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                 int i;
  24                 for (i=0; i<globaldata->Estimators.size(); i++) {
  25                         if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) {
  26                                 if (globaldata->Estimators[i] == "sharedobserved") {
  27                                         rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
  28                                 }
  29                         }
  30                 }
  31
  32                 //reset calc for next command
  33                 globaldata->setCalc("");
  34
  35         }
  36         catch(exception& e) {
  37                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  38                 exit(1);
  39         }
  40         catch(...) {
  41                 cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44
  45 }
  46
  47 //**********************************************************************************************************************
  48
  49 RareFactSharedCommand::~RareFactSharedCommand(){
  50         delete order;
  51         delete input;
  52         delete rCurve;
  53         delete read;
  54 }
  55
  56 //**********************************************************************************************************************
  57
  58 int RareFactSharedCommand::execute(){
  59         try {
  60                 int count = 1;
  61
  62                 //if the users entered no valid calculators don't execute command
  63                 if (rDisplays.size() == 0) { return 0; }
  64
  65                 if (format == "sharedfile") {
  66                         read = new ReadPhilFile(globaldata->inputFileName);
  67                         read->read(&*globaldata);
  68
  69                         input = globaldata->ginput;
  70                         order = input->getSharedOrderVector();
  71                 }else {
  72                         //you are using a list and a groupfile
  73                         read = new ReadPhilFile(globaldata->inputFileName);
  74                         read->read(&*globaldata);
  75
  76                         input = globaldata->ginput;
  77                         SharedList = globaldata->gSharedList;
  78                         order = SharedList->getSharedOrderVector();
  79                 }
  80
  81                 //set users groups
  82                 setGroups();
  83
  84                 while(order != NULL){
  85
  86                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  87                                 //create collectors curve
  88                                 rCurve = new Rarefact(order, rDisplays);
  89                                 convert(globaldata->getFreq(), freq);
  90                                 convert(globaldata->getIters(), nIters);
  91                                 rCurve->getSharedCurve(freq, nIters);
  92
  93                                 delete rCurve;
  94
  95                                 cout << order->getLabel() << '\t' << count << endl;
  96                         }
  97
  98                         //get next line to process
  99                         if (format == "sharedfile") {
 100                                 order = input->getSharedOrderVector();
 101                         }else {
 102                                 //you are using a list and a groupfile
 103                                 SharedList = input->getSharedListVector(); //get new list vector to process
 104                                 if (SharedList != NULL) {
 105                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 106                                 }else {
 107                                         break;
 108                                 }
 109                         }
 110
 111                         count++;
 112                 }
 113
 114                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 115
 116                 //reset groups parameter
 117                 globaldata->Groups.clear();  globaldata->setGroups("");
 118
 119                 return 0;
 120         }
 121         catch(exception& e) {
 122                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 123                 exit(1);
 124         }
 125         catch(...) {
 126                 cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 127                 exit(1);
 128         }
 129 }
 130
 131
 132 //**********************************************************************************************************************
 133
 134 void RareFactSharedCommand::setGroups() {
 135         try {
 136                 //if the user has not entered specific groups to analyze then do them all
 137                 if (globaldata->Groups.size() != 0) {
 138                         if (globaldata->Groups[0] != "all") {
 139                                 //check that groups are valid
 140                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 141                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 142                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 143                                                 // erase the invalid group from globaldata->Groups
 144                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 145                                         }
 146                                 }
 147
 148                                 //if the user only entered invalid groups
 149                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 150                                         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;
 151                                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 152                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 153                                         }
 154                                 }
 155                         }else{//user has enter "all" and wants the default groups
 156                                 globaldata->Groups.clear();
 157                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 158                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 159                                 }
 160                                 globaldata->setGroups("");
 161                         }
 162                 }else {
 163                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 164                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 165                         }
 166                 }
 167
 168         }
 169         catch(exception& e) {
 170                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 171                 exit(1);
 172         }
 173         catch(...) {
 174                 cout << "An unknown error has occurred in the RareFactSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 175                 exit(1);
 176         }
 177
 178 }
 179 /***********************************************************/
 180