heatmapsimcommand.cpp

   1 /*
   2  *  heatmapsimcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "heatmapsimcommand.h"
  11 #include "sharedjabund.h"
  12 #include "sharedsorabund.h"
  13 #include "sharedjclass.h"
  14 #include "sharedsorclass.h"
  15 #include "sharedjest.h"
  16 #include "sharedsorest.h"
  17 #include "sharedthetayc.h"
  18 #include "sharedthetan.h"
  19 #include "sharedmorisitahorn.h"
  20 #include "sharedbraycurtis.h"
  21
  22
  23 //**********************************************************************************************************************
  24
  25 HeatMapSimCommand::HeatMapSimCommand(){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 validCalculator = new ValidCalculators();
  29                 heatmap = new HeatMapSim();
  30
  31                 int i;
  32                 for (i=0; i<globaldata->Estimators.size(); i++) {
  33                         if (validCalculator->isValidCalculator("heat", globaldata->Estimators[i]) == true) {
  34                                 if (globaldata->Estimators[i] == "jabund") {
  35                                         heatCalculators.push_back(new JAbund());
  36                                 }else if (globaldata->Estimators[i] == "sorabund") {
  37                                         heatCalculators.push_back(new SorAbund());
  38                                 }else if (globaldata->Estimators[i] == "jclass") {
  39                                         heatCalculators.push_back(new Jclass());
  40                                 }else if (globaldata->Estimators[i] == "sorclass") {
  41                                         heatCalculators.push_back(new SorClass());
  42                                 }else if (globaldata->Estimators[i] == "jest") {
  43                                         heatCalculators.push_back(new Jest());
  44                                 }else if (globaldata->Estimators[i] == "sorest") {
  45                                         heatCalculators.push_back(new SorEst());
  46                                 }else if (globaldata->Estimators[i] == "thetayc") {
  47                                         heatCalculators.push_back(new ThetaYC());
  48                                 }else if (globaldata->Estimators[i] == "thetan") {
  49                                         heatCalculators.push_back(new ThetaN());
  50                                 }else if (globaldata->Estimators[i] == "morisitahorn") {
  51                                         heatCalculators.push_back(new MorHorn());
  52                                 }else if (globaldata->Estimators[i] == "braycurtis") {
  53                                         heatCalculators.push_back(new BrayCurtis());
  54                                 }
  55                         }
  56                 }
  57
  58                 //reset calc for next command
  59                 globaldata->setCalc("");
  60
  61
  62         }
  63         catch(exception& e) {
  64                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function HeatMapSimCommand. 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 HeatMapSimCommand class function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73
  74 HeatMapSimCommand::~HeatMapSimCommand(){
  75         delete input;
  76         delete read;
  77         delete heatmap;
  78 }
  79
  80 //**********************************************************************************************************************
  81
  82 int HeatMapSimCommand::execute(){
  83         try {
  84                 int count = 1;
  85
  86                 //if the users entered no valid calculators don't execute command
  87                 if (heatCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; }
  88
  89                 //you have groups
  90                 read = new ReadOTUFile(globaldata->inputFileName);
  91                 read->read(&*globaldata);
  92
  93                 input = globaldata->ginput;
  94                 lookup = input->getSharedRAbundVectors();
  95                 vector<SharedRAbundVector*> lastLookup = lookup;
  96
  97                 if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0;}
  98
  99                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 100                 set<string> processedLabels;
 101                 set<string> userLabels = globaldata->labels;
 102                 set<int> userLines = globaldata->lines;
 103
 104
 105                 //as long as you are not at the end of the file or done wih the lines you want
 106                 while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 107
 108                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
 109
 110                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
 111                                 heatmap->getPic(lookup, heatCalculators);
 112
 113                                 processedLabels.insert(lookup[0]->getLabel());
 114                                 userLabels.erase(lookup[0]->getLabel());
 115                                 userLines.erase(count);
 116                         }
 117
 118                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
 119                                 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 120                                 heatmap->getPic(lastLookup, heatCalculators);
 121
 122                                 processedLabels.insert(lastLookup[0]->getLabel());
 123                                 userLabels.erase(lastLookup[0]->getLabel());
 124                         }
 125
 126                         //prevent memory leak
 127                         if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
 128                         lastLookup = lookup;
 129
 130                         //get next line to process
 131                         lookup = input->getSharedRAbundVectors();
 132                         count++;
 133                 }
 134
 135                 //output error messages about any remaining user labels
 136                 set<string>::iterator it;
 137                 bool needToRun = false;
 138                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 139                         cout << "Your file does not include the label "<< *it;
 140                         if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 141                                 cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 142                                 needToRun = true;
 143                         }else {
 144                                 cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 145                         }
 146                 }
 147
 148                 //run last line if you need to
 149                 if (needToRun == true)  {
 150                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 151                         heatmap->getPic(lastLookup, heatCalculators);
 152                 }
 153
 154                 for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 155
 156                 //reset groups parameter
 157                 globaldata->Groups.clear();
 158                 globaldata->setGroups("");
 159
 160                 return 0;
 161         }
 162         catch(exception& e) {
 163                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 164                 exit(1);
 165         }
 166         catch(...) {
 167                 cout << "An unknown error has occurred in the HeatMapSimCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 168                 exit(1);
 169         }
 170 }
 171
 172 //**********************************************************************************************************************