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
  13 //**********************************************************************************************************************
  14
  15 RareFactSharedCommand::RareFactSharedCommand(){
  16         try {
  17                 globaldata = GlobalData::getInstance();
  18                 string fileNameRoot;
  19                 fileNameRoot = getRootName(globaldata->inputFileName);
  20                 format = globaldata->getFormat();
  21                 validCalculator = new ValidCalculators();
  22
  23                 setGroups();
  24
  25                 int i;
  26                 for (i=0; i<globaldata->Estimators.size(); i++) {
  27                         if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) {
  28                                 if (globaldata->Estimators[i] == "sharedobserved") {
  29                                         rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
  30                                 }
  31                         }
  32                 }
  33
  34                 //reset calc for next command
  35                 globaldata->setCalc("");
  36
  37         }
  38         catch(exception& e) {
  39                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  40                 exit(1);
  41         }
  42         catch(...) {
  43                 cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  44                 exit(1);
  45         }
  46
  47 }
  48
  49 //**********************************************************************************************************************
  50
  51 RareFactSharedCommand::~RareFactSharedCommand(){
  52         delete order;
  53         delete input;
  54         delete rCurve;
  55         delete read;
  56 }
  57
  58 //**********************************************************************************************************************
  59
  60 int RareFactSharedCommand::execute(){
  61         try {
  62                 int count = 1;
  63
  64                 //if the users entered no valid calculators don't execute command
  65                 if (rDisplays.size() == 0) { return 0; }
  66
  67                 if (format == "sharedfile") {
  68                         read = new ReadPhilFile(globaldata->inputFileName);
  69                         read->read(&*globaldata);
  70
  71                         input = globaldata->ginput;
  72                         order = input->getSharedOrderVector();
  73                 }else {
  74                         //you are using a list and a groupfile
  75                         read = new ReadPhilFile(globaldata->inputFileName);
  76                         read->read(&*globaldata);
  77
  78                         input = globaldata->ginput;
  79                         SharedList = globaldata->gSharedList;
  80                         order = SharedList->getSharedOrderVector();
  81                 }
  82
  83                 while(order != NULL){
  84
  85                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  86                                 //create collectors curve
  87                                 rCurve = new Rarefact(order, rDisplays);
  88                                 convert(globaldata->getFreq(), freq);
  89                                 convert(globaldata->getIters(), nIters);
  90                                 rCurve->getSharedCurve(freq, nIters);
  91
  92                                 delete rCurve;
  93
  94                                 cout << order->getLabel() << '\t' << count << endl;
  95                         }
  96
  97                         //get next line to process
  98                         if (format == "sharedfile") {
  99                                 order = input->getSharedOrderVector();
 100                         }else {
 101                                 //you are using a list and a groupfile
 102                                 SharedList = input->getSharedListVector(); //get new list vector to process
 103                                 if (SharedList != NULL) {
 104                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 105                                 }else {
 106                                         break;
 107                                 }
 108                         }
 109
 110                         count++;
 111                 }
 112
 113                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 114
 115                 //reset groups parameter
 116                 globaldata->Groups.clear();  globaldata->setGroups("");
 117
 118                 return 0;
 119         }
 120         catch(exception& e) {
 121                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 122                 exit(1);
 123         }
 124         catch(...) {
 125                 cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 126                 exit(1);
 127         }
 128 }
 129
 130
 131 //**********************************************************************************************************************
 132
 133 void RareFactSharedCommand::setGroups() {
 134         try {
 135                 //if the user has not entered specific groups to analyze then do them all
 136                 if (globaldata->Groups.size() != 0) {
 137                         if (globaldata->Groups[0] != "all") {
 138                                 //check that groups are valid
 139                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 140                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 141                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 142                                                 // erase the invalid group from globaldata->Groups
 143                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 144                                         }
 145                                 }
 146
 147                                 //if the user only entered invalid groups
 148                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 149                                         cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
 150                                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 151                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 152                                         }
 153                                 }
 154                         }else{//user has enter "all" and wants the default groups
 155                                 globaldata->Groups.clear();
 156                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 157                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 158                                 }
 159                                 globaldata->setGroups("");
 160                         }
 161                 }else {
 162                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 163                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 164                         }
 165                 }
 166
 167         }
 168         catch(exception& e) {
 169                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 170                 exit(1);
 171         }
 172         catch(...) {
 173                 cout << "An unknown error has occurred in the RareFactSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 174                 exit(1);
 175         }
 176
 177 }
 178 /***********************************************************/
 179