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 #include "database.hpp"
  12 #include "sequence.hpp"
  13 #include "distancedb.hpp"
  14
  15
  16 /**************************************************************************************************/
  17
  18 DistanceDB::DistanceDB(string fastaFileName, string distanceFileName) : Database(fastaFileName) {
  19
  20         ifstream inputData;
  21         openInputFile(distanceFileName, inputData);
  22         int numCandSeqs=count(istreambuf_iterator<char>(inputData),istreambuf_iterator<char>(), '\n');  //      count the number of
  23         inputData.seekg(0);                                                                                                                                             //      sequences
  24
  25         hit closestMatch;
  26         string candidateSeqName;
  27         string junk;
  28
  29         mostSimSequenceVector.resize(numCandSeqs);
  30
  31         for(int i=0;i<numCandSeqs;i++){
  32                 inputData >> candidateSeqName >> closestMatch.seqName >> closestMatch.indexNumber >> closestMatch.simScore;
  33                 mostSimSequenceVector[i] = closestMatch;
  34         }
  35         mothurOut(toString(numCandSeqs)); mothurOutEndLine();
  36         searchIndex = 0;
  37         inputData.close();
  38 }
  39
  40 /**************************************************************************************************/
  41
  42 Sequence DistanceDB::findClosestSequence(Sequence* candidateSeq){
  43
  44         hit simAccession = mostSimSequenceVector[searchIndex];
  45 //      string candidateSeqName, closestMatchSeqName, junk;
  46 //      int closestMatchIndexNumber;
  47 //      float closestMatchSimScore;
  48 //
  49 //      inputData >> candidateSeqName >> closestMatchSeqName >> closestMatchIndexNumber >> closestMatchSimScore;
  50 //      getline(inputData, junk);
  51
  52 //      searchScore = 100. * closestMatchSimScore;
  53
  54         searchScore = 100. * simAccession.simScore;
  55         searchIndex++;
  56 //      return templateSequences[closestMatchIndexNumber];
  57         if (templateValid) {  return templateSequences[simAccession.indexNumber];       }
  58         else {  return emptySequence;   }
  59
  60 }
  61
  62 /**************************************************************************************************/