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                 delete read;
  61
  62                 input = globaldata->ginput;
  63                 SharedList = globaldata->gSharedList;
  64                 string lastLabel = SharedList->getLabel();
  65                 vector<SharedRAbundVector*> lookup;
  66
  67                 if (SharedList->getNumSeqs() != groupMap->getNumSeqs()) {
  68                         mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine();
  69
  70                         //delete memory
  71                         for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
  72                                 delete it3->second;
  73                         }
  74                         delete SharedList;
  75                         globaldata->gSharedList = NULL;
  76
  77                         return(0);
  78                 }
  79
  80                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  81                 set<string> processedLabels;
  82                 set<string> userLabels = globaldata->labels;
  83                 set<int> userLines = globaldata->lines;
  84
  85
  86                 while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
  87
  88
  89                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
  90
  91                                         lookup = SharedList->getSharedRAbundVector();
  92                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
  93
  94                                         printSharedData(lookup); //prints info to the .shared file
  95                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  96
  97                                         processedLabels.insert(SharedList->getLabel());
  98                                         userLabels.erase(SharedList->getLabel());
  99                                         userLines.erase(count);
 100                         }
 101
 102                         if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
 103                                         delete SharedList;
 104                                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 105
 106                                         lookup = SharedList->getSharedRAbundVector();
 107                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 108
 109                                         printSharedData(lookup); //prints info to the .shared file
 110                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 111
 112                                         processedLabels.insert(SharedList->getLabel());
 113                                         userLabels.erase(SharedList->getLabel());
 114                         }
 115
 116
 117                         lastLabel = SharedList->getLabel();
 118
 119                         delete SharedList;
 120                         SharedList = input->getSharedListVector(); //get new list vector to process
 121
 122                         count++;
 123                 }
 124
 125                 //output error messages about any remaining user labels
 126                 set<string>::iterator it;
 127                 bool needToRun = false;
 128                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 129                         if (processedLabels.count(lastLabel) != 1) {
 130                                 needToRun = true;
 131                         }
 132                 }
 133
 134                 //run last line if you need to
 135                 if (needToRun == true)  {
 136                         if (SharedList != NULL) {       delete SharedList;      }
 137                         SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 138
 139                         lookup = SharedList->getSharedRAbundVector();
 140                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 141
 142                         printSharedData(lookup); //prints info to the .shared file
 143                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 144                         delete SharedList;
 145                 }
 146
 147                 globaldata->gSharedList = NULL;
 148
 149                 out.close();
 150
 151                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 152                         delete it3->second;
 153                 }
 154
 155
 156                 return 0;
 157         }
 158         catch(exception& e) {
 159                 errorOut(e, "SharedCommand", "execute");
 160                 exit(1);
 161         }
 162 }
 163 //**********************************************************************************************************************
 164 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 165         try {
 166
 167                 //initialize bin values
 168                 for (int i = 0; i < thislookup.size(); i++) {
 169                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 170                         thislookup[i]->print(out);
 171
 172                         RAbundVector rav = thislookup[i]->getRAbundVector();
 173                         openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
 174                         rav.print(*(filehandles[thislookup[i]->getGroup()]));
 175                         (*(filehandles[thislookup[i]->getGroup()])).close();
 176                 }
 177
 178         }
 179         catch(exception& e) {
 180                 errorOut(e, "SharedCommand", "printSharedData");
 181                 exit(1);
 182         }
 183 }
 184
 185 //**********************************************************************************************************************
 186
 187 SharedCommand::~SharedCommand(){
 188         //delete list;
 189
 190
 191 }
 192
 193 //**********************************************************************************************************************