alignment.cpp

   1 /*
   2  *  alignment.cpp
   3  *
   4  *  Created by Pat Schloss on 12/15/08.
   5  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   6  *
   7  *  This is a class for an abstract datatype for classes that implement various types of alignment      algorithms.
   8  *      As of 12/18/08 these included alignments based on blastn, needleman-wunsch, and the     Gotoh algorithms
   9  *
  10  */
  11
  12 #include "alignmentcell.hpp"
  13 #include "alignment.hpp"
  14
  15
  16 /**************************************************************************************************/
  17
  18 Alignment::Alignment() {        /*      do nothing      */      }
  19
  20 /**************************************************************************************************/
  21
  22 Alignment::Alignment(int A) : nCols(A), nRows(A) {
  23         try {
  24                 alignment.resize(nRows);                        //      For the Gotoh and Needleman-Wunsch we initialize the dynamic programming
  25                 for(int i=0;i<nRows;i++){                       //      matrix by initializing a matrix that is A x A.  By default we will set A
  26                         alignment[i].resize(nCols);             //      at 2000 for 16S rRNA gene sequences
  27                 }
  28         }
  29         catch(exception& e) {
  30                 errorOut(e, "Alignment", "Alignment");
  31                 exit(1);
  32         }
  33 }
  34
  35 /**************************************************************************************************/
  36
  37 void Alignment::traceBack(){                    //      This traceback routine is used by the dynamic programming algorithms
  38         try {
  39                                                                         //      to fill the values of seqAaln and seqBaln
  40                 seqAaln = "";
  41                 seqBaln = "";
  42                 int row = lB-1;
  43                 int column = lA-1;
  44                 //      seqAstart = 1;
  45                 //      seqAend = column;
  46
  47                 AlignmentCell currentCell = alignment[row][column];     //      Start the traceback from the bottom-right corner of the
  48                 //      matrix
  49
  50                 if(currentCell.prevCell == 'x'){        seqAaln = seqBaln = "NOALIGNMENT";              }//If there's an 'x' in the bottom-
  51                 else{                                                                                           //      right corner bail out because it means nothing got aligned
  52                         while(currentCell.prevCell != 'x'){                             //      while the previous cell isn't an 'x', keep going...
  53
  54                                 if(currentCell.prevCell == 'u'){                        //      if the pointer to the previous cell is 'u', go up in the
  55                                         seqAaln = '-' + seqAaln;                                //      matrix.  this indicates that we need to insert a gap in
  56                                         seqBaln = seqB[row] + seqBaln;                  //      seqA and a base in seqB
  57                                         currentCell = alignment[--row][column];
  58                                 }
  59                                 else if(currentCell.prevCell == 'l'){           //      if the pointer to the previous cell is 'l', go to the left
  60                                         seqBaln = '-' + seqBaln;                                //      in the matrix.  this indicates that we need to insert a gap
  61                                         seqAaln = seqA[column] + seqAaln;               //      in seqB and a base in seqA
  62                                         currentCell = alignment[row][--column];
  63                                 }
  64                                 else{
  65                                         seqAaln = seqA[column] + seqAaln;               //      otherwise we need to go diagonally up and to the left,
  66                                         seqBaln = seqB[row] + seqBaln;                  //      here we add a base to both alignments
  67                                         currentCell = alignment[--row][--column];
  68                                 }
  69                         }
  70                 }
  71
  72                 pairwiseLength = seqAaln.length();
  73                 seqAstart = 1;  seqAend = 0;
  74                 seqBstart = 1;  seqBend = 0;
  75
  76                 for(int i=0;i<seqAaln.length();i++){
  77                         if(seqAaln[i] != '-' && seqBaln[i] == '-')              {       seqAstart++;    }
  78                         else if(seqAaln[i] == '-' && seqBaln[i] != '-') {       seqBstart++;    }
  79                         else                                                                                    {       break;                  }
  80                 }
  81
  82                 pairwiseLength -= (seqAstart + seqBstart - 2);
  83
  84                 for(int i=seqAaln.length()-1; i>=0;i--){
  85                         if(seqAaln[i] != '-' && seqBaln[i] == '-')              {       seqAend++;              }
  86                         else if(seqAaln[i] == '-' && seqBaln[i] != '-') {       seqBend++;              }
  87                         else                                                                                    {       break;                  }
  88                 }
  89                 pairwiseLength -= (seqAend + seqBend);
  90
  91                 seqAend = seqA.length() - seqAend - 1;
  92                 seqBend = seqB.length() - seqBend - 1;
  93         }
  94         catch(exception& e) {
  95                 errorOut(e, "Alignment", "traceBack");
  96                 exit(1);
  97         }
  98 }
  99 /**************************************************************************************************/
 100
 101 Alignment::~Alignment(){
 102         try {
 103                 for (int i = 0; i < alignment.size(); i++) {
 104                         for (int j = (alignment[i].size()-1); j >= 0; j--) {  alignment[i].pop_back();  }
 105                 }
 106         }
 107         catch(exception& e) {
 108                 errorOut(e, "Alignment", "~Alignment");
 109                 exit(1);
 110         }
 111 }
 112
 113 /**************************************************************************************************/
 114
 115 string Alignment::getSeqAAln(){
 116         return seqAaln;                                                                         //      this is called to get the alignment of seqA
 117 }
 118
 119 /**************************************************************************************************/
 120
 121 string Alignment::getSeqBAln(){
 122         return seqBaln;                                                                         //      this is called to get the alignment of seqB
 123 }
 124
 125 /**************************************************************************************************/
 126
 127 int Alignment::getCandidateStartPos(){
 128         return seqAstart;                                                                       //      this is called to report the quality of the alignment
 129 }
 130
 131 /**************************************************************************************************/
 132
 133 int Alignment::getCandidateEndPos(){
 134         return seqAend;                                                                         //      this is called to report the quality of the alignment
 135 }
 136
 137 /**************************************************************************************************/
 138
 139 int Alignment::getTemplateStartPos(){
 140         return seqBstart;                                                                       //      this is called to report the quality of the alignment
 141 }
 142
 143 /**************************************************************************************************/
 144
 145 int Alignment::getTemplateEndPos(){
 146         return seqBend;                                                                         //      this is called to report the quality of the alignment
 147 }
 148
 149 /**************************************************************************************************/
 150
 151 int Alignment::getPairwiseLength(){
 152         return pairwiseLength;                                                          //      this is the pairwise alignment length
 153 }
 154
 155 /**************************************************************************************************/
 156
 157 //int Alignment::getLongestTemplateGap(){
 158 //
 159 //      int length = seqBaln.length();
 160 //      int longGap = 0;
 161 //      int gapLength = 0;
 162 //
 163 //      int start = seqAstart;
 164 //      if(seqAstart < seqBstart){      start = seqBstart;      }
 165 //      for(int i=seqAstart;i<length;i++){
 166 //              if(seqBaln[i] == '-'){
 167 //                      gapLength++;
 168 //              }
 169 //              else{
 170 //                      if(gapLength > 0){
 171 //                              if(gapLength > longGap){        longGap = gapLength;    }
 172 //                      }
 173 //                      gapLength = 0;
 174 //              }
 175 //      }
 176 //      return longGap;
 177 //}
 178
 179 /**************************************************************************************************/