Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / tree / UPGMA / RootedClusterTree.cpp

diff --git a/website/archive/binaries/mac/src/clustalw/src/tree/UPGMA/RootedClusterTree.cpp b/website/archive/binaries/mac/src/clustalw/src/tree/UPGMA/RootedClusterTree.cpp
deleted file mode 100644 (file)
index b2ae6e5..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/tree/UPGMA/RootedClusterTree.cpp
+++ /dev/null
@@ -1,222 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifdef HAVE_CONFIG_H
-    #include "config.h"
-#endif
-#include "RootedClusterTree.h"
-#include "../../general/OutputFile.h"
-#include "UPGMAAlgorithm.h"
-#include "RootedTreeOutput.h"
-//#include "../RandomGenerator.h"
-namespace clustalw
-{
-
-auto_ptr<AlignmentSteps> RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, 
-                                           int seq1, int nSeqs, string& phylipName)
-{
-    OutputFile phylipPhyTreeFile;
-    auto_ptr<AlignmentSteps> progSteps;
-    try
-    {
-        // Test to see if the inputs are valid
-        if(seq1 < 1 || nSeqs < 1)
-        {
-            cerr << "Invalid inputs into treeFromDistMatrix \n"
-                 << "seq1 = " << seq1 << " nSeqs = " << nSeqs << "\n"
-                 << "Need to end program!\n";
-            exit(1); 
-            return progSteps;
-        }
-
-        float dist;
-        string path;
-        verbose = false;
-        firstSeq = seq1;
-        lastSeq = firstSeq + nSeqs - 1;
-    
-        SeqInfo info;
-        info.firstSeq = firstSeq;
-        info.lastSeq = lastSeq;
-        info.numSeqs = nSeqs;
-
-        utilityObject->getPath(userParameters->getSeqName(), &path);
-        
-        if(nSeqs >= 2)
-        {
-            string name = phylipName;
-            if(!phylipPhyTreeFile.openFile(&name, 
-                             "\nEnter name for new GUIDE TREE           file  ", &path, "dnd",
-                             "Guide tree"))
-            {
-                return progSteps;
-            }
-            phylipName = name;                    
-        }
-        else
-        {
-            return progSteps;
-        }
-                
-        RootedTreeOutput outputTree(&info);
-        
-        ofstream* ptrToFile = phylipPhyTreeFile.getPtrToFile();
-        
-        if (nSeqs == 2)
-        {
-            dist = (*distMat)(firstSeq, firstSeq + 1) / 2.0;
-            if(ptrToFile->is_open())
-            {
-                (*ptrToFile) <<  "(" << alignPtr->getName(firstSeq) << ":" 
-                             << setprecision(5)
-                             << dist << "," << alignPtr->getName(firstSeq + 1) << ":" 
-                             << setprecision(5) << dist <<");\n";
-            }
-            progSteps.reset(new AlignmentSteps);
-            vector<int> groups;
-            groups.resize(nSeqs + 1, 0);
-            groups[1] = 1;
-            groups[2] = 2;
-        }
-        else
-        {
-            UPGMAAlgorithm clusAlgorithm;
-            progSteps = clusAlgorithm.generateTree(phyloTree, distMat, &info, false);
-            outputTree.printPhylipTree(phyloTree, ptrToFile, alignPtr, distMat);
-        }
-        return progSteps;
-    }
-    catch(const exception &ex)
-    {
-        cerr << "ERROR: Error has occured in treeFromDistMatrix. " 
-             << "Need to terminate program.\n"
-             << ex.what();
-        exit(1);   
-    }
-    catch(...)
-    {
-        cerr << "ERROR: Error has occured in treeFromDistMatrix. " 
-             << "Need to terminate program.\n";      
-        exit(1);  
-    }
-}
-
-void RootedClusterTree::treeFromAlignment(TreeNames* treeNames, Alignment *alignPtr)
-{
-    try
-    {
-        OutputFile phylipPhyTreeFile;   
-        OutputFile clustalPhyTreeFile;
-        OutputFile distancesPhyTreeFile;
-        OutputFile nexusPhyTreeFile;
-        OutputFile pimFile;
-        
-        RootedGuideTree phyloTree;
-        
-        string path;
-        int j;
-        int overspill = 0;
-        int totalDists;
-        numSeqs = alignPtr->getNumSeqs(); // NOTE class variable
-        
-        /**
-         * Check if numSeqs is ok
-         */
-        if(!checkIfConditionsMet(numSeqs, 2))
-        {
-            return;
-        }
-              
-        firstSeq = 1;
-        lastSeq = numSeqs;
-        
-        // The SeqInfo struct is passed to reduce the number of parameters passed!
-        SeqInfo info;
-        info.firstSeq = firstSeq;
-        info.lastSeq = lastSeq;
-        info.numSeqs = numSeqs;
-    
-        RootedTreeOutput outputTree(&info); // No bootstrap!
-
-        utilityObject->getPath(userParameters->getSeqName(), &path);
-
-        /**
-         * Open the required output files.
-         */
-        if(!openFilesForTreeFromAlignment(&clustalPhyTreeFile, &phylipPhyTreeFile, 
-                        &distancesPhyTreeFile, &nexusPhyTreeFile, &pimFile, treeNames, &path))
-        {
-            return; // Problem opeing one of the files, cannot continue!
-        } 
-    
-        int _lenFirstSeq = alignPtr->getSeqLength(firstSeq);
-    
-        bootPositions.clear();
-        bootPositions.resize(_lenFirstSeq + 2);
-
-        for (j = 1; j <= _lenFirstSeq; ++j)
-        {
-            bootPositions[j] = j;
-        }
-
-        /**
-         * Calculate quickDist and overspill
-         */
-        overspill = calcQuickDistMatForAll(clustalPhyTreeFile.getPtrToFile(),
-                       phylipPhyTreeFile.getPtrToFile(), nexusPhyTreeFile.getPtrToFile(),
-                       pimFile.getPtrToFile(), distancesPhyTreeFile.getPtrToFile(), alignPtr);
-
-        // check if any distances overflowed the distance corrections 
-        if (overspill > 0)
-        {
-            totalDists = (numSeqs *(numSeqs - 1)) / 2;
-            overspillMessage(overspill, totalDists);
-        }
-
-        if (userParameters->getOutputTreeClustal())
-        {
-            verbose = true;
-        }
-        // Turn on file output 
-    
-
-        if (userParameters->getOutputTreeClustal() ||
-            userParameters->getOutputTreePhylip() 
-            || userParameters->getOutputTreeNexus())
-        {
-            UPGMAAlgorithm clusAlgorithm;
-            clusAlgorithm.setVerbose(true);
-            clusAlgorithm.generateTree(&phyloTree, quickDistMat.get(), &info, false,
-                                       clustalPhyTreeFile.getPtrToFile());
-            clusAlgorithm.setVerbose(false);
-        }
-
-        if (userParameters->getOutputTreePhylip())
-        {
-            outputTree.printPhylipTree(&phyloTree, phylipPhyTreeFile.getPtrToFile(), alignPtr,
-                                        quickDistMat.get());
-        }
-
-        if (userParameters->getOutputTreeNexus())
-        {
-            outputTree.printNexusTree(&phyloTree, nexusPhyTreeFile.getPtrToFile(), alignPtr, 
-                                       quickDistMat.get());
-        }
-    
-        /** Free up resources!!!!! */
-    
-        treeGaps.clear();
-        bootPositions.clear();
-          
-    }
-    catch(const exception& ex)
-    {
-        cerr << ex.what() << endl;
-        utilityObject->error("Terminating program. Cannot continue\n");
-        exit(1);    
-    }
-}
-                                
-}