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() {        m = MothurOut::getInstance(); /*        do nothing      */      }
  19
  20 /**************************************************************************************************/
  21
  22 Alignment::Alignment(int A) : nCols(A), nRows(A) {
  23         try {
  24
  25                 m = MothurOut::getInstance();
  26                 alignment.resize(nRows);                        //      For the Gotoh and Needleman-Wunsch we initialize the dynamic programming
  27                 for(int i=0;i<nRows;i++){                       //      matrix by initializing a matrix that is A x A.  By default we will set A
  28                         alignment[i].resize(nCols);             //      at 2000 for 16S rRNA gene sequences
  29                 }
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "Alignment", "Alignment");
  33                 exit(1);
  34         }
  35 }
  36 /**************************************************************************************************/
  37 void Alignment::resize(int A) {
  38         try {
  39                 nCols = A;
  40                 nRows = A;
  41
  42                 alignment.resize(nRows);
  43                 for(int i=0;i<nRows;i++){
  44                         alignment[i].resize(nCols);
  45                 }
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "Alignment", "resize");
  49                 exit(1);
  50         }
  51 }
  52 /**************************************************************************************************/
  53
  54 void Alignment::traceBack(){                    //      This traceback routine is used by the dynamic programming algorithms
  55         try {
  56                                                                         //      to fill the values of seqAaln and seqBaln
  57                 seqAaln = "";
  58                 seqBaln = "";
  59                 int row = lB-1;
  60                 int column = lA-1;
  61                 //      seqAstart = 1;
  62                 //      seqAend = column;
  63
  64                 AlignmentCell currentCell = alignment[row][column];     //      Start the traceback from the bottom-right corner of the
  65                 //      matrix
  66
  67                 if(currentCell.prevCell == 'x'){        seqAaln = seqBaln = "NOALIGNMENT";              }//If there's an 'x' in the bottom-
  68                 else{                                                                                           //      right corner bail out because it means nothing got aligned
  69                         while(currentCell.prevCell != 'x'){                             //      while the previous cell isn't an 'x', keep going...
  70
  71                                 if(currentCell.prevCell == 'u'){                        //      if the pointer to the previous cell is 'u', go up in the
  72                                         seqAaln = '-' + seqAaln;                                //      matrix.  this indicates that we need to insert a gap in
  73                                         seqBaln = seqB[row] + seqBaln;                  //      seqA and a base in seqB
  74                                         currentCell = alignment[--row][column];
  75                                 }
  76                                 else if(currentCell.prevCell == 'l'){           //      if the pointer to the previous cell is 'l', go to the left
  77                                         seqBaln = '-' + seqBaln;                                //      in the matrix.  this indicates that we need to insert a gap
  78                                         seqAaln = seqA[column] + seqAaln;               //      in seqB and a base in seqA
  79                                         currentCell = alignment[row][--column];
  80                                 }
  81                                 else{
  82                                         seqAaln = seqA[column] + seqAaln;               //      otherwise we need to go diagonally up and to the left,
  83                                         seqBaln = seqB[row] + seqBaln;                  //      here we add a base to both alignments
  84                                         currentCell = alignment[--row][--column];
  85                                 }
  86                         }
  87                 }
  88
  89                 pairwiseLength = seqAaln.length();
  90                 seqAstart = 1;  seqAend = 0;
  91                 seqBstart = 1;  seqBend = 0;
  92
  93                 for(int i=0;i<seqAaln.length();i++){
  94                         if(seqAaln[i] != '-' && seqBaln[i] == '-')              {       seqAstart++;    }
  95                         else if(seqAaln[i] == '-' && seqBaln[i] != '-') {       seqBstart++;    }
  96                         else                                                                                    {       break;                  }
  97                 }
  98
  99                 pairwiseLength -= (seqAstart + seqBstart - 2);
 100
 101                 for(int i=seqAaln.length()-1; i>=0;i--){
 102                         if(seqAaln[i] != '-' && seqBaln[i] == '-')              {       seqAend++;              }
 103                         else if(seqAaln[i] == '-' && seqBaln[i] != '-') {       seqBend++;              }
 104                         else                                                                                    {       break;                  }
 105                 }
 106                 pairwiseLength -= (seqAend + seqBend);
 107
 108                 seqAend = seqA.length() - seqAend - 1;
 109                 seqBend = seqB.length() - seqBend - 1;
 110         }
 111         catch(exception& e) {
 112                 m->errorOut(e, "Alignment", "traceBack");
 113                 exit(1);
 114         }
 115 }
 116 /**************************************************************************************************/
 117
 118 Alignment::~Alignment(){
 119         try {
 120                 for (int i = 0; i < alignment.size(); i++) {
 121                         for (int j = (alignment[i].size()-1); j >= 0; j--) {  alignment[i].pop_back();  }
 122                 }
 123         }
 124         catch(exception& e) {
 125                 m->errorOut(e, "Alignment", "~Alignment");
 126                 exit(1);
 127         }
 128 }
 129
 130 /**************************************************************************************************/
 131
 132 string Alignment::getSeqAAln(){
 133         return seqAaln;                                                                         //      this is called to get the alignment of seqA
 134 }
 135
 136 /**************************************************************************************************/
 137
 138 string Alignment::getSeqBAln(){
 139         return seqBaln;                                                                         //      this is called to get the alignment of seqB
 140 }
 141
 142 /**************************************************************************************************/
 143
 144 int Alignment::getCandidateStartPos(){
 145         return seqAstart;                                                                       //      this is called to report the quality of the alignment
 146 }
 147
 148 /**************************************************************************************************/
 149
 150 int Alignment::getCandidateEndPos(){
 151         return seqAend;                                                                         //      this is called to report the quality of the alignment
 152 }
 153
 154 /**************************************************************************************************/
 155
 156 int Alignment::getTemplateStartPos(){
 157         return seqBstart;                                                                       //      this is called to report the quality of the alignment
 158 }
 159
 160 /**************************************************************************************************/
 161
 162 int Alignment::getTemplateEndPos(){
 163         return seqBend;                                                                         //      this is called to report the quality of the alignment
 164 }
 165
 166 /**************************************************************************************************/
 167
 168 int Alignment::getPairwiseLength(){
 169         return pairwiseLength;                                                          //      this is the pairwise alignment length
 170 }
 171
 172 /**************************************************************************************************/
 173
 174 //int Alignment::getLongestTemplateGap(){
 175 //
 176 //      int length = seqBaln.length();
 177 //      int longGap = 0;
 178 //      int gapLength = 0;
 179 //
 180 //      int start = seqAstart;
 181 //      if(seqAstart < seqBstart){      start = seqBstart;      }
 182 //      for(int i=seqAstart;i<length;i++){
 183 //              if(seqBaln[i] == '-'){
 184 //                      gapLength++;
 185 //              }
 186 //              else{
 187 //                      if(gapLength > 0){
 188 //                              if(gapLength > longGap){        longGap = gapLength;    }
 189 //                      }
 190 //                      gapLength = 0;
 191 //              }
 192 //      }
 193 //      return longGap;
 194 //}
 195
 196 /**************************************************************************************************/