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                 validCalculator = new ValidCalculators();
  23
  24                 int i;
  25                 for (i=0; i<globaldata->Estimators.size(); i++) {
  26                         if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) {
  27                                 if (globaldata->Estimators[i] == "sharedobserved") {
  28                                         rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
  29                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  30                                         rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
  31                                 }
  32
  33                         }
  34                 }
  35
  36                 //reset calc for next command
  37                 globaldata->setCalc("");
  38
  39         }
  40         catch(exception& e) {
  41                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44         catch(...) {
  45                 cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  46                 exit(1);
  47         }
  48
  49 }
  50
  51 //**********************************************************************************************************************
  52
  53 RareFactSharedCommand::~RareFactSharedCommand(){
  54         delete order;
  55         delete input;
  56         delete rCurve;
  57         delete read;
  58 }
  59
  60 //**********************************************************************************************************************
  61
  62 int RareFactSharedCommand::execute(){
  63         try {
  64                 int count = 1;
  65
  66                 //if the users entered no valid calculators don't execute command
  67                 if (rDisplays.size() == 0) { return 0; }
  68
  69                 if (format == "sharedfile") {
  70                         read = new ReadPhilFile(globaldata->inputFileName);
  71                         read->read(&*globaldata);
  72
  73                         input = globaldata->ginput;
  74                         order = input->getSharedOrderVector();
  75                 }else {
  76                         //you are using a list and a groupfile
  77                         read = new ReadPhilFile(globaldata->inputFileName);
  78                         read->read(&*globaldata);
  79
  80                         input = globaldata->ginput;
  81                         SharedList = globaldata->gSharedList;
  82                         order = SharedList->getSharedOrderVector();
  83                 }
  84
  85                 //set users groups
  86                 setGroups();
  87
  88                 while(order != NULL){
  89
  90                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  91                                 //create collectors curve
  92                                 rCurve = new Rarefact(order, rDisplays);
  93                                 convert(globaldata->getFreq(), freq);
  94                                 convert(globaldata->getIters(), nIters);
  95                                 rCurve->getSharedCurve(freq, nIters);
  96
  97                                 delete rCurve;
  98
  99                                 cout << order->getLabel() << '\t' << count << endl;
 100                         }
 101
 102                         //get next line to process
 103                         if (format == "sharedfile") {
 104                                 order = input->getSharedOrderVector();
 105                         }else {
 106                                 //you are using a list and a groupfile
 107                                 SharedList = input->getSharedListVector(); //get new list vector to process
 108                                 if (SharedList != NULL) {
 109                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 110                                 }else {
 111                                         break;
 112                                 }
 113                         }
 114
 115                         count++;
 116                 }
 117
 118                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 119
 120                 //reset groups parameter
 121                 globaldata->Groups.clear();  globaldata->setGroups("");
 122
 123                 return 0;
 124         }
 125         catch(exception& e) {
 126                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 127                 exit(1);
 128         }
 129         catch(...) {
 130                 cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 131                 exit(1);
 132         }
 133 }
 134
 135
 136 //**********************************************************************************************************************
 137
 138 void RareFactSharedCommand::setGroups() {
 139         try {
 140                 //if the user has not entered specific groups to analyze then do them all
 141                 if (globaldata->Groups.size() != 0) {
 142                         if (globaldata->Groups[0] != "all") {
 143                                 //check that groups are valid
 144                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 145                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 146                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 147                                                 // erase the invalid group from globaldata->Groups
 148                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 149                                         }
 150                                 }
 151
 152                                 //if the user only entered invalid groups
 153                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 154                                         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;
 155                                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 156                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 157                                         }
 158                                 }
 159                         }else{//user has enter "all" and wants the default groups
 160                                 globaldata->Groups.clear();
 161                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 162                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 163                                 }
 164                                 globaldata->setGroups("");
 165                         }
 166                 }else {
 167                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 168                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 169                         }
 170                 }
 171
 172         }
 173         catch(exception& e) {
 174                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 175                 exit(1);
 176         }
 177         catch(...) {
 178                 cout << "An unknown error has occurred in the RareFactSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 179                 exit(1);
 180         }
 181
 182 }
 183 /***********************************************************/
 184