sharedcommand.cpp

   1 /*
   2  *  sharedcommand.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 "sharedcommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 SharedCommand::SharedCommand(){
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17
  18                 //getting output filename
  19                 filename = globaldata->inputFileName;
  20                 filename = getRootName(filename);
  21                 filename = filename + "shared";
  22                 openOutputFile(filename, out);
  23         }
  24         catch(exception& e) {
  25                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  26                 exit(1);
  27         }
  28         catch(...) {
  29                 cout << "An unknown error has occurred in the SharedCommand class function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  30                 exit(1);
  31         }
  32
  33 }
  34 //**********************************************************************************************************************
  35
  36 int SharedCommand::execute(){
  37         try {
  38                 globaldata = GlobalData::getInstance();
  39                 int count = 1;
  40                 string errorOff = "no error";
  41
  42                 //read in listfile
  43                 read = new ReadOTUFile(globaldata->inputFileName);
  44                 read->read(&*globaldata);
  45                 input = globaldata->ginput;
  46                 SharedList = globaldata->gSharedList;
  47                 SharedListVector* lastList = SharedList;
  48
  49                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  50                 set<string> processedLabels;
  51                 set<string> userLabels = globaldata->labels;
  52                 set<int> userLines = globaldata->lines;
  53
  54                 shared = new Shared();
  55
  56                 while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
  57
  58
  59                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
  60
  61                                         shared->getSharedVectors(SharedList); //fills sharedGroups with new info and updates sharedVector
  62                                         printSharedData(); //prints info to the .shared file
  63
  64                                         processedLabels.insert(SharedList->getLabel());
  65                                         userLabels.erase(SharedList->getLabel());
  66                                         userLines.erase(count);
  67                         }
  68
  69                         if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
  70                                         shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
  71                                         printSharedData(); //prints info to the .shared file
  72
  73                                         processedLabels.insert(lastList->getLabel());
  74                                         userLabels.erase(lastList->getLabel());
  75                         }
  76
  77                         if (count != 1) { delete lastList; }
  78                         lastList = SharedList;
  79
  80                         SharedList = input->getSharedListVector(); //get new list vector to process
  81                 }
  82
  83                 //output error messages about any remaining user labels
  84                 set<string>::iterator it;
  85                 bool needToRun = false;
  86                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
  87                         //cout << "Your file does not include the label "<< *it;
  88                         if (processedLabels.count(lastList->getLabel()) != 1) {
  89                                 //cout << ". I will use " << lastList->getLabel() << "." << endl;
  90                                 needToRun = true;
  91                         }else {
  92                                 //cout << ". Please refer to " << lastList->getLabel() << "." << endl;
  93                         }
  94                 }
  95
  96                 //run last line if you need to
  97                 if (needToRun == true)  {
  98                         shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
  99                         printSharedData(); //prints info to the .shared file
 100                 }
 101
 102                 delete lastList;
 103                 delete shared;
 104
 105                 return 0;
 106         }
 107         catch(exception& e) {
 108                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 109                 exit(1);
 110         }
 111         catch(...) {
 112                 cout << "An unknown error has occurred in the SharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 113                 exit(1);
 114         }
 115
 116 }
 117 //**********************************************************************************************************************
 118 void SharedCommand::printSharedData() {
 119         try {
 120                 //prints out horizontally
 121                 for (it = shared->sharedGroups.begin(); it != shared->sharedGroups.end(); it++) {
 122                         out << it->second->getLabel() << "\t" << it->first << "\t"; //prints out label and groupname
 123                         it->second->print(out); // prints sharedrabundvector
 124                 }
 125         }
 126         catch(exception& e) {
 127                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 128                 exit(1);
 129         }
 130         catch(...) {
 131                 cout << "An unknown error has occurred in the SharedCommand class function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 132                 exit(1);
 133         }
 134
 135 }
 136
 137 //**********************************************************************************************************************
 138
 139 SharedCommand::~SharedCommand(){
 140         //delete list;
 141         delete read;
 142
 143 }
 144
 145 //**********************************************************************************************************************