heatmapcommand.cpp

   1 /*
   2  *  heatmapcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/25/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "heatmapcommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14
  15 HeatMapCommand::HeatMapCommand(){
  16         try {
  17                 globaldata = GlobalData::getInstance();
  18                 format = globaldata->getFormat();
  19         }
  20         catch(exception& e) {
  21                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  22                 exit(1);
  23         }
  24         catch(...) {
  25                 cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  26                 exit(1);
  27         }
  28 }
  29 //**********************************************************************************************************************
  30
  31 HeatMapCommand::~HeatMapCommand(){
  32         delete input;
  33         delete read;
  34 }
  35
  36 //**********************************************************************************************************************
  37
  38 int HeatMapCommand::execute(){
  39         try {
  40                 int count = 1;
  41
  42                 if (format == "sharedfile") {
  43                         //you have groups
  44                         read = new ReadPhilFile(globaldata->inputFileName);
  45                         read->read(&*globaldata);
  46
  47                         input = globaldata->ginput;
  48                         order = input->getSharedOrderVector();
  49                 }else if (format == "shared") {
  50                         //you are using a list and a groupfile
  51                         read = new ReadPhilFile(globaldata->inputFileName);
  52                         read->read(&*globaldata);
  53
  54                         input = globaldata->ginput;
  55                         SharedList = globaldata->gSharedList;
  56                         order = SharedList->getSharedOrderVector();
  57                 }else if (format == "list") {
  58                         //you are using just a list file and have only one group
  59                         read = new ReadPhilFile(globaldata->inputFileName);
  60                         read->read(&*globaldata);
  61
  62                         ordersingle = globaldata->gorder;
  63                         input = globaldata->ginput;
  64                 }
  65
  66                 if (format != "list") {
  67                         while(order != NULL){
  68
  69                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  70
  71                                         cout << order->getLabel() << '\t' << count << endl;
  72 //call heatmap class to make file
  73                                 }
  74
  75                                 //get next line to process
  76                                 if (format == "sharedfile") {
  77                                         order = input->getSharedOrderVector();
  78                                 }else {
  79                                         //you are using a list and a groupfile
  80                                         SharedList = input->getSharedListVector(); //get new list vector to process
  81                                         if (SharedList != NULL) {
  82                                                 order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
  83                                         }else {
  84                                                 break;
  85                                         }
  86                                 }
  87                                 count++;
  88                         }
  89
  90                         //reset groups parameter
  91                         globaldata->Groups.clear();  globaldata->setGroups("");
  92
  93                 }else{
  94                         while(ordersingle != NULL){
  95
  96                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  97
  98                                         cout << order->getLabel() << '\t' << count << endl;
  99 //call heatmap class to make file
 100                                 }
 101
 102                                 ordersingle = (input->getOrderVector());
 103                                 count++;
 104                         }
 105                 }
 106
 107                 return 0;
 108         }
 109         catch(exception& e) {
 110                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 111                 exit(1);
 112         }
 113         catch(...) {
 114                 cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 115                 exit(1);
 116         }
 117 }
 118
 119 //**********************************************************************************************************************
 120