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/**
* 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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