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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/**
* This is the interface class to all the substitution matrices.
* It provides the matrices in a form that the rest of the program can use.
* It is also used to store the user defined matrix. This will be used mainly as an interface
* to the matrices defined in matrices.h.
* The way this class will work is the user can read in matrix series or a single matrix,
* or they can select one of the matrix series (e.g Blosum). This will then be used in the
* alignment stages. There are separate matrices for amino acid pairwise and progressive,
* and for DNA alignments both pairwise and progressive.
* It is possible to have a series of matrices that are user defined for amino acid
* progressive ONLY!!
* A single matrix is choosen for pairwise and for DNA alignments.
* This class does 3 jobs. It reads in matrices from files/arrays, it provides
* matrices in the formats that are used in the alignment stage, it allows users to select
* which matrices they would like to use.
*/
#ifndef SUBMATRIX_H
#define SUBMATRIX_H
#include <vector>
#include <string>
#include "../general/clustalw.h"
#include "../general/userparams.h"
#include "../general/utils.h"
#include "../general/Array2D.h"
namespace clustalw
{
using namespace std;
typedef vector<short> Xref;
typedef vector<short> Matrix;
class SubMatrix
{
public:
/* Functions */
SubMatrix();
~SubMatrix();
bool getUserMatFromFile(char *str, int alignResidueType, int alignType);
bool getAAScoreMatFromFile(char *str);
bool getDNAScoreMatFromFile(char *str);
bool getQTLowScoreMatFromFile(char *fileName, bool dna);
bool getUserMatSeriesFromFile(char *str);
void setCurrentNameAndNum(string _matrixName, int _matrixNum, int alignResidueType,
int alignType);
int getMatrixNumForMenu(int alignResidueType, int alignType);
int getPairwiseMatrix(int matrix[NUMRES][NUMRES], PairScaleValues& scale,
int& matAvg);
int getProfileAlignMatrix(int matrix[NUMRES][NUMRES], double pcid, int minLen,
PrfScaleValues& scaleParam, int& matAvg);
int getAlnScoreMatrix(int matrix[NUMRES][NUMRES]);
// Access functions for the interactive menu.
int getMatrixNum();
int getDNAMatrixNum();
int getPWMatrixNum();
int getPWDNAMatrixNum();
void getQTMatrixForHistogram(int matrix[NUMRES][NUMRES]);
// NOTE Qt
int getQTAAHistMatNum(){return QTAAHistMatNum;};
int getQTDNAHistMatNum(){return QTDNAHistMatNum;};
void setQTAAHistMatNum(int num){QTAAHistMatNum = num;};
void setQTDNAHistMatNum(int num){QTDNAHistMatNum = num;};
void getQTMatrixForLowScoreSeg(int matrix[NUMRES][NUMRES]);
int getQTsegmentDNAMatNum(){return QTsegmentDNAMatNum;}
void setQTsegmentDNAMatNum(int dnaMat){QTsegmentDNAMatNum = dnaMat;}
int getQTsegmentAAMatNum(){return QTsegmentAAMatNum;}
void setQTsegmentAAMatNum(int aaMat){QTsegmentAAMatNum = aaMat;}
void tempInterface(int alignResidueType, int alignType);
void setValuesToDefault();
/* Attributes */
private:
/* Functions */
int getMatrix(Matrix* matPtr, Xref* xref, int matrix[NUMRES][NUMRES],
bool negFlag, int scale, bool minimise = false);
int readMatrixSeries(const char *fileName, Matrix& userMat, Xref& xref);
int readUserMatrix(const char *fileName, Matrix& userMat, Xref& xref);
int getArgs(char *inline1, char *args[], int max);
void setUpCrossReferences();
bool commentline(char* line);
// The functions below are purely for testing purposes.
void printGetMatrixResults(int mat[NUMRES][NUMRES]);
void compareMatrices(int mat1[NUMRES][NUMRES], int mat2[NUMRES][NUMRES]);
void printInFormat(vector<short>& temp, char* name = "tempfile.out");
void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
Matrix* getUserMatAddress(int alignResidueType, int alignType);
Xref* getUserXrefAddress(int alignResidueType, int alignType);
void checkResidueAndAlignType(int alignResidueType, int alignType);
/* Attributes */
bool userSeries;
int matrixNum;
int DNAMatrixNum;
int pwMatrixNum;
int pwDNAMatrixNum;
string* matrixName;
string* DNAMatrixName;
string* pwMatrixName;
string* pwDNAMatrixName;
// Matrix cross references.
Xref defaultDNAXref;
Xref defaultAAXref;
Xref DNAXref; // User defined dna xref
Xref AAXref;
Xref pwAAXref; // pairwise
Xref pwDNAXref;
Xref QTscoreXref;
Xref QTscoreDNAXref;
Xref QTsegmentDNAXref;
Xref QTsegmentAAXref;
vector<Xref> AAXrefseries;
vector<Matrix> userMatSeries;
Matrix userMat;
Matrix pwUserMat;
Matrix userDNAMat;
Matrix pwUserDNAMat;
Matrix QTscoreUserMatrix;
Matrix QTscoreUserDNAMatrix;
Matrix QTsegmentDNAMatrix;
Matrix QTsegmentAAMatrix;
/* These are vectors to store the matrices defined in matrices.h */
const int sizenAAMatrix;
const int sizeDNAMatrix;
Matrix* blosum30mtVec;
Matrix* blosum40mtVec;
Matrix* blosum45mtVec;
Matrix* blosum62mt2Vec;
Matrix* blosum80mtVec;
Matrix* pam20mtVec;
Matrix* pam60mtVec;
Matrix* pam120mtVec;
Matrix* pam350mtVec;
Matrix* idmatVec;
Matrix* gon40mtVec;
Matrix* gon80mtVec;
Matrix* gon120mtVec;
Matrix* gon160mtVec;
Matrix* gon250mtVec;
Matrix* gon350mtVec;
Matrix* clustalvdnamtVec;
Matrix* swgapdnamtVec;
int matrixAvgScore; // NOTE Needed by other classes.
UserMatrixSeries matSeries;
string line2;
int QTDNAHistMatNum;
int QTAAHistMatNum;
int QTsegmentDNAMatNum;
int QTsegmentAAMatNum;
// Temp, to hold current selection
Matrix* mat;
Xref* xref;
Matrix* _matPtr;
Xref* _matXref;
};
}
#endif
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