+++ /dev/null
-/**
- * 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
-
git://source.jalview.org / jabaws.git / blobdiff