binaries/src/clustalw/src/tree/ClusterTree.h

   1 /**
   2  * Author: Mark Larkin
   3  *
   4  * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
   5  */
   6 /**
   7  * This is the interface class for the clustering part of the code. The 3 public functions
   8  * are the 3 things that can be done. 1) Generate a tree from alignment (treeFromAlignment),
   9  * 2) Generate a tree from a distance matrix (treeFromDistMatrix), or
  10  * 3) Bootstrap a tree (bootstrapTree).
  11  **/
  12 #ifndef CLUSTALTREEBASE_H
  13 #define CLUSTALTREEBASE_H
  14
  15 #include <fstream>
  16 #include <memory>
  17 #include <iostream>
  18 #include <vector>
  19 #include <exception>
  20 #include "../alignment/Alignment.h"
  21 #include "NJTree.h"
  22 #include "ClusterTreeOutput.h"
  23 #include "../general/OutputFile.h"
  24 #include "ClusterTreeAlgorithm.h"
  25 #include <string>
  26
  27 namespace clustalw
  28 {
  29 class OutputFile;
  30
  31 class ClusterTree
  32 {
  33     public:
  34         /* Functions */
  35         ClusterTree();
  36         /* Attributes */
  37
  38     protected: // This is because we will have a derived class that needs these.
  39         /* Functions */
  40         void overspillMessage(int overspill,int total_dists);
  41         void treeGapDelete(clustalw::Alignment *alignPtr);
  42         int dnaDistanceMatrix(ofstream* treeFile, clustalw::Alignment *alignPtr);
  43         int protDistanceMatrix(ofstream* treeFile, clustalw::Alignment *alignPtr);
  44         bool isAmbiguity(int c);
  45         void calcPercIdentity(ofstream* pfile, clustalw::Alignment *alignPtr);
  46         void compareTree(clustalw::PhyloTree* tree1, clustalw::PhyloTree* tree2, vector<int>* hits, int n);
  47         //string getOutputFileName(const string prompt, string path,
  48         //                              const string fileExtension);
  49         bool transition(int base1, int base2);
  50         void distanceMatrixOutput(ofstream* outFile, clustalw::DistMatrix* matToPrint,
  51                                   clustalw::Alignment *alignPtr);
  52         bool openFilesForBootstrap(clustalw::OutputFile* clustalFile, clustalw::OutputFile* phylipFile,
  53                          clustalw::OutputFile* nexusFile, clustalw::TreeNames* treeNames, string* path);
  54         bool openFilesForTreeFromAlignment(clustalw::OutputFile* clustalFile, clustalw::OutputFile* phylipFile,
  55                             clustalw::OutputFile* distFile, clustalw::OutputFile* nexusFile, clustalw::OutputFile* pimFile,
  56                             clustalw::TreeNames* treeNames, string* path);
  57         int calcQuickDistMatForAll(ofstream* clustalFile, ofstream* phylipFile,
  58                                    ofstream* nexusFile, ofstream* pimFile,
  59                                    ofstream* distFile, clustalw::Alignment* alignPtr);
  60
  61         int calcQuickDistMatForSubSet(ofstream* clustalFile, ofstream* phylipFile,
  62                                       ofstream* nexusFile, clustalw::Alignment* alignPtr,
  63                                       bool inBootLoop = false);
  64         void printBootstrapHeaderToClustalFile(ofstream* clustalFile);
  65         void promptForBoolSeedAndNumTrials();
  66         void printErrorMessageForBootstrap(int totalOverspill, int totalDists, int nfails);
  67         bool checkIfConditionsMet(int numSeqs, int min);
  68         /* Attributes */
  69         ClusterTreeAlgorithm* clusAlgorithm;
  70         auto_ptr<clustalw::DistMatrix> quickDistMat;
  71
  72         vector<int> bootTotals;
  73         vector<int> bootPositions;
  74         bool verbose;
  75         vector<int> treeGaps;
  76         int numSeqs;
  77         int firstSeq;
  78         int lastSeq;
  79         string bootstrapPrompt;
  80         string bootstrapFileTypeMsg;
  81 };
  82
  83 }
  84 #endif