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71 lines
1.8 KiB
C++
71 lines
1.8 KiB
C++
/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
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***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
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trimAl v1.4: a tool for automated alignment trimming in large-scale
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phylogenetics analyses.
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2009-2015 Capella-Gutierrez S. and Gabaldon, T.
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[scapella, tgabaldon]@crg.es
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This file is part of trimAl.
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trimAl is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, the last available version.
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trimAl is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with trimAl. If not, see <http://www.gnu.org/licenses/>.
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***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
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***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
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#ifndef SIMILARITYMATRIX_H
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#define SIMILARITYMATRIX_H
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#include <math.h>
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#include <ctype.h>
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#include <stdlib.h>
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#include <string>
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#include <iostream>
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#include <iomanip>
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#include <fstream>
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#include "defines.h"
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class similarityMatrix{
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int *vhash;
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float **simMat;
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float **distMat;
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int numPositions;
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private:
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void memoryAllocation(int);
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void memoryDeletion();
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public:
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similarityMatrix();
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~similarityMatrix();
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bool loadSimMatrix(char *);
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void defaultAASimMatrix();
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void defaultNTSimMatrix();
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void defaultNTDegeneratedSimMatrix();
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void alternativeSimilarityMatrices(int, int);
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float getDistance(char, char);
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void printMatrix();
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};
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#endif
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