fastamap.cpp

   1 /*
   2  *  fastamap.cpp
   3  *  mothur
   4  *
   5  *  Created by Sarah Westcott on 1/16/09.
   6  *  Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "fastamap.h"
  11
  12 /*******************************************************************************/
  13  FastaMap::FastaMap(ifstream& in) {
  14         //int numberOfSequences = 0;
  15
  16         string name, sequence, line;
  17         sequence = "";
  18
  19         getline(in, line);
  20         name = line.substr(1, line.length());  //rips off '>'
  21
  22         //read through file
  23         while (getline(in, line)) {
  24                 if (isalnum(line.at(0))){  //if it's a sequence line
  25                         sequence += line;
  26                 }
  27                 else{
  28                         //input sequence info into map
  29                         it = data.find(sequence);
  30                         if (it == data.end()) {         //it's unique.
  31                                 data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
  32                                 data[sequence].groupnumber = 1;
  33                                 data[sequence].names = name;
  34                         }else { // its a duplicate.
  35                                 data[sequence].names += "," + name;
  36                                 data[sequence].groupnumber++;
  37                         }
  38                         name = (line.substr(1, (line.npos))); //The line you just read is a new name so rip off '>'
  39                 }
  40         }
  41
  42         //store last sequence and name info.
  43         it = data.find(sequence);
  44         if (it == data.end()) {         //it's unique.
  45                 data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
  46                 data[sequence].groupnumber = 1;
  47                 data[sequence].names = name;
  48         }else { // its a duplicate.
  49                 data[sequence].names += "," + name;
  50                 data[sequence].groupnumber++;
  51         }
  52 }
  53 /*******************************************************************************/
  54 string FastaMap::getGroupName(string seq) {  //pass a sequence name get its group
  55         return data[seq].groupname;
  56 }
  57 /*******************************************************************************/
  58 int FastaMap::getGroupNumber(string seq) {  //pass a sequence name get number of sequence in its group
  59         return data[seq].groupnumber;
  60 }
  61 /*******************************************************************************/
  62 string FastaMap::getNames(string seq) { //pass a sequence get the string of names in the group separated by ','s.
  63         return data[seq].names;
  64 }
  65 /*******************************************************************************/
  66 void FastaMap::push_back(string seq, string Name) {//sequencename, name
  67         data[seq].groupname = Name;
  68         data[seq].groupnumber = 1;
  69         data[seq].names = Name;
  70 }
  71 /*******************************************************************************/
  72 void FastaMap::clear() { //clears out data
  73         data.clear();
  74 }
  75 /*******************************************************************************/
  76 int FastaMap::size(){ //returns datas size which is the number of unique sequences
  77         return data.size();
  78 }
  79 /*******************************************************************************/
  80 void FastaMap::print(ostream&){ //prints data
  81
  82 }
  83 /*******************************************************************************/