rarefactsharedcommand.cpp

   1 /*
   2  *  rarefactsharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/6/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactsharedcommand.h"
  11 #include "sharedsobs.h"
  12 #include "sharednseqs.h"
  13
  14 //**********************************************************************************************************************
  15
  16 RareFactSharedCommand::RareFactSharedCommand(){
  17         try {
  18                 globaldata = GlobalData::getInstance();
  19                 string fileNameRoot;
  20                 fileNameRoot = getRootName(globaldata->inputFileName);
  21                 format = globaldata->getFormat();
  22                 convert(globaldata->getFreq(), freq);
  23                 convert(globaldata->getIters(), nIters);
  24                 validCalculator = new ValidCalculators();
  25
  26                 int i;
  27                 for (i=0; i<globaldata->Estimators.size(); i++) {
  28                         if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) {
  29                                 if (globaldata->Estimators[i] == "sharedobserved") {
  30                                         rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
  31                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  32                                         rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
  33                                 }
  34
  35                         }
  36                 }
  37
  38                 //reset calc for next command
  39                 globaldata->setCalc("");
  40
  41         }
  42         catch(exception& e) {
  43                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  44                 exit(1);
  45         }
  46         catch(...) {
  47                 cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  48                 exit(1);
  49         }
  50
  51 }
  52
  53 //**********************************************************************************************************************
  54
  55 RareFactSharedCommand::~RareFactSharedCommand(){
  56         delete input;
  57         delete rCurve;
  58         delete read;
  59 }
  60
  61 //**********************************************************************************************************************
  62
  63 int RareFactSharedCommand::execute(){
  64         try {
  65                 int count = 1;
  66
  67                 //if the users entered no valid calculators don't execute command
  68                 if (rDisplays.size() == 0) { return 0; }
  69
  70                 read = new ReadOTUFile(globaldata->inputFileName);
  71                 read->read(&*globaldata);
  72
  73                 input = globaldata->ginput;
  74                 lookup = input->getSharedRAbundVectors();
  75                 vector<SharedRAbundVector*> lastLookup = lookup;
  76
  77                 if (lookup.size() < 2) {
  78                         cout << "I cannot run the command without at least 2 valid groups.";
  79                         for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
  80                         return 0;
  81                 }
  82
  83                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  84                 set<string> processedLabels;
  85                 set<string> userLabels = globaldata->labels;
  86
  87                 //as long as you are not at the end of the file or done wih the lines you want
  88                 while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
  89
  90                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
  91
  92                                 rCurve = new Rarefact(lookup, rDisplays);
  93                                 rCurve->getSharedCurve(freq, nIters);
  94                                 delete rCurve;
  95
  96                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
  97                                 processedLabels.insert(lookup[0]->getLabel());
  98                                 userLabels.erase(lookup[0]->getLabel());
  99                         }
 100
 101                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
 102                                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 103                                         rCurve = new Rarefact(lastLookup, rDisplays);
 104                                         rCurve->getSharedCurve(freq, nIters);
 105                                         delete rCurve;
 106
 107                                         processedLabels.insert(lastLookup[0]->getLabel());
 108                                         userLabels.erase(lastLookup[0]->getLabel());
 109                         }
 110
 111                         //prevent memory leak
 112                         if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
 113                         lastLookup = lookup;
 114
 115                         //get next line to process
 116                         lookup = input->getSharedRAbundVectors();
 117                         count++;
 118                 }
 119
 120                 //output error messages about any remaining user labels
 121                 set<string>::iterator it;
 122                 bool needToRun = false;
 123                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 124                         cout << "Your file does not include the label "<< *it;
 125                         if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 126                                 cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 127                                 needToRun = true;
 128                         }else {
 129                                 cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 130                         }
 131                 }
 132
 133                 //run last line if you need to
 134                 if (needToRun == true)  {
 135                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 136                         rCurve = new Rarefact(lastLookup, rDisplays);
 137                         rCurve->getSharedCurve(freq, nIters);
 138                         delete rCurve;
 139                 }
 140
 141                 for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 142
 143                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 144
 145                 //reset groups parameter
 146                 globaldata->Groups.clear();  globaldata->setGroups("");
 147
 148                 return 0;
 149         }
 150         catch(exception& e) {
 151                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 152                 exit(1);
 153         }
 154         catch(...) {
 155                 cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 156                 exit(1);
 157         }
 158 }
 159
 160
 161 //**********************************************************************************************************************