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