venncommand.cpp

   1 /*
   2  *  venncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venncommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 #include "jackknife.h"
  15 #include "sharedsobscollectsummary.h"
  16 #include "sharedchao1.h"
  17 #include "sharedace.h"
  18
  19
  20 //**********************************************************************************************************************
  21
  22 VennCommand::VennCommand(){
  23         try {
  24                 globaldata = GlobalData::getInstance();
  25                 format = globaldata->getFormat();
  26                 validCalculator = new ValidCalculators();
  27
  28                 int i;
  29
  30                 if (format == "list") {
  31                         for (i=0; i<globaldata->Estimators.size(); i++) {
  32                                 if (validCalculator->isValidCalculator("vennsingle", globaldata->Estimators[i]) == true) {
  33                                         if (globaldata->Estimators[i] == "sobs") {
  34                                                 vennCalculators.push_back(new Sobs());
  35                                         }else if (globaldata->Estimators[i] == "chao") {
  36                                                 vennCalculators.push_back(new Chao1());
  37                                         }else if (globaldata->Estimators[i] == "ace") {
  38                                                 convert(globaldata->getAbund(), abund);
  39                                                 if(abund < 5)
  40                                                         abund = 10;
  41                                                 vennCalculators.push_back(new Ace(abund));
  42                                         }else if (globaldata->Estimators[i] == "jack") {
  43                                                 vennCalculators.push_back(new Jackknife());
  44                                         }
  45                                 }
  46                         }
  47                 }else {
  48                         for (i=0; i<globaldata->Estimators.size(); i++) {
  49                                 if (validCalculator->isValidCalculator("vennshared", globaldata->Estimators[i]) == true) {
  50                                         if (globaldata->Estimators[i] == "sharedsobs") {
  51                                                 vennCalculators.push_back(new SharedSobsCS());
  52                                         }else if (globaldata->Estimators[i] == "sharedchao") {
  53                                                 vennCalculators.push_back(new SharedChao1());
  54                                         }else if (globaldata->Estimators[i] == "sharedace") {
  55                                                 vennCalculators.push_back(new SharedAce());
  56                                         }
  57                                 }
  58                         }
  59                 }
  60
  61                 venn = new Venn();
  62
  63                 //reset calc for next command
  64                 globaldata->setCalc("");
  65
  66
  67         }
  68         catch(exception& e) {
  69                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  70                 exit(1);
  71         }
  72         catch(...) {
  73                 cout << "An unknown error has occurred in the VennCommand class function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78
  79 VennCommand::~VennCommand(){
  80         delete input;
  81         delete read;
  82         delete venn;
  83 }
  84
  85 //**********************************************************************************************************************
  86
  87 int VennCommand::execute(){
  88         try {
  89                 int count = 1;
  90
  91                 //if the users entered no valid calculators don't execute command
  92                 if (vennCalculators.size() == 0) { return 0; }
  93
  94                 if (format == "sharedfile") {
  95                         //you have groups
  96                         read = new ReadPhilFile(globaldata->inputFileName);
  97                         read->read(&*globaldata);
  98
  99                         input = globaldata->ginput;
 100                         order = input->getSharedOrderVector();
 101                 }else if (format == "shared") {
 102                         //you are using a list and a groupfile
 103                         read = new ReadPhilFile(globaldata->inputFileName);
 104                         read->read(&*globaldata);
 105
 106                         input = globaldata->ginput;
 107                         SharedList = globaldata->gSharedList;
 108                         order = SharedList->getSharedOrderVector();
 109                 }else if (format == "list") {
 110                         //you are using just a list file and have only one group
 111                         read = new ReadPhilFile(globaldata->inputFileName);
 112                         read->read(&*globaldata);
 113
 114                         ordersingle = globaldata->gorder;
 115                         input = globaldata->ginput;
 116                 }
 117
 118
 119                 if (format != "list") {
 120
 121                         setGroups();
 122
 123                         while(order != NULL){
 124
 125                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 126
 127                                         cout << order->getLabel() << '\t' << count << endl;
 128                                         venn->getPic(order, vennCalculators);
 129
 130                                 }
 131
 132                                 //get next line to process
 133                                 if (format == "sharedfile") {
 134                                         order = input->getSharedOrderVector();
 135                                 }else {
 136                                         //you are using a list and a groupfile
 137                                         SharedList = input->getSharedListVector(); //get new list vector to process
 138                                         if (SharedList != NULL) {
 139                                                 order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 140                                         }else {
 141                                                 break;
 142                                         }
 143                                 }
 144                                 count++;
 145                         }
 146
 147                         //reset groups parameter
 148                         globaldata->Groups.clear();  globaldata->setGroups("");
 149
 150                 }else{
 151                         while(ordersingle != NULL){
 152
 153                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){
 154
 155                                         cout << ordersingle->getLabel() << '\t' << count << endl;
 156                                         venn->getPic(ordersingle, vennCalculators);
 157
 158                                 }
 159
 160                                 ordersingle = (input->getOrderVector());
 161                                 count++;
 162                         }
 163                 }
 164
 165                 return 0;
 166         }
 167         catch(exception& e) {
 168                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 169                 exit(1);
 170         }
 171         catch(...) {
 172                 cout << "An unknown error has occurred in the VennCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 173                 exit(1);
 174         }
 175 }
 176
 177 //**********************************************************************************************************************
 178 void VennCommand::setGroups() {
 179         try {
 180                 //if the user has not entered specific groups to analyze then do them all
 181                 if (globaldata->Groups.size() != 0) {
 182                         if (globaldata->Groups[0] != "all") {
 183                                 //check that groups are valid
 184                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 185                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 186                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 187                                                 // erase the invalid group from globaldata->Groups
 188                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 189                                         }
 190                                 }
 191
 192                                 //if the user only entered invalid groups
 193                                 if (globaldata->Groups.size() == 0) {
 194                                         if (globaldata->gGroupmap->namesOfGroups.size() > 4) {
 195                                                 cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using the first four groups in your groupfile." << endl;
 196                                                 for (int i = 0; i < 4; i++) {
 197                                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 198                                                 }
 199                                         }else {
 200                                                 cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
 201                                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 202                                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 203                                                 }
 204                                         }
 205
 206                                 }
 207                         }else{//user has enter "all" and wants the default groups
 208                                 globaldata->Groups.clear();
 209                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 210                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 211                                 }
 212                                 globaldata->setGroups("");
 213                         }
 214                 }else {
 215                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 216                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 217                         }
 218                 }
 219
 220
 221                 //check to make sure their are only 3 groups
 222                 if (globaldata->Groups.size() > 4) {
 223                         cout << "You may only use up to 4 groups at a time with this command.  I will choose the first four and disregard the rest." << endl;
 224                         for (int i = 4; i < globaldata->Groups.size(); i++) {
 225                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 226                         }
 227                 }
 228
 229         }
 230         catch(exception& e) {
 231                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 232                 exit(1);
 233         }
 234         catch(...) {
 235                 cout << "An unknown error has occurred in the VennCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 236                 exit(1);
 237         }
 238
 239 }
 240 /***********************************************************/
 241