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 "sharedbdiversity.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
  33
  34
  35 //**********************************************************************************************************************
  36
  37 CollectSharedCommand::CollectSharedCommand(){
  38         try {
  39                 globaldata = GlobalData::getInstance();
  40                 string fileNameRoot;
  41                 fileNameRoot = getRootName(globaldata->inputFileName);
  42                 format = globaldata->getFormat();
  43                 validCalculator = new ValidCalculators();
  44
  45                 int i;
  46                 for (i=0; i<globaldata->Estimators.size(); i++) {
  47                         if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) {
  48                                 if (globaldata->Estimators[i] == "sharedchao") {
  49                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
  50                                 }else if (globaldata->Estimators[i] == "sharedsobs") {
  51                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
  52                                 }else if (globaldata->Estimators[i] == "sharedace") {
  53                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
  54                                 }else if (globaldata->Estimators[i] == "sharedjabund") {
  55                                         cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund")));
  56                                 }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
  57                                         cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund")));
  58                                 }else if (globaldata->Estimators[i] == "sharedjclass") {
  59                                         cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass")));
  60                                 }else if (globaldata->Estimators[i] == "sharedsorclass") {
  61                                         cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass")));
  62                                 }else if (globaldata->Estimators[i] == "sharedjest") {
  63                                         cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest")));
  64                                 }else if (globaldata->Estimators[i] == "sharedsorest") {
  65                                         cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest")));
  66                                 }else if (globaldata->Estimators[i] == "sharedthetayc") {
  67                                         cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
  68                                 }else if (globaldata->Estimators[i] == "sharedthetan") {
  69                                         cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
  70                                 }else if (globaldata->Estimators[i] == "sharedkstest") {
  71                                         cDisplays.push_back(new CollectDisplay(new SharedKSTest(), new SharedOneColumnFile(fileNameRoot+"shared.kstest")));
  72                                 }else if (globaldata->Estimators[i] == "sharedbdiversity") {
  73                                         cDisplays.push_back(new CollectDisplay(new SharedBDiversity(), new SharedOneColumnFile(fileNameRoot+"shared.bdiversity")));
  74                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  75                                         cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
  76                                 }else if (globaldata->Estimators[i] == "sharedochiai") {
  77                                         cDisplays.push_back(new CollectDisplay(new SharedOchiai(), new SharedOneColumnFile(fileNameRoot+"shared.ochiai")));
  78                                 }else if (globaldata->Estimators[i] == "sharedanderberg") {
  79                                         cDisplays.push_back(new CollectDisplay(new SharedAnderberg(), new SharedOneColumnFile(fileNameRoot+"shared.anderberg")));
  80                                 }else if (globaldata->Estimators[i] == "sharedkulczynski") {
  81                                         cDisplays.push_back(new CollectDisplay(new SharedKulczynski(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynski")));
  82                                 }else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
  83                                         cDisplays.push_back(new CollectDisplay(new SharedKulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynskicody")));
  84                                 }else if (globaldata->Estimators[i] == "sharedlennon") {
  85                                         cDisplays.push_back(new CollectDisplay(new SharedLennon(), new SharedOneColumnFile(fileNameRoot+"shared.lennon")));
  86                                 }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
  87                                         cDisplays.push_back(new CollectDisplay(new SharedMorHorn(), new SharedOneColumnFile(fileNameRoot+"shared.morisitahorn")));
  88                                 }else if (globaldata->Estimators[i] == "sharedbraycurtis") {
  89                                         cDisplays.push_back(new CollectDisplay(new SharedBrayCurtis(), new SharedOneColumnFile(fileNameRoot+"shared.braycurtis")));
  90                                 }
  91                         }
  92                 }
  93
  94                 //reset calc for next command
  95                 globaldata->setCalc("");
  96
  97         }
  98         catch(exception& e) {
  99                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 100                 exit(1);
 101         }
 102         catch(...) {
 103                 cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 104                 exit(1);
 105         }
 106
 107 }
 108
 109 //**********************************************************************************************************************
 110
 111 CollectSharedCommand::~CollectSharedCommand(){
 112         delete order;
 113         delete input;
 114         delete cCurve;
 115         delete read;
 116 }
 117
 118 //**********************************************************************************************************************
 119
 120 int CollectSharedCommand::execute(){
 121         try {
 122                 int count = 1;
 123
 124                 //if the users entered no valid calculators don't execute command
 125                 if (cDisplays.size() == 0) { return 0; }
 126
 127                 if (format == "sharedfile") {
 128                         read = new ReadPhilFile(globaldata->inputFileName);
 129                         read->read(&*globaldata);
 130
 131                         input = globaldata->ginput;
 132                         order = input->getSharedOrderVector();
 133                 }else {
 134                         //you are using a list and a groupfile
 135                         read = new ReadPhilFile(globaldata->inputFileName);
 136                         read->read(&*globaldata);
 137
 138                         input = globaldata->ginput;
 139                         SharedList = globaldata->gSharedList;
 140                         order = SharedList->getSharedOrderVector();
 141                 }
 142                 set<string> orderList;
 143
 144                 //set users groups
 145                 setGroups();
 146
 147                 while(order != NULL){
 148                         orderList.insert(order->getLabel());
 149                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 150                                 //create collectors curve
 151                                 cCurve = new Collect(order, cDisplays);
 152                                 convert(globaldata->getFreq(), freq);
 153                                 cCurve->getSharedCurve(freq);
 154
 155                                 delete cCurve;
 156
 157                                 cout << order->getLabel() << '\t' << count << endl;
 158                         }
 159
 160                         //get next line to process
 161                         if (format == "sharedfile") {
 162                                 order = input->getSharedOrderVector();
 163                         }else {
 164                                 //you are using a list and a groupfile
 165                                 SharedList = input->getSharedListVector(); //get new list vector to process
 166                                 if (SharedList != NULL) {
 167                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 168                                 }else {
 169                                         break;
 170                                 }
 171                         }
 172
 173                         count++;
 174                 }
 175                 set<string>::iterator i;
 176                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 177                         if(orderList.count(*i) == 0)
 178                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 179                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 180
 181                 //reset groups parameter
 182                 globaldata->Groups.clear();  globaldata->setGroups("");
 183
 184                 return 0;
 185         }
 186         catch(exception& e) {
 187                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 188                 exit(1);
 189         }
 190         catch(...) {
 191                 cout << "An unknown error has occurred in the CollectSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 192                 exit(1);
 193         }
 194 }
 195
 196
 197 //**********************************************************************************************************************
 198 void CollectSharedCommand::setGroups() {
 199         try {
 200                 //if the user has not entered specific groups to analyze then do them all
 201                 if (globaldata->Groups.size() != 0) {
 202                         if (globaldata->Groups[0] != "all") {
 203                                 //check that groups are valid
 204                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 205                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 206                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 207                                                 // erase the invalid group from globaldata->Groups
 208                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 209                                         }
 210                                 }
 211
 212                                 //if the user only entered invalid groups
 213                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 214                                         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;
 215                                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 216                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 217                                         }
 218                                 }
 219                         }else{//user has enter "all" and wants the default groups
 220                                 globaldata->Groups.clear();
 221                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 222                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 223                                 }
 224                                 globaldata->setGroups("");
 225                         }
 226                 }else {
 227                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 228                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 229                         }
 230                 }
 231
 232         }
 233         catch(exception& e) {
 234                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 235                 exit(1);
 236         }
 237         catch(...) {
 238                 cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 239                 exit(1);
 240         }
 241
 242 }
 243 /***********************************************************/
 244