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                 groupMap = globaldata->gGroupmap;
  25
  26                 //fill filehandles with neccessary ofstreams
  27                 int i;
  28                 ofstream* temp;
  29                 for (i=0; i<groupMap->getNumGroups(); i++) {
  30                         temp = new ofstream;
  31                         filehandles[groupMap->namesOfGroups[i]] = temp;
  32                 }
  33
  34                 //set fileroot
  35                 fileroot = getRootName(globaldata->getListFile());
  36
  37                 //clears file before we start to write to it below
  38                 for (int i=0; i<groupMap->getNumGroups(); i++) {
  39                         remove((fileroot + groupMap->namesOfGroups[i] + ".rabund").c_str());
  40                 }
  41
  42         }
  43         catch(exception& e) {
  44                 errorOut(e, "SharedCommand", "SharedCommand");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49
  50 int SharedCommand::execute(){
  51         try {
  52
  53                 //lookup.clear();
  54                 int count = 1;
  55                 string errorOff = "no error";
  56
  57                 //read in listfile
  58                 read = new ReadOTUFile(globaldata->inputFileName);
  59                 read->read(&*globaldata);
  60
  61                 input = globaldata->ginput;
  62                 SharedList = globaldata->gSharedList;
  63                 string lastLabel = SharedList->getLabel();
  64                 vector<SharedRAbundVector*> lookup;
  65
  66                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  67                 set<string> processedLabels;
  68                 set<string> userLabels = globaldata->labels;
  69                 set<int> userLines = globaldata->lines;
  70
  71
  72                 while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
  73
  74
  75                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
  76
  77                                         lookup = SharedList->getSharedRAbundVector();
  78                                         mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
  79
  80                                         printSharedData(lookup); //prints info to the .shared file
  81                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  82
  83                                         processedLabels.insert(SharedList->getLabel());
  84                                         userLabels.erase(SharedList->getLabel());
  85                                         userLines.erase(count);
  86                         }
  87
  88                         if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
  89                                         delete SharedList;
  90                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
  91
  92                                         lookup = SharedList->getSharedRAbundVector();
  93                                         mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
  94
  95                                         printSharedData(lookup); //prints info to the .shared file
  96                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  97
  98                                         processedLabels.insert(SharedList->getLabel());
  99                                         userLabels.erase(SharedList->getLabel());
 100                         }
 101
 102
 103                         lastLabel = SharedList->getLabel();
 104
 105                         delete SharedList;
 106                         SharedList = input->getSharedListVector(); //get new list vector to process
 107
 108                         count++;
 109                 }
 110
 111                 //output error messages about any remaining user labels
 112                 set<string>::iterator it;
 113                 bool needToRun = false;
 114                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 115                         if (processedLabels.count(lastLabel) != 1) {
 116                                 needToRun = true;
 117                         }
 118                 }
 119
 120                 //run last line if you need to
 121                 if (needToRun == true)  {
 122                         delete SharedList;
 123                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 124
 125                         lookup = SharedList->getSharedRAbundVector();
 126                         mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
 127
 128                         printSharedData(lookup); //prints info to the .shared file
 129                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 130                         delete SharedList;
 131                 }
 132
 133                 globaldata->gSharedList = NULL;
 134                 delete read;
 135
 136                 out.close();
 137
 138                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 139                         delete it3->second;
 140                 }
 141
 142
 143                 return 0;
 144         }
 145         catch(exception& e) {
 146                 errorOut(e, "SharedCommand", "execute");
 147                 exit(1);
 148         }
 149 }
 150 //**********************************************************************************************************************
 151 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 152         try {
 153
 154                 //initialize bin values
 155                 for (int i = 0; i < thislookup.size(); i++) {
 156                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 157                         thislookup[i]->print(out);
 158
 159                         openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
 160                         (*filehandles[thislookup[i]->getGroup()]) << thislookup[i]->getLabel()  << '\t' << thislookup[i]->getGroup()  << '\t';
 161                         thislookup[i]->print(*(filehandles[thislookup[i]->getGroup()]));
 162                         (*(filehandles[thislookup[i]->getGroup()])).close();
 163                 }
 164
 165         }
 166         catch(exception& e) {
 167                 errorOut(e, "SharedCommand", "printSharedData");
 168                 exit(1);
 169         }
 170 }
 171
 172 //**********************************************************************************************************************
 173
 174 SharedCommand::~SharedCommand(){
 175         //delete list;
 176
 177
 178 }
 179
 180 //**********************************************************************************************************************