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 <<<<<<< collectsharedcommand.cpp
  23 #include "sharedkstest.h"
  24 #include "sharedbdiversity.h"
  25 =======
  26 #include "sharednseqs.h"
  27 #include "sharedochiai.h"
  28 #include "sharedanderberg.h"
  29 #include "sharedkulczynski.h"
  30 #include "sharedkulczynskicody.h"
  31 #include "sharedlennon.h"
  32 #include "sharedmorisitahorn.h"
  33 #include "sharedbraycurtis.h"
  34 >>>>>>> 1.13
  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
  47                 int i;
  48                 for (i=0; i<globaldata->Estimators.size(); i++) {
  49                         if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) {
  50                                 if (globaldata->Estimators[i] == "sharedchao") {
  51                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
  52                                 }else if (globaldata->Estimators[i] == "sharedsobs") {
  53                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
  54                                 }else if (globaldata->Estimators[i] == "sharedace") {
  55                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
  56                                 }else if (globaldata->Estimators[i] == "sharedjabund") {
  57                                         cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund")));
  58                                 }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
  59                                         cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund")));
  60                                 }else if (globaldata->Estimators[i] == "sharedjclass") {
  61                                         cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass")));
  62                                 }else if (globaldata->Estimators[i] == "sharedsorclass") {
  63                                         cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass")));
  64                                 }else if (globaldata->Estimators[i] == "sharedjest") {
  65                                         cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest")));
  66                                 }else if (globaldata->Estimators[i] == "sharedsorest") {
  67                                         cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest")));
  68                                 }else if (globaldata->Estimators[i] == "sharedthetayc") {
  69                                         cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
  70                                 }else if (globaldata->Estimators[i] == "sharedthetan") {
  71                                         cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
  72                                 }else if (globaldata->Estimators[i] == "sharedkstest") {
  73                                         cDisplays.push_back(new CollectDisplay(new SharedKSTest(), new SharedOneColumnFile(fileNameRoot+"shared.kstest")));
  74                                 }else if (globaldata->Estimators[i] == "sharedbdiversity") {
  75                                         cDisplays.push_back(new CollectDisplay(new SharedBDiversity(), new SharedOneColumnFile(fileNameRoot+"shared.bdiversity")));
  76                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  77                                         cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
  78                                 }else if (globaldata->Estimators[i] == "sharedochiai") {
  79                                         cDisplays.push_back(new CollectDisplay(new SharedOchiai(), new SharedOneColumnFile(fileNameRoot+"shared.ochiai")));
  80                                 }else if (globaldata->Estimators[i] == "sharedanderberg") {
  81                                         cDisplays.push_back(new CollectDisplay(new SharedAnderberg(), new SharedOneColumnFile(fileNameRoot+"shared.anderberg")));
  82                                 }else if (globaldata->Estimators[i] == "sharedkulczynski") {
  83                                         cDisplays.push_back(new CollectDisplay(new SharedKulczynski(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynski")));
  84                                 }else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
  85                                         cDisplays.push_back(new CollectDisplay(new SharedKulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynskicody")));
  86                                 }else if (globaldata->Estimators[i] == "sharedlennon") {
  87                                         cDisplays.push_back(new CollectDisplay(new SharedLennon(), new SharedOneColumnFile(fileNameRoot+"shared.lennon")));
  88                                 }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
  89                                         cDisplays.push_back(new CollectDisplay(new SharedMorHorn(), new SharedOneColumnFile(fileNameRoot+"shared.morisitahorn")));
  90                                 }else if (globaldata->Estimators[i] == "sharedbraycurtis") {
  91                                         cDisplays.push_back(new CollectDisplay(new SharedBrayCurtis(), new SharedOneColumnFile(fileNameRoot+"shared.braycurtis")));
  92                                 }
  93                         }
  94                 }
  95
  96                 //reset calc for next command
  97                 globaldata->setCalc("");
  98
  99         }
 100         catch(exception& e) {
 101                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 102                 exit(1);
 103         }
 104         catch(...) {
 105                 cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 106                 exit(1);
 107         }
 108
 109 }
 110
 111 //**********************************************************************************************************************
 112
 113 CollectSharedCommand::~CollectSharedCommand(){
 114         delete order;
 115         delete input;
 116         delete cCurve;
 117         delete read;
 118 }
 119
 120 //**********************************************************************************************************************
 121
 122 int CollectSharedCommand::execute(){
 123         try {
 124                 int count = 1;
 125
 126                 //if the users entered no valid calculators don't execute command
 127                 if (cDisplays.size() == 0) { return 0; }
 128
 129                 if (format == "sharedfile") {
 130                         read = new ReadPhilFile(globaldata->inputFileName);
 131                         read->read(&*globaldata);
 132
 133                         input = globaldata->ginput;
 134                         order = input->getSharedOrderVector();
 135                 }else {
 136                         //you are using a list and a groupfile
 137                         read = new ReadPhilFile(globaldata->inputFileName);
 138                         read->read(&*globaldata);
 139
 140                         input = globaldata->ginput;
 141                         SharedList = globaldata->gSharedList;
 142                         order = SharedList->getSharedOrderVector();
 143                 }
 144                 set<string> orderList;
 145
 146                 //set users groups
 147                 setGroups();
 148
 149                 while(order != NULL){
 150                         orderList.insert(order->getLabel());
 151                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 152                                 //create collectors curve
 153                                 cCurve = new Collect(order, cDisplays);
 154                                 convert(globaldata->getFreq(), freq);
 155                                 cCurve->getSharedCurve(freq);
 156
 157                                 delete cCurve;
 158
 159                                 cout << order->getLabel() << '\t' << count << endl;
 160                         }
 161
 162                         //get next line to process
 163                         if (format == "sharedfile") {
 164                                 order = input->getSharedOrderVector();
 165                         }else {
 166                                 //you are using a list and a groupfile
 167                                 SharedList = input->getSharedListVector(); //get new list vector to process
 168                                 if (SharedList != NULL) {
 169                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 170                                 }else {
 171                                         break;
 172                                 }
 173                         }
 174
 175                         count++;
 176                 }
 177                 set<string>::iterator i;
 178                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 179                         if(orderList.count(*i) == 0)
 180                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 181                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 182
 183                 //reset groups parameter
 184                 globaldata->Groups.clear();  globaldata->setGroups("");
 185
 186                 return 0;
 187         }
 188         catch(exception& e) {
 189                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 190                 exit(1);
 191         }
 192         catch(...) {
 193                 cout << "An unknown error has occurred in the CollectSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 194                 exit(1);
 195         }
 196 }
 197
 198
 199 //**********************************************************************************************************************
 200 void CollectSharedCommand::setGroups() {
 201         try {
 202                 //if the user has not entered specific groups to analyze then do them all
 203                 if (globaldata->Groups.size() != 0) {
 204                         if (globaldata->Groups[0] != "all") {
 205                                 //check that groups are valid
 206                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 207                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 208                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 209                                                 // erase the invalid group from globaldata->Groups
 210                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 211                                         }
 212                                 }
 213
 214                                 //if the user only entered invalid groups
 215                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 216                                         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;
 217                                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 218                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 219                                         }
 220                                 }
 221                         }else{//user has enter "all" and wants the default groups
 222                                 globaldata->Groups.clear();
 223                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 224                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 225                                 }
 226                                 globaldata->setGroups("");
 227                         }
 228                 }else {
 229                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 230                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 231                         }
 232                 }
 233
 234         }
 235         catch(exception& e) {
 236                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 237                 exit(1);
 238         }
 239         catch(...) {
 240                 cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 241                 exit(1);
 242         }
 243
 244 }
 245 /***********************************************************/
 246