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 "whittaker.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                 convert(globaldata->getFreq(), freq);
  46                 validCalculator = new ValidCalculators();
  47                 util = new SharedUtil();
  48
  49                 int i;
  50                 for (i=0; i<globaldata->Estimators.size(); i++) {
  51                         if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) {
  52                                 if (globaldata->Estimators[i] == "sharedchao") {
  53                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
  54                                 }else if (globaldata->Estimators[i] == "sharedsobs") {
  55                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
  56                                 }else if (globaldata->Estimators[i] == "sharedace") {
  57                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
  58                                 }else if (globaldata->Estimators[i] == "jabund") {
  59                                         cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
  60                                 }else if (globaldata->Estimators[i] == "sorabund") {
  61                                         cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
  62                                 }else if (globaldata->Estimators[i] == "jclass") {
  63                                         cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
  64                                 }else if (globaldata->Estimators[i] == "sorclass") {
  65                                         cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
  66                                 }else if (globaldata->Estimators[i] == "jest") {
  67                                         cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
  68                                 }else if (globaldata->Estimators[i] == "sorest") {
  69                                         cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
  70                                 }else if (globaldata->Estimators[i] == "thetayc") {
  71                                         cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
  72                                 }else if (globaldata->Estimators[i] == "thetan") {
  73                                         cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
  74                                 }else if (globaldata->Estimators[i] == "kstest") {
  75                                         cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
  76                                 }else if (globaldata->Estimators[i] == "whittaker") {
  77                                         cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
  78                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  79                                         cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
  80
  81                                 }else if (globaldata->Estimators[i] == "ochiai") {
  82                                         cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
  83                                 }else if (globaldata->Estimators[i] == "anderberg") {
  84                                         cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
  85                                 }else if (globaldata->Estimators[i] == "skulczynski") {
  86                                         cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
  87                                 }else if (globaldata->Estimators[i] == "kulczynskicody") {
  88                                         cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
  89                                 }else if (globaldata->Estimators[i] == "lennon") {
  90                                         cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
  91                                 }else if (globaldata->Estimators[i] == "morisitahorn") {
  92                                         cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
  93                                 }else if (globaldata->Estimators[i] == "braycurtis") {
  94                                         cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
  95                                 }
  96                         }
  97                 }
  98
  99                 //reset calc for next command
 100                 globaldata->setCalc("");
 101
 102         }
 103         catch(exception& e) {
 104                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 105                 exit(1);
 106         }
 107         catch(...) {
 108                 cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 109                 exit(1);
 110         }
 111
 112 }
 113
 114 //**********************************************************************************************************************
 115
 116 CollectSharedCommand::~CollectSharedCommand(){
 117         delete order;
 118         delete input;
 119         delete cCurve;
 120         delete read;
 121         delete util;
 122 }
 123
 124 //**********************************************************************************************************************
 125
 126 int CollectSharedCommand::execute(){
 127         try {
 128                 int count = 1;
 129
 130                 //if the users entered no valid calculators don't execute command
 131                 if (cDisplays.size() == 0) { return 0; }
 132
 133                 read = new ReadOTUFile(globaldata->inputFileName);
 134                 read->read(&*globaldata);
 135
 136                 input = globaldata->ginput;
 137                 order = input->getSharedOrderVector();
 138                 SharedOrderVector* lastOrder = order;
 139
 140                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 141                 set<string> processedLabels;
 142                 set<string> userLabels = globaldata->labels;
 143                 set<int> userLines = globaldata->lines;
 144
 145                 //set users groups
 146                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
 147                 util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 148
 149                 while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 150
 151                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 152
 153                                 //create collectors curve
 154                                 cCurve = new Collect(order, cDisplays);
 155                                 cCurve->getSharedCurve(freq);
 156                                 delete cCurve;
 157
 158                                 cout << order->getLabel() << '\t' << count << endl;
 159                                 processedLabels.insert(order->getLabel());
 160                                 userLabels.erase(order->getLabel());
 161                                 userLines.erase(count);
 162
 163                         //you have a label the user want that is smaller than this line and the last line has not already been processed
 164                         }
 165
 166                         if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
 167                                 //create collectors curve
 168                                 cCurve = new Collect(lastOrder, cDisplays);
 169                                 cCurve->getSharedCurve(freq);
 170                                 delete cCurve;
 171
 172                                 cout << lastOrder->getLabel() << '\t' << count << endl;
 173                                 processedLabels.insert(lastOrder->getLabel());
 174                                 userLabels.erase(lastOrder->getLabel());
 175                         }
 176
 177                         if (count != 1) { delete lastOrder; }
 178                         lastOrder = order;
 179
 180                         //get next line to process
 181                         order = input->getSharedOrderVector();
 182                         count++;
 183                 }
 184
 185                 //output error messages about any remaining user labels
 186                 set<string>::iterator it;
 187                 bool needToRun = false;
 188                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 189                         cout << "Your file does not include the label "<< *it;
 190                         if (processedLabels.count(lastOrder->getLabel()) != 1) {
 191                                 cout << ". I will use " << lastOrder->getLabel() << "." << endl;
 192                                 needToRun = true;
 193                         }else {
 194                                 cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
 195                         }
 196                 }
 197
 198                 //run last line if you need to
 199                 if (needToRun == true)  {
 200                         cCurve = new Collect(lastOrder, cDisplays);
 201                         cCurve->getCurve(freq);
 202                         delete cCurve;
 203
 204                         cout << lastOrder->getLabel() << '\t' << count << endl;
 205                 }
 206
 207                 delete lastOrder;
 208                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 209
 210                 //reset groups parameter
 211                 globaldata->Groups.clear();  globaldata->setGroups("");
 212
 213                 return 0;
 214         }
 215         catch(exception& e) {
 216                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 217                 exit(1);
 218         }
 219         catch(...) {
 220                 cout << "An unknown error has occurred in the CollectSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 221                 exit(1);
 222         }
 223 }
 224
 225 /***********************************************************/
 226