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         catch(exception& e) {
  22                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  23                 exit(1);
  24         }
  25         catch(...) {
  26                 cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31
  32 HeatMapCommand::~HeatMapCommand(){
  33         delete input;
  34         delete read;
  35         delete heatmap;
  36 }
  37
  38 //**********************************************************************************************************************
  39
  40 int HeatMapCommand::execute(){
  41         try {
  42                 int count = 1;
  43                 RAbundVector* lastRAbund;
  44                 vector<SharedRAbundVector*> lastLookup;
  45
  46                 if (format == "sharedfile") {
  47                         //you have groups
  48                         read = new ReadOTUFile(globaldata->inputFileName);
  49                         read->read(&*globaldata);
  50
  51                         input = globaldata->ginput;
  52                         lookup = input->getSharedRAbundVectors();
  53                         lastLookup = lookup;
  54                 }else if (format == "list") {
  55                         //you are using just a list file and have only one group
  56                         read = new ReadOTUFile(globaldata->inputFileName);
  57                         read->read(&*globaldata);
  58
  59                         rabund = globaldata->rabund;
  60                         lastRAbund = globaldata->rabund;
  61                         input = globaldata->ginput;
  62                 }
  63
  64                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  65                 set<string> processedLabels;
  66                 set<string> userLabels = globaldata->labels;
  67                 set<int> userLines = globaldata->lines;
  68
  69                 if (format != "list") {
  70
  71                         //as long as you are not at the end of the file or done wih the lines you want
  72                         while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
  73
  74                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
  75
  76                                         cout << lookup[0]->getLabel() << '\t' << count << endl;
  77                                         heatmap->getPic(lookup);
  78
  79                                         processedLabels.insert(lookup[0]->getLabel());
  80                                         userLabels.erase(lookup[0]->getLabel());
  81                                         userLines.erase(count);
  82                                 }
  83
  84                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
  85                                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
  86                                         heatmap->getPic(lastLookup);
  87
  88                                         processedLabels.insert(lastLookup[0]->getLabel());
  89                                         userLabels.erase(lastLookup[0]->getLabel());
  90                                 }
  91
  92                                 //prevent memory leak
  93                                 if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
  94                                 lastLookup = lookup;
  95
  96                                 //get next line to process
  97                                 lookup = input->getSharedRAbundVectors();
  98                                 count++;
  99                         }
 100
 101                         //output error messages about any remaining user labels
 102                         set<string>::iterator it;
 103                         bool needToRun = false;
 104                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 105                                 cout << "Your file does not include the label "<< *it;
 106                                 if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 107                                         cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 108                                         needToRun = true;
 109                                 }else {
 110                                         cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 111                                 }
 112                         }
 113
 114                         //run last line if you need to
 115                         if (needToRun == true)  {
 116                                 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 117                                 heatmap->getPic(lastLookup);
 118                         }
 119
 120                         for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 121
 122                         //reset groups parameter
 123                         globaldata->Groups.clear();
 124
 125                 }else{
 126
 127                         while((rabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 128
 129                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(rabund->getLabel()) == 1){
 130
 131                                         cout << rabund->getLabel() << '\t' << count << endl;
 132                                         heatmap->getPic(rabund);
 133
 134                                         processedLabels.insert(rabund->getLabel());
 135                                         userLabels.erase(rabund->getLabel());
 136                                         userLines.erase(count);
 137                                 }
 138
 139                                 if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
 140
 141                                         cout << lastRAbund->getLabel() << '\t' << count << endl;
 142                                         heatmap->getPic(lastRAbund);
 143
 144                                         processedLabels.insert(lastRAbund->getLabel());
 145                                         userLabels.erase(lastRAbund->getLabel());
 146                                 }
 147
 148                                 if (count != 1) { delete lastRAbund; }
 149                                 lastRAbund = rabund;
 150
 151                                 rabund = input->getRAbundVector();
 152                                 count++;
 153                         }
 154
 155                         //output error messages about any remaining user labels
 156                         set<string>::iterator it;
 157                         bool needToRun = false;
 158                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 159                                 cout << "Your file does not include the label "<< *it;
 160                                 if (processedLabels.count(lastRAbund->getLabel()) != 1) {
 161                                         cout << ". I will use " << lastRAbund->getLabel() << "." << endl;
 162                                         needToRun = true;
 163                                 }else {
 164                                         cout << ". Please refer to " << lastRAbund->getLabel() << "." << endl;
 165                                 }
 166                         }
 167
 168                         //run last line if you need to
 169                         if (needToRun == true)  {
 170                                 cout << lastRAbund->getLabel() << '\t' << count << endl;
 171                                 heatmap->getPic(lastRAbund);
 172                         }
 173
 174                         delete lastRAbund;
 175
 176                 }
 177
 178                 globaldata->setGroups("");
 179                 return 0;
 180         }
 181         catch(exception& e) {
 182                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 183                 exit(1);
 184         }
 185         catch(...) {
 186                 cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 187                 exit(1);
 188         }
 189 }
 190
 191 //**********************************************************************************************************************
 192
 193