QueryManager/MatchAligner.cpp File Reference

#include "MatchAligner.h"
#include "SequenceReader.h"
#include "SequenceEncoder.h"
#include <iomanip>

Include dependency graph for MatchAligner.cpp:

Go to the source code of this file.

Functions
void	makeScoreTableDNA (ScoreTable &table)
void	makeScoreTableBlosum62 (ScoreTable &table)
void	print (vector< ScoreType > &v)
void	print (PathMatrix< PathType > &p)

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Function Documentation

void makeScoreTableBlosum62

(

ScoreTable &

table

)

Definition at line 461 of file MatchAligner.cpp.

References blosumResidues, blosumScores, gapExtendScoreBLOSUM, gapStartScoreBLOSUM, numBlosumResidues, and stopCodonScoreBLOSUM.

{

  uchar a[2];
  unsigned short* b = (unsigned short*) &a[0];

  const ScoreType* pScore = blosumScores;


  for (int i(0); i < numBlosumResidues; i++ )
  {
    for (int j(0); j < i; j++ )
    {
      //      cout << i << " " << j << endl; 

      // a[0] = uc, a[1] = uc
      a[0]=blosumResidues[i]; a[1]=blosumResidues[j]; table[ *b ] = *pScore;
      //      cout << a[0] << a[1] << " " table[ *b ] << endl;
      // a[0] = uc, a[1] = lc
      a[1]=tolower(a[1]); table[ *b ] = *pScore;
      // a[0] = lc, a[1] = lc
      a[0]=tolower(a[0]); table[ *b ] = *pScore;
      // a[0] = lc, a[1] = uc
      a[1]=toupper(a[1]); table[ *b ] = *pScore;

      a[0]=blosumResidues[j]; a[1]=blosumResidues[i]; table[ *b ] = *pScore;
      a[1]=tolower(a[1]); table[ *b ] = *pScore;
      a[0]=tolower(a[0]); table[ *b ] = *pScore;
      a[1]=toupper(a[1]); table[ *b ] = *pScore;
     
      ++pScore;
    } // ~for j

    a[0] = blosumResidues[i];
    a[1] = blosumResidues[i]; table[ *b ] = (*pScore); // a0=uc, a1=uc
    a[1] = tolower(a[1]); table[ *b ] = (*pScore);  // a0=uc, a1=lc
    a[1] = '*'; table[ *b ] = stopCodonScoreBLOSUM; // a0=uc, a1=*
    a[1] = '-'; table[ *b ] = gapStartScoreBLOSUM;  // a0=uc, a1=-

    a[0] = tolower(a[0]); 
    a[1] = blosumResidues[i]; table[ *b ] = (*pScore); // a0=lc, a1=uc
    a[1] = tolower(a[1]); table[ *b ] = (*pScore);  // a0=lc, a1=lc
    a[1] = '*'; table[ *b ] = stopCodonScoreBLOSUM; // a0=lc, a1=*
    a[1] = '-'; table[ *b ] = gapStartScoreBLOSUM;  // a0=lc, a1=-

    a[1] = blosumResidues[i];
    a[0] = '*'; table[ *b ] = stopCodonScoreBLOSUM; // a0=*, a1=uc
    a[0] = '-'; table[ *b ] = gapStartScoreBLOSUM;  // a0=-, a1=uc

    a[1] = tolower(a[1]);
    a[0] = '*'; table[ *b ] = stopCodonScoreBLOSUM; // a0=*, a1=lc
    a[0] = '-'; table[ *b ] = gapStartScoreBLOSUM;  // a0=-, a1=lc

    ++pScore;
  } // ~for i

  a[0] = '*'; a[1] = '*'; table[ *b ] = 1;
  a[0] = '*'; a[1] = '-'; table[ *b ] = gapStartScoreBLOSUM;
  a[0] = '-'; a[1] = '*'; table[ *b ] = gapStartScoreBLOSUM;
  a[0] = '-'; a[1] = '-'; table[ *b ] = gapExtendScoreBLOSUM;

} // ~void makeScoreTableBlosum62( ScoreTable& table )

void makeScoreTableDNA

(

ScoreTable &

table

)

Definition at line 401 of file MatchAligner.cpp.

References gapExtendScoreDNA, gapStartScoreDNA, matchScoreDNA, mismatchScoreDNA, and nScoreDNA.

{

  uchar a[2];
  unsigned short* b = (unsigned short*) &a[0];
  //  a[0]=0; a[1]=0;

  const char base[] = {"agct"};

  ScoreType thisScore;
  for (int i(0); i < 4; i++ )
  {
    for (int j(0); j < 4; j++ )
    {
      thisScore = ((i==j) ? matchScoreDNA: mismatchScoreDNA);
      a[0]=base[i]; a[1] = base[j]; table[ *b ] = thisScore;
      a[1] = toupper(base[j]); table[ *b ] = thisScore;
      a[0]=toupper(base[i]); a[1] = base[j]; table[ *b ] = thisScore;
      a[1] = toupper(base[j]); table[ *b ] = thisScore;
    } // ~for j

    a[0]=base[i];  
    a[1] = 'n'; table[ *b ] = nScoreDNA;
    a[1] = 'N'; table[ *b ] = nScoreDNA;
    a[1] = '-'; table[ *b ] = gapStartScoreDNA;

    a[0]=toupper(base[i]);  
    a[1] = 'n'; table[ *b ] = nScoreDNA;
    a[1] = 'N'; table[ *b ] = nScoreDNA;
    a[1] = '-'; table[ *b ] = gapStartScoreDNA;

    a[1]=base[i];  
    a[0] = 'n'; table[ *b ] = nScoreDNA;
    a[0] = 'N'; table[ *b ] = nScoreDNA;
    a[0] = '-'; table[ *b ] = gapStartScoreDNA;

    a[1]=toupper(base[i]);  
    a[0] = 'n'; table[ *b ] = nScoreDNA;
    a[0] = 'N'; table[ *b ] = nScoreDNA;
    a[0] = '-'; table[ *b ] = gapStartScoreDNA;
    


  } // ~for i;

    a[0]='n'; a[1] = 'n'; table[ *b ] = nScoreDNA;
    a[0]='n'; a[1] = 'N'; table[ *b ] = nScoreDNA;
    a[0]='N'; a[1] = 'n'; table[ *b ] = nScoreDNA;
    a[0]='N'; a[1] = 'N'; table[ *b ] = nScoreDNA;

    a[0]='-'; a[1] = 'n'; table[ *b ] = gapStartScoreDNA;
    a[0]='-'; a[1] = 'N'; table[ *b ] = gapStartScoreDNA;
    a[0]='n'; a[1] = '-'; table[ *b ] = gapStartScoreDNA;
    a[0]='N'; a[1] = '-'; table[ *b ] = gapStartScoreDNA;

    a[0]='-'; a[1] = '-'; table[ *b ] = gapExtendScoreDNA;

} // ~void makeScoreTableDNA( ScoreTable& table )

void print

(

PathMatrix< PathType > &

p

)

Definition at line 984 of file MatchAligner.cpp.

References fromN, fromSW, and fromW.

{
  for (int i(0); i< p.front().size(); i++)
  {
    for (vector<vector<PathType> >::iterator j(p.begin());
         j!=p.end();++j)
    {
      cout << (((*j)[i] & fromW)?'-':'.')
           << (((*j)[i] & fromSW)?'/':'.') 
           << (((*j)[i] & fromN)?'|':'.') 
           << "\t";
    } // ~for j   
    cout << endl;
  } // ~for i

} // ~print

void print

(

vector< ScoreType > &

v

)

Definition at line 976 of file MatchAligner.cpp.

Referenced by main().

{
  for( vector<ScoreType>::iterator i(v.begin());i!=v.end();++i)
    cout << "Score: " << *i << endl;

}

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