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                 heatmap = new HeatMap();
  19                 format = globaldata->getFormat();
  20
  21         }
  22         catch(exception& e) {
  23                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  24                 exit(1);
  25         }
  26         catch(...) {
  27                 cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32
  33 HeatMapCommand::~HeatMapCommand(){
  34         delete input;
  35         delete read;
  36         delete heatmap;
  37 }
  38
  39 //**********************************************************************************************************************
  40
  41 int HeatMapCommand::execute(){
  42         try {
  43                 int count = 1;
  44
  45                 if (format == "sharedfile") {
  46                         //you have groups
  47                         read = new ReadPhilFile(globaldata->inputFileName);
  48                         read->read(&*globaldata);
  49
  50                         input = globaldata->ginput;
  51                         order = input->getSharedOrderVector();
  52                 }else if (format == "shared") {
  53                         //you are using a list and a groupfile
  54                         read = new ReadPhilFile(globaldata->inputFileName);
  55                         read->read(&*globaldata);
  56
  57                         input = globaldata->ginput;
  58                         SharedList = globaldata->gSharedList;
  59                         order = SharedList->getSharedOrderVector();
  60                 }else if (format == "list") {
  61                         //you are using just a list file and have only one group
  62                         read = new ReadPhilFile(globaldata->inputFileName);
  63                         read->read(&*globaldata);
  64
  65                         ordersingle = globaldata->gorder;
  66                         input = globaldata->ginput;
  67                 }
  68
  69
  70                 if (format != "list") {
  71
  72                         setGroups();
  73
  74                         while(order != NULL){
  75
  76                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  77
  78                                         cout << order->getLabel() << '\t' << count << endl;
  79                                         heatmap->getPic(order);
  80
  81                                 }
  82
  83                                 //get next line to process
  84                                 if (format == "sharedfile") {
  85                                         order = input->getSharedOrderVector();
  86                                 }else {
  87                                         //you are using a list and a groupfile
  88                                         SharedList = input->getSharedListVector(); //get new list vector to process
  89                                         if (SharedList != NULL) {
  90                                                 order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
  91                                         }else {
  92                                                 break;
  93                                         }
  94                                 }
  95                                 count++;
  96                         }
  97
  98                         //reset groups parameter
  99                         globaldata->Groups.clear();  globaldata->setGroups("");
 100
 101                 }else{
 102                         while(ordersingle != NULL){
 103
 104                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){
 105
 106                                         cout << ordersingle->getLabel() << '\t' << count << endl;
 107                                         heatmap->getPic(ordersingle);
 108
 109                                 }
 110
 111                                 ordersingle = (input->getOrderVector());
 112                                 count++;
 113                         }
 114                 }
 115
 116                 return 0;
 117         }
 118         catch(exception& e) {
 119                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 120                 exit(1);
 121         }
 122         catch(...) {
 123                 cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 124                 exit(1);
 125         }
 126 }
 127
 128 //**********************************************************************************************************************
 129 void HeatMapCommand::setGroups() {
 130         try {
 131                 //if the user has not entered specific groups to analyze then do them all
 132                 if (globaldata->Groups.size() != 0) {
 133                         if (globaldata->Groups[0] != "all") {
 134                                 //check that groups are valid
 135                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 136                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 137                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 138                                                 // erase the invalid group from globaldata->Groups
 139                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 140                                         }
 141                                 }
 142
 143                                 //if the user only entered invalid groups
 144                                 if (globaldata->Groups.size() == 0) {
 145                                         cout << "When using the groups parameter you must have at least 1 valid groups. I will run the command using all the groups in your groupfile." << endl;
 146                                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 147                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 148                                         }
 149                                 }
 150                         }else{//user has enter "all" and wants the default groups
 151                                 globaldata->Groups.clear();
 152                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 153                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 154                                 }
 155                                 globaldata->setGroups("");
 156                         }
 157                 }else {
 158                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 159                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 160                         }
 161                 }
 162
 163         }
 164         catch(exception& e) {
 165                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 166                 exit(1);
 167         }
 168         catch(...) {
 169                 cout << "An unknown error has occurred in the HeatMapCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 170                 exit(1);
 171         }
 172
 173 }
 174 /***********************************************************/
 175