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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/**
* This is the interface class for the clustering part of the code. The 3 public functions
* are the 3 things that can be done. 1) Generate a tree from alignment (treeFromAlignment),
* 2) Generate a tree from a distance matrix (treeFromDistMatrix), or
* 3) Bootstrap a tree (bootstrapTree).
**/
#ifndef CLUSTALTREEBASE_H
#define CLUSTALTREEBASE_H
#include <fstream>
#include <memory>
#include <iostream>
#include <vector>
#include <exception>
#include "../alignment/Alignment.h"
#include "NJTree.h"
#include "ClusterTreeOutput.h"
#include "../general/OutputFile.h"
#include "ClusterTreeAlgorithm.h"
#include <string>
namespace clustalw
{
class OutputFile;
class ClusterTree
{
public:
/* Functions */
ClusterTree();
/* Attributes */
protected: // This is because we will have a derived class that needs these.
/* Functions */
void overspillMessage(int overspill,int total_dists);
void treeGapDelete(clustalw::Alignment *alignPtr);
int dnaDistanceMatrix(ofstream* treeFile, clustalw::Alignment *alignPtr);
int protDistanceMatrix(ofstream* treeFile, clustalw::Alignment *alignPtr);
bool isAmbiguity(int c);
void calcPercIdentity(ofstream* pfile, clustalw::Alignment *alignPtr);
void compareTree(clustalw::PhyloTree* tree1, clustalw::PhyloTree* tree2, vector<int>* hits, int n);
//string getOutputFileName(const string prompt, string path,
// const string fileExtension);
bool transition(int base1, int base2);
void distanceMatrixOutput(ofstream* outFile, clustalw::DistMatrix* matToPrint,
clustalw::Alignment *alignPtr);
bool openFilesForBootstrap(clustalw::OutputFile* clustalFile, clustalw::OutputFile* phylipFile,
clustalw::OutputFile* nexusFile, clustalw::TreeNames* treeNames, string* path);
bool openFilesForTreeFromAlignment(clustalw::OutputFile* clustalFile, clustalw::OutputFile* phylipFile,
clustalw::OutputFile* distFile, clustalw::OutputFile* nexusFile, clustalw::OutputFile* pimFile,
clustalw::TreeNames* treeNames, string* path);
int calcQuickDistMatForAll(ofstream* clustalFile, ofstream* phylipFile,
ofstream* nexusFile, ofstream* pimFile,
ofstream* distFile, clustalw::Alignment* alignPtr);
int calcQuickDistMatForSubSet(ofstream* clustalFile, ofstream* phylipFile,
ofstream* nexusFile, clustalw::Alignment* alignPtr,
bool inBootLoop = false);
void printBootstrapHeaderToClustalFile(ofstream* clustalFile);
void promptForBoolSeedAndNumTrials();
void printErrorMessageForBootstrap(int totalOverspill, int totalDists, int nfails);
bool checkIfConditionsMet(int numSeqs, int min);
/* Attributes */
ClusterTreeAlgorithm* clusAlgorithm;
auto_ptr<clustalw::DistMatrix> quickDistMat;
vector<int> bootTotals;
vector<int> bootPositions;
bool verbose;
vector<int> treeGaps;
int numSeqs;
int firstSeq;
int lastSeq;
string bootstrapPrompt;
string bootstrapFileTypeMsg;
};
}
#endif
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