#ifndef QRMATRIX_H
#define QRMATRIX_H

#include <stdio.h>
#include <math.h>
#include "aaTools.h"
#include "affinityScore.h"
#include "alignment.h"
#include "matrix.h"

class qrMatrix{
  
 public:
  qrMatrix(Alignment *aln);
  qrMatrix() {};
  ~qrMatrix();
  int qrAlgorithm();
  int printColumns();
 private:
  int householder(int currentColumn);       // Householder transformation
  int permuteColumns(int currentColumn);       // column permutation
  float frobeniusNormSeq(int k, int currentRow);
  float frobeniusNormCoord(int j);
  int scaleGapData();
  
 private:
  /*
    Anytime you access the third index from coordMatrix, go through the
    columnList; So coordMatrix[i][j][k] becomes coordMatrix[i][j][columnList[k]];
    This level of indirection eliminates array copying and saves the sequence
    order.
  */
  float ***coordMatrix;
  int *columnList;         // indices for columns which may be permuted
  int cMi;                 // number of residue columns in coordMatrix (alignment column)
  int cMj;                 // number of coordinates for a coordMatrix residue (x,y,z,gap)
  int cMk;                 // number of sequences in coordMatrix
};

#endif