Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / tree / ClusterTree.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/tree/ClusterTree.h b/website/archive/binaries/mac/src/clustalw/src/tree/ClusterTree.h
deleted file mode 100644 (file)
index c0d83a4..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/tree/ClusterTree.h
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@@ -1,84 +0,0 @@
-/**
- * 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