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