readtreecommand.cpp

   1 /*
   2  *  readtreecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/23/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readtreecommand.h"
  11
  12 //**********************************************************************************************************************
  13 ReadTreeCommand::ReadTreeCommand(){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 filename = globaldata->inputFileName;
  17
  18                 //read in group map info.
  19                 treeMap = new TreeMap(globaldata->getGroupFile());
  20                 treeMap->readMap();
  21
  22                 //memory leak prevention
  23                 //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
  24                 globaldata->gTreemap = treeMap;
  25
  26                 //get names in tree
  27                 globaldata->parseTreeFile();
  28
  29                 read = new ReadNewickTree(filename);
  30
  31         }
  32         catch(exception& e) {
  33                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  34                 exit(1);
  35         }
  36         catch(...) {
  37                 cout << "An unknown error has occurred in the ReadTreeCommand class function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  38                 exit(1);
  39         }
  40 }
  41
  42 //**********************************************************************************************************************
  43
  44 ReadTreeCommand::~ReadTreeCommand(){
  45         delete read;
  46 }
  47
  48 //**********************************************************************************************************************
  49
  50 int ReadTreeCommand::execute(){
  51         try {
  52                 int readOk;
  53
  54                 readOk = read->read();
  55
  56                 if (readOk != 0) { cout << "Read Terminated." << endl; globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
  57
  58                 vector<Tree*> T = globaldata->gTree;
  59
  60                 //assemble users trees
  61                 for (int i = 0; i < T.size(); i++) {
  62                         T[i]->assembleTree();
  63                 }
  64
  65                 //output any names that are in names file but not in tree
  66                 if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
  67                         for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
  68                                 //is that name in the tree?
  69                                 int count = 0;
  70                                 for (int j = 0; j < globaldata->Treenames.size(); j++) {
  71                                         if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
  72                                         count++;
  73                                 }
  74
  75                                 //then you did not find it so report it
  76                                 if (count == globaldata->Treenames.size()) {
  77                                         cout << treeMap->namesOfSeqs[i] << " is in your namefile and not in your tree. It will be disregarded." << endl;
  78                                 }
  79                         }
  80                 }
  81
  82                 return 0;
  83         }
  84         catch(exception& e) {
  85                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  86                 exit(1);
  87         }
  88         catch(...) {
  89                 cout << "An unknown error has occurred in the ReadTreeCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  90                 exit(1);
  91         }
  92 }
  93
  94 //**********************************************************************************************************************