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
  12 //**********************************************************************************************************************
  13
  14 VennCommand::VennCommand(){
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17                 venn = new Venn();
  18                 format = globaldata->getFormat();
  19
  20         }
  21         catch(exception& e) {
  22                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  23                 exit(1);
  24         }
  25         catch(...) {
  26                 cout << "An unknown error has occurred in the VennCommand class function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31
  32 VennCommand::~VennCommand(){
  33         delete input;
  34         delete read;
  35         delete venn;
  36 }
  37
  38 //**********************************************************************************************************************
  39
  40 int VennCommand::execute(){
  41         try {
  42                 int count = 1;
  43
  44                 if (format == "sharedfile") {
  45                         //you have groups
  46                         read = new ReadPhilFile(globaldata->inputFileName);
  47                         read->read(&*globaldata);
  48
  49                         input = globaldata->ginput;
  50                         order = input->getSharedOrderVector();
  51                 }else if (format == "shared") {
  52                         //you are using a list and a groupfile
  53                         read = new ReadPhilFile(globaldata->inputFileName);
  54                         read->read(&*globaldata);
  55
  56                         input = globaldata->ginput;
  57                         SharedList = globaldata->gSharedList;
  58                         order = SharedList->getSharedOrderVector();
  59                 }else if (format == "list") {
  60                         //you are using just a list file and have only one group
  61                         read = new ReadPhilFile(globaldata->inputFileName);
  62                         read->read(&*globaldata);
  63
  64                         ordersingle = globaldata->gorder;
  65                         input = globaldata->ginput;
  66                 }
  67
  68
  69                 if (format != "list") {
  70
  71                         setGroups();
  72
  73                         while(order != NULL){
  74
  75                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  76
  77                                         cout << order->getLabel() << '\t' << count << endl;
  78                                         venn->getPic(order);
  79
  80                                 }
  81
  82                                 //get next line to process
  83                                 if (format == "sharedfile") {
  84                                         order = input->getSharedOrderVector();
  85                                 }else {
  86                                         //you are using a list and a groupfile
  87                                         SharedList = input->getSharedListVector(); //get new list vector to process
  88                                         if (SharedList != NULL) {
  89                                                 order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
  90                                         }else {
  91                                                 break;
  92                                         }
  93                                 }
  94                                 count++;
  95                         }
  96
  97                         //reset groups parameter
  98                         globaldata->Groups.clear();  globaldata->setGroups("");
  99
 100                 }else{
 101                         while(ordersingle != NULL){
 102
 103                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){
 104
 105                                         cout << ordersingle->getLabel() << '\t' << count << endl;
 106                                         venn->getPic(ordersingle);
 107
 108                                 }
 109
 110                                 ordersingle = (input->getOrderVector());
 111                                 count++;
 112                         }
 113                 }
 114
 115                 return 0;
 116         }
 117         catch(exception& e) {
 118                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 119                 exit(1);
 120         }
 121         catch(...) {
 122                 cout << "An unknown error has occurred in the VennCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 123                 exit(1);
 124         }
 125 }
 126
 127 //**********************************************************************************************************************
 128 void VennCommand::setGroups() {
 129         try {
 130                 //if the user has not entered specific groups to analyze then do them all
 131                 if (globaldata->Groups.size() != 0) {
 132                         if (globaldata->Groups[0] != "all") {
 133                                 //check that groups are valid
 134                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 135                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 136                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 137                                                 // erase the invalid group from globaldata->Groups
 138                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 139                                         }
 140                                 }
 141
 142                                 //if the user only entered invalid groups
 143                                 if (globaldata->Groups.size() == 0) {
 144                                         if (globaldata->gGroupmap->namesOfGroups.size() > 4) {
 145                                                 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;
 146                                                 for (int i = 0; i < 4; i++) {
 147                                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 148                                                 }
 149                                         }else {
 150                                                 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;
 151                                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 152                                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 153                                                 }
 154                                         }
 155
 156                                 }
 157                         }else{//user has enter "all" and wants the default groups
 158                                 globaldata->Groups.clear();
 159                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 160                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 161                                 }
 162                                 globaldata->setGroups("");
 163                         }
 164                 }else {
 165                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 166                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 167                         }
 168                 }
 169
 170
 171                 //check to make sure their are only 3 groups
 172                 if (globaldata->Groups.size() > 4) {
 173                         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;
 174                         for (int i = 4; i < globaldata->Groups.size(); i++) {
 175                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 176                         }
 177                 }
 178
 179         }
 180         catch(exception& e) {
 181                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 182                 exit(1);
 183         }
 184         catch(...) {
 185                 cout << "An unknown error has occurred in the VennCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 186                 exit(1);
 187         }
 188
 189 }
 190 /***********************************************************/
 191