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 "sharednseqs.h"
  23 #include "sharedochiai.h"
  24 #include "sharedanderberg.h"
  25 #include "sharedkulczynski.h"
  26 #include "sharedkulczynskicody.h"
  27 #include "sharedlennon.h"
  28 #include "sharedmorisitahorn.h"
  29 #include "sharedbraycurtis.h"
  30
  31
  32 //**********************************************************************************************************************
  33
  34 CollectSharedCommand::CollectSharedCommand(){
  35         try {
  36                 globaldata = GlobalData::getInstance();
  37                 string fileNameRoot;
  38                 fileNameRoot = getRootName(globaldata->inputFileName);
  39                 format = globaldata->getFormat();
  40                 validCalculator = new ValidCalculators();
  41
  42                 int i;
  43                 for (i=0; i<globaldata->Estimators.size(); i++) {
  44                         if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) {
  45                                 if (globaldata->Estimators[i] == "sharedchao") {
  46                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
  47                                 }else if (globaldata->Estimators[i] == "sharedsobs") {
  48                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
  49                                 }else if (globaldata->Estimators[i] == "sharedace") {
  50                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
  51                                 }else if (globaldata->Estimators[i] == "sharedjabund") {
  52                                         cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund")));
  53                                 }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
  54                                         cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund")));
  55                                 }else if (globaldata->Estimators[i] == "sharedjclass") {
  56                                         cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass")));
  57                                 }else if (globaldata->Estimators[i] == "sharedsorclass") {
  58                                         cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass")));
  59                                 }else if (globaldata->Estimators[i] == "sharedjest") {
  60                                         cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest")));
  61                                 }else if (globaldata->Estimators[i] == "sharedsorest") {
  62                                         cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest")));
  63                                 }else if (globaldata->Estimators[i] == "sharedthetayc") {
  64                                         cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
  65                                 }else if (globaldata->Estimators[i] == "sharedthetan") {
  66                                         cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
  67                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  68                                         cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
  69                                 }else if (globaldata->Estimators[i] == "sharedochiai") {
  70                                         cDisplays.push_back(new CollectDisplay(new SharedOchiai(), new SharedOneColumnFile(fileNameRoot+"shared.ochiai")));
  71                                 }else if (globaldata->Estimators[i] == "sharedanderberg") {
  72                                         cDisplays.push_back(new CollectDisplay(new SharedAnderberg(), new SharedOneColumnFile(fileNameRoot+"shared.anderberg")));
  73                                 }else if (globaldata->Estimators[i] == "sharedkulczynski") {
  74                                         cDisplays.push_back(new CollectDisplay(new SharedKulczynski(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynski")));
  75                                 }else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
  76                                         cDisplays.push_back(new CollectDisplay(new SharedKulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynskicody")));
  77                                 }else if (globaldata->Estimators[i] == "sharedlennon") {
  78                                         cDisplays.push_back(new CollectDisplay(new SharedLennon(), new SharedOneColumnFile(fileNameRoot+"shared.lennon")));
  79                                 }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
  80                                         cDisplays.push_back(new CollectDisplay(new SharedMorHorn(), new SharedOneColumnFile(fileNameRoot+"shared.morisitahorn")));
  81                                 }else if (globaldata->Estimators[i] == "sharedbraycurtis") {
  82                                         cDisplays.push_back(new CollectDisplay(new SharedBrayCurtis(), new SharedOneColumnFile(fileNameRoot+"shared.braycurtis")));
  83                                 }
  84                         }
  85                 }
  86
  87                 //reset calc for next command
  88                 globaldata->setCalc("");
  89
  90         }
  91         catch(exception& e) {
  92                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  93                 exit(1);
  94         }
  95         catch(...) {
  96                 cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  97                 exit(1);
  98         }
  99
 100 }
 101
 102 //**********************************************************************************************************************
 103
 104 CollectSharedCommand::~CollectSharedCommand(){
 105         delete order;
 106         delete input;
 107         delete cCurve;
 108         delete read;
 109 }
 110
 111 //**********************************************************************************************************************
 112
 113 int CollectSharedCommand::execute(){
 114         try {
 115                 int count = 1;
 116
 117                 //if the users entered no valid calculators don't execute command
 118                 if (cDisplays.size() == 0) { return 0; }
 119
 120                 if (format == "sharedfile") {
 121                         read = new ReadPhilFile(globaldata->inputFileName);
 122                         read->read(&*globaldata);
 123
 124                         input = globaldata->ginput;
 125                         order = input->getSharedOrderVector();
 126                 }else {
 127                         //you are using a list and a groupfile
 128                         read = new ReadPhilFile(globaldata->inputFileName);
 129                         read->read(&*globaldata);
 130
 131                         input = globaldata->ginput;
 132                         SharedList = globaldata->gSharedList;
 133                         order = SharedList->getSharedOrderVector();
 134                 }
 135                 set<string> orderList;
 136
 137                 //set users groups
 138                 setGroups();
 139
 140                 while(order != NULL){
 141                         orderList.insert(order->getLabel());
 142                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 143                                 //create collectors curve
 144                                 cCurve = new Collect(order, cDisplays);
 145                                 convert(globaldata->getFreq(), freq);
 146                                 cCurve->getSharedCurve(freq);
 147
 148                                 delete cCurve;
 149
 150                                 cout << order->getLabel() << '\t' << count << endl;
 151                         }
 152
 153                         //get next line to process
 154                         if (format == "sharedfile") {
 155                                 order = input->getSharedOrderVector();
 156                         }else {
 157                                 //you are using a list and a groupfile
 158                                 SharedList = input->getSharedListVector(); //get new list vector to process
 159                                 if (SharedList != NULL) {
 160                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 161                                 }else {
 162                                         break;
 163                                 }
 164                         }
 165
 166                         count++;
 167                 }
 168                 set<string>::iterator i;
 169                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 170                         if(orderList.count(*i) == 0)
 171                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 172                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 173
 174                 //reset groups parameter
 175                 globaldata->Groups.clear();  globaldata->setGroups("");
 176
 177                 return 0;
 178         }
 179         catch(exception& e) {
 180                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 181                 exit(1);
 182         }
 183         catch(...) {
 184                 cout << "An unknown error has occurred in the CollectSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 185                 exit(1);
 186         }
 187 }
 188
 189
 190 //**********************************************************************************************************************
 191 void CollectSharedCommand::setGroups() {
 192         try {
 193                 //if the user has not entered specific groups to analyze then do them all
 194                 if (globaldata->Groups.size() != 0) {
 195                         if (globaldata->Groups[0] != "all") {
 196                                 //check that groups are valid
 197                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 198                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 199                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 200                                                 // erase the invalid group from globaldata->Groups
 201                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 202                                         }
 203                                 }
 204
 205                                 //if the user only entered invalid groups
 206                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 207                                         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;
 208                                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 209                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 210                                         }
 211                                 }
 212                         }else{//user has enter "all" and wants the default groups
 213                                 globaldata->Groups.clear();
 214                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 215                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 216                                 }
 217                                 globaldata->setGroups("");
 218                         }
 219                 }else {
 220                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 221                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 222                         }
 223                 }
 224
 225         }
 226         catch(exception& e) {
 227                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 228                 exit(1);
 229         }
 230         catch(...) {
 231                 cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 232                 exit(1);
 233         }
 234
 235 }
 236 /***********************************************************/
 237