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(string option){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 abort = false;
  17
  18                 //allow user to run help
  19                 if(option == "help") { help(); abort = true; }
  20
  21                 else {
  22                         //valid paramters for this command
  23                         string Array[] =  {"tree","group"};
  24                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  25
  26                         parser = new OptionParser();
  27                         parser->parse(option, parameters);  delete parser;
  28
  29                         ValidParameters* validParameter = new ValidParameters();
  30
  31                         //check to make sure all parameters are valid for command
  32                         for (it = parameters.begin(); it != parameters.end(); it++) {
  33                                 if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  34                         }
  35
  36                         globaldata->newRead();
  37
  38                         //check for required parameters
  39                         treefile = validParameter->validFile(parameters, "tree", true);
  40                         if (treefile == "not open") { abort = true; }
  41                         else if (treefile == "not found") { treefile = ""; cout << "tree is a required parameter for the read.tree command." << endl; abort = true;  }
  42                         else {  globaldata->setTreeFile(treefile);  globaldata->setFormat("tree");      }
  43
  44                         groupfile = validParameter->validFile(parameters, "group", true);
  45                         if (groupfile == "not open") { abort = true; }
  46                         else if (groupfile == "not found") { groupfile = ""; cout << "group is a required parameter for the read.tree command." << endl; abort = true;  }
  47                         else {
  48                                 globaldata->setGroupFile(groupfile);
  49                                 //read in group map info.
  50                                 treeMap = new TreeMap(groupfile);
  51                                 treeMap->readMap();
  52                                 globaldata->gTreemap = treeMap;
  53                         }
  54
  55                         if (abort == false) {
  56                                 filename = treefile;
  57                                 read = new ReadNewickTree(filename);
  58                         }
  59
  60                         delete validParameter;
  61                 }
  62         }
  63         catch(exception& e) {
  64                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67         catch(...) {
  68                 cout << "An unknown error has occurred in the ReadTreeCommand class function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73
  74 void ReadTreeCommand::help(){
  75         try {
  76                 cout << "The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. " << "\n";
  77                 cout << "It also must be run before using the parsimony command, unless you are using the randomtree parameter." << "\n";
  78                 cout << "The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile)." << "\n";
  79                 cout << "The tree and group parameters are both required." << "\n";
  80                 cout << "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile)." << "\n" << "\n";
  81         }
  82         catch(exception& e) {
  83                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  84                 exit(1);
  85         }
  86         catch(...) {
  87                 cout << "An unknown error has occurred in the ReadTreeCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  88                 exit(1);
  89         }
  90 }
  91
  92 //**********************************************************************************************************************
  93
  94 ReadTreeCommand::~ReadTreeCommand(){
  95         delete read;
  96 }
  97
  98 //**********************************************************************************************************************
  99
 100 int ReadTreeCommand::execute(){
 101         try {
 102
 103                 if (abort == true) { return 0; }
 104
 105                 int readOk;
 106
 107                 readOk = read->read();
 108
 109                 if (readOk != 0) { cout << "Read Terminated." << endl; globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
 110
 111                 vector<Tree*> T = globaldata->gTree;
 112
 113                 //assemble users trees
 114                 for (int i = 0; i < T.size(); i++) {
 115                         T[i]->assembleTree();
 116                 }
 117
 118                 //output any names that are in names file but not in tree
 119                 if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
 120                         for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
 121                                 //is that name in the tree?
 122                                 int count = 0;
 123                                 for (int j = 0; j < globaldata->Treenames.size(); j++) {
 124                                         if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
 125                                         count++;
 126                                 }
 127
 128                                 //then you did not find it so report it
 129                                 if (count == globaldata->Treenames.size()) {
 130                                         cout << treeMap->namesOfSeqs[i] << " is in your namefile and not in your tree. It will be disregarded." << endl;
 131                                 }
 132                         }
 133                 }
 134
 135                 return 0;
 136         }
 137         catch(exception& e) {
 138                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 139                 exit(1);
 140         }
 141         catch(...) {
 142                 cout << "An unknown error has occurred in the ReadTreeCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 143                 exit(1);
 144         }
 145 }
 146
 147 //**********************************************************************************************************************