shared.cpp

   1 /*
   2  *  shared.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 12/5/08.
   6  *  Copyright 2008 Schloss Lab Umass Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "shared.h"
  11
  12 /**************************************************************************************************/
  13
  14 Shared::Shared(){
  15    globaldata = GlobalData::getInstance();
  16 }
  17
  18 /**************************************************************************************************/
  19 void Shared::getSharedVectors(int index, SharedListVector* list) {
  20                 string label, group;
  21                 int i,j;
  22                 label = list->getLabel();
  23
  24                 sharedGroups.clear();  //removes old info.
  25
  26                 //initalize sharedGroups
  27                 for (j=0; j<globaldata->gGroupmap->getNumGroups(); j++) {//for each group
  28                         group = globaldata->gGroupmap->namesOfGroups[j];
  29                         sharedGroups[group] = new SharedRAbundVector();
  30                         sharedGroups[group]->setLabel(label);
  31                         for (i = 0; i<list->size(); i++) { //for each otu
  32                                 sharedGroups[group]->push_back(0, i, group); //initialize to 0.
  33                         }
  34                 }
  35
  36                 //fills sharedGroups
  37                 for (i = 0; i<list->size(); i++) {
  38                         parse(i, list);
  39                 }
  40
  41                 //updates sharedVector
  42                 sharedRAbund.push_back(sharedGroups);
  43 }
  44
  45
  46
  47 /***********************************************************************/
  48 void Shared::parse(int index, SharedListVector* list) {
  49
  50                 string prefix, suffix, groupsName;
  51                 suffix = list->get(index);
  52
  53                 while (suffix.find_first_of(',') != -1) {//while you still have sequences
  54                         prefix = suffix.substr(0,suffix.find_first_of(','));
  55                         if ((suffix.find_first_of(',')+1) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
  56                                 suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
  57                         }
  58                         groupsName = globaldata->gGroupmap->getGroup(prefix);
  59                         if (groupsName != "not found") {
  60                                 sharedGroups[groupsName]->set(index, (sharedGroups[groupsName]->getAbundance(index) + 1), groupsName); //increment shared vector for that group
  61                         }else {
  62                                 cerr << "Error: Sequence '" << prefix << "' was not found in the group file, please correct\n";
  63                         }
  64                 }
  65
  66                 //save last name after comma
  67                 groupsName = globaldata->gGroupmap->getGroup(suffix);
  68                 if (groupsName != "not found") {
  69                         sharedGroups[groupsName]->set(index, ((sharedGroups[groupsName]->getAbundance(index)) + 1), groupsName); //increment shared vector for that group
  70                 }else {
  71                         cerr << "Error: Sequence '" << suffix << "' was not found in the group file, please correct\n";
  72                 }
  73         }