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                 errorOut(e, "SharedCommand", "SharedCommand");
  26                 exit(1);
  27         }
  28 }
  29 //**********************************************************************************************************************
  30
  31 int SharedCommand::execute(){
  32         try {
  33
  34                 mothurOut("creating sharedfile..."); mothurOutEndLine();
  35                 //lookup.clear();
  36                 int count = 1;
  37                 string errorOff = "no error";
  38
  39                 //read in listfile
  40                 read = new ReadOTUFile(globaldata->inputFileName);
  41                 read->read(&*globaldata);
  42
  43                 input = globaldata->ginput;
  44                 SharedList = globaldata->gSharedList;
  45                 string lastLabel = SharedList->getLabel();
  46                 vector<SharedRAbundVector*> lookup;
  47
  48                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  49                 set<string> processedLabels;
  50                 set<string> userLabels = globaldata->labels;
  51                 set<int> userLines = globaldata->lines;
  52
  53
  54                 while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
  55
  56
  57                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
  58                                         lookup = SharedList->getSharedRAbundVector();
  59                                         printSharedData(lookup); //prints info to the .shared file
  60                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  61
  62                                         processedLabels.insert(SharedList->getLabel());
  63                                         userLabels.erase(SharedList->getLabel());
  64                                         userLines.erase(count);
  65                         }
  66
  67                         if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
  68                                         delete SharedList;
  69                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
  70
  71                                         lookup = SharedList->getSharedRAbundVector();
  72                                         printSharedData(lookup); //prints info to the .shared file
  73                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  74
  75                                         processedLabels.insert(SharedList->getLabel());
  76                                         userLabels.erase(SharedList->getLabel());
  77                         }
  78
  79
  80                         lastLabel = SharedList->getLabel();
  81
  82                         delete SharedList;
  83                         SharedList = input->getSharedListVector(); //get new list vector to process
  84
  85                         count++;
  86                 }
  87
  88                 //output error messages about any remaining user labels
  89                 set<string>::iterator it;
  90                 bool needToRun = false;
  91                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
  92                         if (processedLabels.count(lastLabel) != 1) {
  93                                 needToRun = true;
  94                         }
  95                 }
  96
  97                 //run last line if you need to
  98                 if (needToRun == true)  {
  99                         delete SharedList;
 100                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 101
 102                         lookup = SharedList->getSharedRAbundVector();
 103                         printSharedData(lookup); //prints info to the .shared file
 104                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 105                         delete SharedList;
 106                 }
 107
 108                 globaldata->gSharedList = NULL;
 109                 delete read;
 110
 111                 out.close();
 112
 113                 mothurOut("complete."); mothurOutEndLine();
 114                 return 0;
 115         }
 116         catch(exception& e) {
 117                 errorOut(e, "SharedCommand", "execute");
 118                 exit(1);
 119         }
 120 }
 121 //**********************************************************************************************************************
 122 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 123         try {
 124
 125                 //initialize bin values
 126                 for (int i = 0; i < thislookup.size(); i++) {
 127                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 128                         thislookup[i]->print(out);
 129                 }
 130
 131         }
 132         catch(exception& e) {
 133                 errorOut(e, "SharedCommand", "printSharedData");
 134                 exit(1);
 135         }
 136 }
 137
 138 //**********************************************************************************************************************
 139
 140 SharedCommand::~SharedCommand(){
 141         //delete list;
 142
 143
 144 }
 145
 146 //**********************************************************************************************************************