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(SharedListVector* list) {
  20                 string label, group;
  21                 int i,j;
  22                 label = list->getLabel();
  23
  24                 for (it = sharedGroups.begin(); it != sharedGroups.end(); it++) {  delete it->second;  }
  25                 sharedGroups.clear();  //removes old info.
  26
  27                 //initalize sharedGroups
  28                 for (j=0; j<globaldata->gGroupmap->getNumGroups(); j++) {//for each group
  29                         group = globaldata->gGroupmap->namesOfGroups[j];
  30                         sharedGroups[group] = new SharedRAbundVector();
  31                         sharedGroups[group]->setLabel(label);
  32                         for (i = 0; i<list->size(); i++) { //for each otu
  33                                 sharedGroups[group]->push_back(0, i, group); //initialize to 0.
  34                         }
  35                 }
  36
  37                 //fills sharedGroups
  38                 for (i = 0; i<list->size(); i++) {
  39                         parse(i, list);
  40                 }
  41
  42                 //updates sharedVector
  43                 //sharedRAbund.push_back(sharedGroups);
  44 }
  45
  46
  47
  48 /***********************************************************************/
  49 void Shared::parse(int index, SharedListVector* list) {
  50
  51                 string prefix, suffix, groupsName;
  52                 suffix = list->get(index);
  53
  54                 while (suffix.find_first_of(',') != -1) {//while you still have sequences
  55                         prefix = suffix.substr(0,suffix.find_first_of(','));
  56                         if ((suffix.find_first_of(',')+1) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
  57                                 suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
  58                         }
  59                         groupsName = globaldata->gGroupmap->getGroup(prefix);
  60                         if (groupsName != "not found") {
  61                                 sharedGroups[groupsName]->set(index, (sharedGroups[groupsName]->getAbundance(index) + 1), groupsName); //increment shared vector for that group
  62                         }else {
  63                                 cerr << "Error: Sequence '" << prefix << "' was not found in the group file, please correct\n";
  64                         }
  65                 }
  66
  67                 //save last name after comma
  68                 groupsName = globaldata->gGroupmap->getGroup(suffix);
  69                 if (groupsName != "not found") {
  70                         sharedGroups[groupsName]->set(index, ((sharedGroups[groupsName]->getAbundance(index)) + 1), groupsName); //increment shared vector for that group
  71                 }else {
  72                         cerr << "Error: Sequence '" << suffix << "' was not found in the group file, please correct\n";
  73                 }
  74         }