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118 lines
3.2 KiB
C++
118 lines
3.2 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 STATISTICSFILES_H
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#define STATISTICSFILES_H
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#include <iostream>
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#include <iomanip>
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#include "utils.h"
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using namespace std;
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/** \brief Class containing a sequences matrix
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*
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* This class stores the alignment sequences matrix. It provides
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* methods to \b build the sequences matrix and print the matrix.
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* It also provides methods for look to a column in the matrix and
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* for look to value at the position (row, column) in the matrix.
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*/
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class sequencesMatrix {
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int resNumber;
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int seqsNumber;
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/* Sequences Matrix */
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int **matrix;
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/* Sequences Name */
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string *seqsName;
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public:
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/* Constructors */
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/** \brief Null constructor.
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*
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* This construction method initializates all attributes
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* of the new object with 0 or NULL value.
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*/
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sequencesMatrix(void);
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/* Copy constructor */
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sequencesMatrix(string *, string *, int, int);
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sequencesMatrix &operator=(const sequencesMatrix &);
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/* Destructor */
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/** \brief Destructor.
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*
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* Destruction method that frees, if exists, previously allocated memory.
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*/
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~sequencesMatrix();
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/* Basics Operations. */
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/** \brief Sequences Matrix printing method.
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*
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* Method that prints the alignment sequences matrix.
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*/
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void printMatrix();
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/** \brief Column for looking to method.
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* \param column Column number at sequences matrix.
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* \param numResidueseqMatrix Vector where storage a column's sequences matrix.
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*
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* Method that storages a column's sequences matrix in a vector.
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*/
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void getColumn(int, int *);
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/** \brief Column for looking to method.
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* \param value to look in a row's sequences matrix.
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* \param row where to look for a value.
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* \param numResidueseqMatrix Vector where storage a column's sequences matrix.
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*
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* Method that looks to value in a row and storages a column's, corresponding to row,
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* sequences matrix in a vector.
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*/
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void getColumn(int, int, int *);
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void setOrder(int *);
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void removeColumns(int, int, int *, int *);
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bool getSequence(string, int *);
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int getSeqNumber(void);
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int getResidNumber(void);
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};
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#endif
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