - profile1NumSeqs >= 2)
- {
- generateTreeFromDistMatNJ(distMat, alignPtr, profile1NumSeqs + 1,
- numSeqs - profile1NumSeqs, p2TreeName, success);
- }
- }
-
- if (userParameters->getNewTree1File() || userParameters->getNewTree2File())
- {
- *success = false;
- return;
- }
- // MSA->CALCPAIRWISE
-
- MSA* msaObj = new MSA();
-
- int count = msaObj->calcPairwiseForProfileAlign(alignPtr, distMat);
-
- if (count == 0)
- {
- *success = false;
- return;
- }
-
- Tree groupTree1, groupTree2;
- int status = 0;
-
- if (profile1NumSeqs >= 2)
- {
- status = groupTree1.readTree(alignPtr, p1TreeName->c_str(), 0, profile1NumSeqs);
- if (status == 0)
- {
- *success = false;
- return;
- }
- }
-
- groupTree1.calcSeqWeights(0, profile1NumSeqs, p1Weights);
-
- if (profile1NumSeqs >= 2)
- {
- groupTree1.clearTree(NULL);
- }
-
- if (numSeqs - profile1NumSeqs >= 2)
- {
- status = groupTree2.readTree(alignPtr, p2TreeName->c_str(), profile1NumSeqs, numSeqs);
- if (status == 0)
- {
- *success = false;
- return;
- }
- }
-
- groupTree2.calcSeqWeights(profile1NumSeqs, numSeqs, p2Weights);
-
-
- /* clear the memory for the phylogenetic tree */
-
- if (numSeqs - profile1NumSeqs >= 2)
- {
- groupTree2.clearTree(NULL);
- }
-
- /**
- * Convert distances to similarities!!!!!!
- */
- for (int i = 1; i < numSeqs; i++)
- {
- for (int j = i + 1; j <= numSeqs; j++)
- {
- (*distMat)(i, j) = 100.0 - (*distMat)(i, j) * 100.0;
- (*distMat)(j, i) = (*distMat)(i, j);
- }
- }
-
- *success = true;
-
-}
-
-void
-TreeInterface::generateTreeFromDistMatNJ(DistMatrix* distMat, Alignment *alignPtr,
- int seq1, int nSeqs,
- string* phylipName, bool* success)
-{
- string copyOfPhylipName = string(*phylipName);
-
- if (nSeqs >= 2)
- {
- UnRootedClusterTree* clusterTree = new UnRootedClusterTree;
- clusterTree->treeFromDistMatrix(distMat, alignPtr, seq1, nSeqs, copyOfPhylipName);
-
- *phylipName = copyOfPhylipName;
- // AW: message outputted by OutputFile function
- // utilityObject->info("Guide tree file created: [%s]",
- // phylipName->c_str());
- delete clusterTree;
- }
- *success = true;
-}
-
-auto_ptr<AlignmentSteps>
-TreeInterface::getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
- DistMatrix* distMat, string* treeName,
- vector<int>* seqWeights, int fSeq, int numSeqs,
- bool* success)
-{
- auto_ptr<AlignmentSteps> progSteps;
- Tree groupTree;
- if(numSeqs == 1)
- {
- utilityObject->info("Only 1 sequence, cannot do multiple alignment\n");
- *success = false;
- return progSteps;
- }
- int status;
- status = readTreeAndCalcWeightsNJ(&groupTree, alignPtr, distMat, treeName,
- seqWeights, fSeq, numSeqs);
-
- if (status == 0)
- {
- *success = false;
- return progSteps;
- }
-
- progSteps = groupTree.createSets(0, numSeqs);
- int _numSteps = progSteps->getNumSteps();
- utilityObject->info("There are %d groups", _numSteps);
- // clear the memory used for the phylogenetic tree
-
- if (numSeqs >= 2)
- {
- groupTree.clearTree(NULL);
- }
-
- *success = true;
-
- return progSteps;
-
-}
-
-/**
- * UPGMA functions
- *
- */
-
-
-auto_ptr<AlignmentSteps>
-TreeInterface::getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
- DistMatrix* distMat, Alignment *alignPtr,
- int seq1, int nSeqs, string* phylipName, bool* success)
-{
- auto_ptr<AlignmentSteps> progSteps;
- RootedGuideTree guideTree;
-
- progSteps = generateTreeFromDistMatUPGMA(&guideTree, distMat, alignPtr, seq1, nSeqs,
- phylipName, success);
-
- guideTree.calcSeqWeights(0, nSeqs, seqWeights);
-
- distMat->makeSimilarityMatrix();
-
- return progSteps;
-}
-
-auto_ptr<AlignmentSteps> TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success)
-{
- auto_ptr<AlignmentSteps> progSteps;
- string copyOfPhylipName = string(*phylipName);
-
- if (nSeqs >= 2)
- {
- RootedClusterTree clusterTree;
- progSteps = clusterTree.treeFromDistMatrix(guideTree, distMat, alignPtr, seq1,
- nSeqs, copyOfPhylipName);
-
- *phylipName = copyOfPhylipName;
- // AW: message outputted by OutputFile function
- // utilityObject->info("Guide tree file created: [%s]",
- // phylipName->c_str());
- }
- *success = true;
- return progSteps;
-}
-
-void TreeInterface::getWeightsFromDistMatUPGMA(vector<int>* seqWeights, DistMatrix* distMat,
- Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success)
-{
- getWeightsAndStepsFromDistMatUPGMA(seqWeights, distMat, alignPtr,
- seq1, nSeqs, phylipName, success);
-}
-
-/**
- * The function getWeightsForProfileAlignUPGMA is used to generate the sequence weights
- * that will be used in a profile alignment. It also recalculates the distance matrix, and
- * then returns it as a similarity matrix. This function uses the NJ code to read in a tree
- * from a file if we are using a previous tree. This is because that part of the code is able
- * to do the finding of the root etc.
- */
-void TreeInterface::getWeightsForProfileAlignUPGMA(Alignment* alignPtr, DistMatrix* distMat,
- string* p1TreeName, vector<int>* p1Weights, string* p2TreeName,
- vector<int>* p2Weights, int numSeqs, int profile1NumSeqs, bool useTree1,
- bool useTree2, bool* success)
-{
- int status = 0;
-
- if(useTree1)
- {
- // Use the code to read in the tree and get the seqWeights
- Tree groupTree1;
- if (profile1NumSeqs >= 2)
- {
- status = groupTree1.readTree(alignPtr, p1TreeName->c_str(), 0, profile1NumSeqs);
- if (status == 0)
- {
- *success = false;
- return;
- }
- }
- groupTree1.calcSeqWeights(0, profile1NumSeqs, p1Weights);
-
- if (profile1NumSeqs >= 2)
- {
- groupTree1.clearTree(NULL);
- }
- }
- else
- {
- if (profile1NumSeqs >= 2)
- {
- RootedGuideTree guideTree;
- generateTreeFromDistMatUPGMA(&guideTree, distMat, alignPtr, 1, profile1NumSeqs,
- p1TreeName, success);
- guideTree.calcSeqWeights(0, profile1NumSeqs, p1Weights);
- }
- }
-
- if(useTree2)
- {
- Tree groupTree2;
- if (numSeqs - profile1NumSeqs >= 2)
- {
- status = groupTree2.readTree(alignPtr, p2TreeName->c_str(),
- profile1NumSeqs, numSeqs);
- if (status == 0)
- {
- *success = false;
- return;
- }
- }
- groupTree2.calcSeqWeights(profile1NumSeqs, numSeqs, p2Weights);
-
- if (numSeqs - profile1NumSeqs >= 2)
- {
- groupTree2.clearTree(NULL);
- }
- }
- else
- {
- if(numSeqs - profile1NumSeqs >= 2)
- {
- RootedGuideTree guideTree;
- generateTreeFromDistMatUPGMA(&guideTree, distMat, alignPtr, profile1NumSeqs + 1,
- numSeqs - profile1NumSeqs, p2TreeName, success);
- guideTree.calcSeqWeights(profile1NumSeqs, numSeqs, p2Weights);
- }
- }
-
- if (userParameters->getNewTree1File() || userParameters->getNewTree2File())
- {
- *success = false;
- return;
- }
-
- MSA* msaObj = new MSA();
-
- int count = msaObj->calcPairwiseForProfileAlign(alignPtr, distMat);
-
- delete msaObj;
-
- if (count == 0)
- {
- *success = false;
- return;
- }
-
- /**
- * Convert distances to similarities!!!!!!
- */
- distMat->makeSimilarityMatrix();
-
- *success = true;
-
-}
-
-/**
- * Mark 10-5-2007: Bug fix # 42
- * The following function is to be used only for calculating the weights for the Qt
- * low scoring segments.
- */
-void TreeInterface::getWeightsForQtLowScore(vector<int>* seqWeights, DistMatrix* distMat,
- Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success)
-{
- string copyOfPhylipName = string(*phylipName);
- int _nSeqs = nSeqs;
- int status = 0;
-
- generateTreeFromDistMatNJ(distMat, alignPtr, seq1, _nSeqs, phylipName, success);
-
- Tree groupTree;
-
- status = 0;
- if (_nSeqs >= 2)
- {
- status = groupTree.readTree(alignPtr, phylipName->c_str(), seq1 - 1,
- seq1 + _nSeqs-1); // mark 22-5-07
- if(status == 0)
- {
- *success = false;
- return;
- }
- else
- {
- *success = true;
- }
- }
-
- groupTree.calcSeqWeights(seq1 - 1, seq1 + _nSeqs - 1, seqWeights); // mark 23-5-07
-}
-
-}
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