+++ /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.
- *
- *
- */
-#ifndef TREEINTERFACE_H
-#define TREEINTERFACE_H
-
-#include <vector>
-#include <string>
-#include <memory>
-#include "AlignmentSteps.h"
-#include "../alignment/Alignment.h"
-#include "../general/clustalw.h"
-
-namespace clustalw
-{
-
-using namespace std;
-class Tree;
-class RootedGuideTree;
-
-class TreeInterface
-{
- public:
- /**
- * This function will be used to generate the phylogenetic tree from the distMat using
- * either UPGMA or NJ. It will then calculate the seqWeights and the steps.
- * Note the Distmat
- * will be in similarity form after this. It will no longer be distances!!!!!
- */
- auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
- DistMatrix* distMat,
- Alignment *alignPtr,
- int seq1, int nSeqs,
- string* phylipName, bool* success);
- /**
- * This will be called by sequencesAlignToProfile and QTcalcWeightsForLowScoreSeg
- */
- void getWeightsFromDistMat(vector<int>* seqWeights, DistMatrix* distMat,
- Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success);
-
- void getWeightsForQtLowScore(vector<int>* seqWeights, DistMatrix* distMat,
- Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success);
-
- /**
- * This function will be called from doAlignUseOldTree
- */
- auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
- DistMatrix* distMat, string* treeName,
- vector<int>* seqWeights, int fSeq,
- int numSeqs, bool* success);
-
- /**
- * This function will be called from sequencesAlignToProfile, it doesnt calc the
- * steps.
- */
- int getWeightsFromGuideTree(Alignment* alignPtr, DistMatrix* distMat,
- string* treeName, vector<int>* seqWeights, int fSeq,
- int nSeqs, bool* success);
- /**
- * This function is used to generate 2 guide trees for the profile align part.
- * IT must be done on its own. It calls calcPairwiseForProfileAlign in MSA.
- * It is called by profileAlign and removeFirstIterate.
- */
- void 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);
- /**
- * This function is used to generate the guide tree from the distance matrix.
- * It doesnt return
- * any seqWeights or AlignmentSteps. It will be used by doGuideTreeOnly
- */
- void generateTreeFromDistMat(DistMatrix* distMat, Alignment *alignPtr,
- int seq1, int nSeqs,
- string* phylipName, bool* success);
-
- /**
- * This function is to simply to call either the UPGMA or NJ version of
- * this function, and print out all the trees. It will be called
- * from phylogeneticTree in the clustal class.
- */
- void treeFromAlignment(TreeNames* treeNames, Alignment *alignPtr);
-
- /**
- * This function will be used to bootstrap the tree and output the results.
- * It will use either
- * UPGMA or NJ for the bootstrapping, depending on what is selected.
- */
- void bootstrapTree(TreeNames* treeNames, Alignment *alignPtr);
-
- private:
- auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
- DistMatrix* distMat,
- Alignment *alignPtr,
- int seq1, int nSeqs,
- string* phylipName, bool* success);
-
- auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
- Alignment *alignPtr, string* treeName,
- vector<int>* seqWeights,
- int fSeq, int nSeqs, bool* success);
-
- int readTreeAndCalcWeightsNJ(Tree* groupTree, Alignment* alignPtr,
- DistMatrix* distMat, string* treeName, vector<int>* seqWeights,
- int fSeq, int nSeqs);
-
- int getWeightsFromGuideTreeNJ(Alignment* alignPtr, DistMatrix* distMat,
- string* treeName, vector<int>* seqWeights, int fSeq,
- int nSeqs, bool* success);
-
- void getWeightsFromDistMatNJ(vector<int>* seqWeights, DistMatrix* distMat,
- Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success);
-
- void 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);
-
- void generateTreeFromDistMatNJ(DistMatrix* distMat, Alignment *alignPtr,
- int seq1, int nSeqs, string* phylipName, bool* success);
-
- auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
- DistMatrix* distMat, string* treeName,
- vector<int>* seqWeights, int fSeq, int numSeqs, bool* success);
-
- /** UPGMA functions */
- auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
- DistMatrix* distMat, Alignment *alignPtr,
- int seq1, int nSeqs, string* phylipName, bool* success);
-
- auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
- DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success);
-
- void getWeightsFromDistMatUPGMA(vector<int>* seqWeights, DistMatrix* distMat,
- Alignment *alignPtr, int seq1, int nSeqs,
- string* phylipName, bool* success);
-
- void 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);
-};
-}
-#endif
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