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
  39                 cout << "creating sharedfile...";
  40                 //lookup.clear();
  41                 int count = 1;
  42                 string errorOff = "no error";
  43
  44                 //read in listfile
  45                 read = new ReadOTUFile(globaldata->inputFileName);
  46                 read->read(&*globaldata);
  47
  48                 input = globaldata->ginput;
  49                 SharedList = globaldata->gSharedList;
  50                 string lastLabel = SharedList->getLabel();
  51                 vector<SharedRAbundVector*> 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
  59                 while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
  60
  61
  62                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
  63                                         lookup = SharedList->getSharedRAbundVector();
  64                                         printSharedData(lookup); //prints info to the .shared file
  65                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  66
  67                                         processedLabels.insert(SharedList->getLabel());
  68                                         userLabels.erase(SharedList->getLabel());
  69                                         userLines.erase(count);
  70                         }
  71
  72                         if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
  73                                         delete SharedList;
  74                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
  75
  76                                         lookup = SharedList->getSharedRAbundVector();
  77                                         printSharedData(lookup); //prints info to the .shared file
  78                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  79
  80                                         processedLabels.insert(SharedList->getLabel());
  81                                         userLabels.erase(SharedList->getLabel());
  82                         }
  83
  84
  85                         lastLabel = SharedList->getLabel();
  86
  87                         delete SharedList;
  88                         SharedList = input->getSharedListVector(); //get new list vector to process
  89
  90                         count++;
  91                 }
  92
  93                 //output error messages about any remaining user labels
  94                 set<string>::iterator it;
  95                 bool needToRun = false;
  96                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
  97                         //cout << "Your file does not include the label "<< *it;
  98                         if (processedLabels.count(lastLabel) != 1) {
  99                                 //cout << ". I will use " << lastList->getLabel() << "." << endl;
 100                                 needToRun = true;
 101                         }else {
 102                                 //cout << ". Please refer to " << lastList->getLabel() << "." << endl;
 103                         }
 104                 }
 105
 106                 //run last line if you need to
 107                 if (needToRun == true)  {
 108                         delete SharedList;
 109                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 110
 111                         lookup = SharedList->getSharedRAbundVector();
 112                         printSharedData(lookup); //prints info to the .shared file
 113                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 114                         delete SharedList;
 115                 }
 116
 117                 globaldata->gSharedList = NULL;
 118                 delete read;
 119
 120                 out.close();
 121
 122                 cout << "complete." << endl;
 123                 return 0;
 124         }
 125         catch(exception& e) {
 126                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 127                 exit(1);
 128         }
 129         catch(...) {
 130                 cout << "An unknown error has occurred in the SharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 131                 exit(1);
 132         }
 133
 134 }
 135 //**********************************************************************************************************************
 136 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 137         try {
 138
 139                 //initialize bin values
 140                 for (int i = 0; i < thislookup.size(); i++) {
 141                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 142                         thislookup[i]->print(out);
 143                 }
 144
 145         }
 146         catch(exception& e) {
 147                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 148                 exit(1);
 149         }
 150         catch(...) {
 151                 cout << "An unknown error has occurred in the SharedCommand class function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 152                 exit(1);
 153         }
 154
 155 }
 156
 157 //**********************************************************************************************************************
 158
 159 SharedCommand::~SharedCommand(){
 160         //delete list;
 161
 162
 163 }
 164
 165 //**********************************************************************************************************************