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                 //lookup.clear();
  40                 int count = 1;
  41                 string errorOff = "no error";
  42
  43                 //read in listfile
  44                 read = new ReadOTUFile(globaldata->inputFileName);
  45                 read->read(&*globaldata);
  46
  47                 input = globaldata->ginput;
  48                 SharedList = globaldata->gSharedList;
  49                 SharedListVector* lastList = SharedList;
  50                 //lookup = SharedList->getSharedRAbundVector();
  51                 //vector<SharedRAbundVector*> lastLookup = lookup;
  52
  53                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  54                 set<string> processedLabels;
  55                 set<string> userLabels = globaldata->labels;
  56                 set<int> userLines = globaldata->lines;
  57
  58                 shared = new Shared();
  59
  60                 while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
  61
  62
  63                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
  64
  65                                         shared->getSharedVectors(SharedList); //fills sharedGroups with new info and updates sharedVector
  66                                         printSharedData(); //prints info to the .shared file
  67
  68                                         processedLabels.insert(SharedList->getLabel());
  69                                         userLabels.erase(SharedList->getLabel());
  70                                         userLines.erase(count);
  71                         }
  72
  73                         if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
  74                                         shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
  75                                         printSharedData(); //prints info to the .shared file
  76
  77                                         processedLabels.insert(lastList->getLabel());
  78                                         userLabels.erase(lastList->getLabel());
  79                         }
  80
  81                         if (count != 1) { delete lastList; }
  82                         lastList = SharedList;
  83                         SharedList = input->getSharedListVector(); //get new list vector to process
  84
  85                         //if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
  86                         //lastLookup = lookup;
  87                         //if (SharedList != NULL) { lookup = SharedList->getSharedRAbundVector(); }
  88                 }
  89
  90                 //output error messages about any remaining user labels
  91                 set<string>::iterator it;
  92                 bool needToRun = false;
  93                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
  94                         //cout << "Your file does not include the label "<< *it;
  95                         if (processedLabels.count(lastList->getLabel()) != 1) {
  96                                 //cout << ". I will use " << lastList->getLabel() << "." << endl;
  97                                 needToRun = true;
  98                         }else {
  99                                 //cout << ". Please refer to " << lastList->getLabel() << "." << endl;
 100                         }
 101                 }
 102
 103                 //run last line if you need to
 104                 if (needToRun == true)  {
 105                         shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
 106                         printSharedData(); //prints info to the .shared file
 107                 }
 108
 109                 delete lastList;
 110                 delete shared;
 111                 out.close();
 112
 113                 return 0;
 114         }
 115         catch(exception& e) {
 116                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 117                 exit(1);
 118         }
 119         catch(...) {
 120                 cout << "An unknown error has occurred in the SharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 121                 exit(1);
 122         }
 123
 124 }
 125 //**********************************************************************************************************************
 126 void SharedCommand::printSharedData() {
 127         try {
 128
 129                 ///for (int i = 0; i < thislookup.size(); i++) {
 130                 //      out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 131 //cout << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;
 132                 //      thislookup[i]->print(out);
 133         //      }
 134                 //prints out horizontally
 135                 for (it = shared->sharedGroups.begin(); it != shared->sharedGroups.end(); it++) {
 136                         out << it->second->getLabel() << "\t" << it->first << "\t"; //prints out label and groupname
 137                         it->second->print(out); // prints sharedrabundvector
 138                 }
 139         }
 140         catch(exception& e) {
 141                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 142                 exit(1);
 143         }
 144         catch(...) {
 145                 cout << "An unknown error has occurred in the SharedCommand class function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 146                 exit(1);
 147         }
 148
 149 }
 150
 151 //**********************************************************************************************************************
 152
 153 SharedCommand::~SharedCommand(){
 154         //delete list;
 155         delete read;
 156
 157 }
 158
 159 //**********************************************************************************************************************