collectsharedcommand.cpp

   1 /*
   2  *  collectsharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "collectsharedcommand.h"
  11 #include "sharedsobscollectsummary.h"
  12 #include "sharedchao1.h"
  13 #include "sharedace.h"
  14 #include "sharedjabund.h"
  15 #include "sharedsorabund.h"
  16 #include "sharedjclass.h"
  17 #include "sharedsorclass.h"
  18 #include "sharedjest.h"
  19 #include "sharedsorest.h"
  20 #include "sharedthetayc.h"
  21 #include "sharedthetan.h"
  22 #include "sharedkstest.h"
  23 #include "whittaker.h"
  24 #include "sharednseqs.h"
  25 #include "sharedochiai.h"
  26 #include "sharedanderbergs.h"
  27 #include "sharedkulczynski.h"
  28 #include "sharedkulczynskicody.h"
  29 #include "sharedlennon.h"
  30 #include "sharedmorisitahorn.h"
  31 #include "sharedbraycurtis.h"
  32 #include "sharedjackknife.h"
  33 #include "sharedwhittaker.h"
  34
  35
  36
  37 //**********************************************************************************************************************
  38
  39 CollectSharedCommand::CollectSharedCommand(){
  40         try {
  41                 globaldata = GlobalData::getInstance();
  42                 string fileNameRoot;
  43                 fileNameRoot = getRootName(globaldata->inputFileName);
  44                 format = globaldata->getFormat();
  45                 validCalculator = new ValidCalculators();
  46                 util = new SharedUtil();
  47
  48                 int i;
  49                 for (i=0; i<globaldata->Estimators.size(); i++) {
  50                         if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) {
  51                                 if (globaldata->Estimators[i] == "sharedchao") {
  52                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
  53                                 }else if (globaldata->Estimators[i] == "sharedsobs") {
  54                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
  55                                 }else if (globaldata->Estimators[i] == "sharedace") {
  56                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
  57                                 }else if (globaldata->Estimators[i] == "jabund") {
  58                                         cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
  59                                 }else if (globaldata->Estimators[i] == "sorabund") {
  60                                         cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
  61                                 }else if (globaldata->Estimators[i] == "jclass") {
  62                                         cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
  63                                 }else if (globaldata->Estimators[i] == "sorclass") {
  64                                         cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
  65                                 }else if (globaldata->Estimators[i] == "jest") {
  66                                         cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
  67                                 }else if (globaldata->Estimators[i] == "sorest") {
  68                                         cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
  69                                 }else if (globaldata->Estimators[i] == "thetayc") {
  70                                         cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
  71                                 }else if (globaldata->Estimators[i] == "thetan") {
  72                                         cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
  73                                 }else if (globaldata->Estimators[i] == "kstest") {
  74                                         cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
  75                                 }else if (globaldata->Estimators[i] == "whittaker") {
  76                                         cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
  77                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  78                                         cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
  79
  80                                 }else if (globaldata->Estimators[i] == "ochiai") {
  81                                         cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
  82                                 }else if (globaldata->Estimators[i] == "anderberg") {
  83                                         cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
  84                                 }else if (globaldata->Estimators[i] == "skulczynski") {
  85                                         cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
  86                                 }else if (globaldata->Estimators[i] == "kulczynskicody") {
  87                                         cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
  88                                 }else if (globaldata->Estimators[i] == "lennon") {
  89                                         cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
  90                                 }else if (globaldata->Estimators[i] == "morisitahorn") {
  91                                         cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
  92                                 }else if (globaldata->Estimators[i] == "braycurtis") {
  93                                         cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
  94                                 }
  95                         }
  96                 }
  97
  98                 //reset calc for next command
  99                 globaldata->setCalc("");
 100
 101         }
 102         catch(exception& e) {
 103                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 104                 exit(1);
 105         }
 106         catch(...) {
 107                 cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 108                 exit(1);
 109         }
 110
 111 }
 112
 113 //**********************************************************************************************************************
 114
 115 CollectSharedCommand::~CollectSharedCommand(){
 116         delete order;
 117         delete input;
 118         delete cCurve;
 119         delete read;
 120         delete util;
 121 }
 122
 123 //**********************************************************************************************************************
 124
 125 int CollectSharedCommand::execute(){
 126         try {
 127                 int count = 1;
 128
 129                 //if the users entered no valid calculators don't execute command
 130                 if (cDisplays.size() == 0) { return 0; }
 131
 132                 if (format == "sharedfile") {
 133                         read = new ReadOTUFile(globaldata->inputFileName);
 134                         read->read(&*globaldata);
 135
 136                         input = globaldata->ginput;
 137                         order = input->getSharedOrderVector();
 138                 }else {
 139                         //you are using a list and a groupfile
 140                         read = new ReadOTUFile(globaldata->inputFileName);
 141                         read->read(&*globaldata);
 142
 143                         input = globaldata->ginput;
 144                         SharedList = globaldata->gSharedList;
 145                         order = SharedList->getSharedOrderVector();
 146                 }
 147                 set<string> orderList;
 148
 149                 //set users groups
 150                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
 151                 util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 152
 153                 while(order != NULL){
 154                         orderList.insert(order->getLabel());
 155                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 156                                 //create collectors curve
 157                                 cCurve = new Collect(order, cDisplays);
 158                                 convert(globaldata->getFreq(), freq);
 159                                 cCurve->getSharedCurve(freq);
 160
 161                                 delete cCurve;
 162
 163                                 cout << order->getLabel() << '\t' << count << endl;
 164                         }
 165
 166                         //get next line to process
 167                         if (format == "sharedfile") {
 168                                 order = input->getSharedOrderVector();
 169                         }else {
 170                                 //you are using a list and a groupfile
 171                                 SharedList = input->getSharedListVector(); //get new list vector to process
 172                                 if (SharedList != NULL) {
 173                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 174                                 }else {
 175                                         break;
 176                                 }
 177                         }
 178
 179                         count++;
 180                 }
 181                 set<string>::iterator i;
 182                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 183                         if(orderList.count(*i) == 0)
 184                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 185                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 186
 187                 //reset groups parameter
 188                 globaldata->Groups.clear();  globaldata->setGroups("");
 189
 190                 return 0;
 191         }
 192         catch(exception& e) {
 193                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 194                 exit(1);
 195         }
 196         catch(...) {
 197                 cout << "An unknown error has occurred in the CollectSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 198                 exit(1);
 199         }
 200 }
 201
 202 /***********************************************************/
 203