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                         OptionParser parser(option);
  27                         map<string, string> parameters = parser.getParameters();
  28
  29                         ValidParameters validParameter;
  30
  31                         //check to make sure all parameters are valid for command
  32                         for (map<string, string>::iterator 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 = ""; mothurOut("tree is a required parameter for the read.tree command."); mothurOutEndLine(); 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 = ""; mothurOut("group is a required parameter for the read.tree command."); mothurOutEndLine(); 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                 }
  61         }
  62         catch(exception& e) {
  63                 errorOut(e, "ReadTreeCommand", "ReadTreeCommand");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68
  69 void ReadTreeCommand::help(){
  70         try {
  71                 mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n");
  72                 mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
  73                 mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
  74                 mothurOut("The tree and group parameters are both required.\n");
  75                 mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
  76         }
  77         catch(exception& e) {
  78                 errorOut(e, "ReadTreeCommand", "help");
  79                 exit(1);
  80         }
  81 }
  82
  83 //**********************************************************************************************************************
  84
  85 ReadTreeCommand::~ReadTreeCommand(){
  86         if (abort == false) { delete read; }
  87 }
  88
  89 //**********************************************************************************************************************
  90
  91 int ReadTreeCommand::execute(){
  92         try {
  93
  94                 if (abort == true) { return 0; }
  95
  96                 int readOk;
  97
  98                 readOk = read->read();
  99
 100                 if (readOk != 0) { mothurOut("Read Terminated."); mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
 101
 102                 vector<Tree*> T = globaldata->gTree;
 103
 104                 //assemble users trees
 105                 for (int i = 0; i < T.size(); i++) {
 106                         T[i]->assembleTree();
 107                 }
 108
 109                 //output any names that are in names file but not in tree
 110                 if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
 111                         for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
 112                                 //is that name in the tree?
 113                                 int count = 0;
 114                                 for (int j = 0; j < globaldata->Treenames.size(); j++) {
 115                                         if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
 116                                         count++;
 117                                 }
 118
 119                                 //then you did not find it so report it
 120                                 if (count == globaldata->Treenames.size()) {
 121                                         mothurOut(treeMap->namesOfSeqs[i] + " is in your namefile and not in your tree. It will be disregarded."); mothurOutEndLine();
 122                                 }
 123                         }
 124                 }
 125
 126                 return 0;
 127         }
 128         catch(exception& e) {
 129                 errorOut(e, "ReadTreeCommand", "execute");
 130                 exit(1);
 131         }
 132 }
 133
 134 //**********************************************************************************************************************