distancedb.cpp

   1 /*
   2  *  distancedb.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 12/29/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10
  11 using namespace std;
  12
  13
  14 #include "database.hpp"
  15 #include "sequence.hpp"
  16 #include "distancedb.hpp"
  17
  18
  19 /**************************************************************************************************/
  20
  21 DistanceDB::DistanceDB(string fastaFileName, string distanceFileName) : Database(fastaFileName) {
  22
  23         ifstream inputData;
  24         openInputFile(distanceFileName, inputData);
  25         int numCandSeqs=count(istreambuf_iterator<char>(inputData),istreambuf_iterator<char>(), '\n');  //      count the number of
  26         inputData.seekg(0);                                                                                                                                             //      sequences
  27
  28         hit closestMatch;
  29         string candidateSeqName;
  30         string junk;
  31
  32         mostSimSequenceVector.resize(numCandSeqs);
  33
  34         for(int i=0;i<numCandSeqs;i++){
  35                 inputData >> candidateSeqName >> closestMatch.seqName >> closestMatch.indexNumber >> closestMatch.simScore;
  36 //              getline(inputData, junk);
  37                 mostSimSequenceVector[i] = closestMatch;
  38         }
  39         cout << numCandSeqs << endl;
  40         searchIndex = 0;
  41         inputData.close();
  42 }
  43
  44 /**************************************************************************************************/
  45
  46 Sequence* DistanceDB::findClosestSequence(Sequence* candidateSeq){
  47
  48         hit simAccession = mostSimSequenceVector[searchIndex];
  49 //      string candidateSeqName, closestMatchSeqName, junk;
  50 //      int closestMatchIndexNumber;
  51 //      float closestMatchSimScore;
  52 //
  53 //      inputData >> candidateSeqName >> closestMatchSeqName >> closestMatchIndexNumber >> closestMatchSimScore;
  54 //      getline(inputData, junk);
  55
  56 //      searchScore = 100. * closestMatchSimScore;
  57
  58         searchScore = 100. * simAccession.simScore;
  59         searchIndex++;
  60 //      return templateSequences[closestMatchIndexNumber];
  61         return templateSequences[simAccession.indexNumber];
  62
  63 }
  64
  65 /**************************************************************************************************/