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113 lines
3.6 KiB
C++
113 lines
3.6 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 STATISTICS_CONSERVATION_H
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#define STATISTICS_CONSERVATION_H
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#include <math.h>
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#include <iostream>
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#include <iomanip>
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#include "similarityMatrix.h"
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#include "statisticsGaps.h"
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#include "defines.h"
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#include "utils.h"
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using namespace std;
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/* ***************************************************************************************************************** */
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/* Header Class File: StatisticsConservation. */
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/* ***************************************************************************************************************** */
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class statisticsConservation{
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private:
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/* Number of columns and sequences of the alignment */
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int columns;
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int sequences;
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/* Sequence's Datatype: DNA, RNA or Amino Acids. */
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int dataType;
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/* Half window size */
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int halfWindow;
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/* Conservation vectors */
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float *Q;
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float *MDK;
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float *MDK_Window;
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/* Identity weight matrix between alignment rows */
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float **matrixIdentity;
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/* Similarity matrix used to conservation calculations */
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similarityMatrix *simMatrix;
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/* Private methods */
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/* Computes the matrix identity between alignment's columns. */
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void calculateMatrixIdentity(string *alignmentMatrix);
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public:
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/* Constructors without any parameters */
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statisticsConservation(void);
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/* Constructors using parameters */
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statisticsConservation(string *, int, int, int);
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/* Destroyer */
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~statisticsConservation(void);
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/* This methods allows us compute the alignment's conservation's values. */
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bool calculateVectors(string *, int *);
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/* Allows us compute the conservationWindow's values. */
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bool applyWindow(int);
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/* Returns if a windows size value has been defined or not. */
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bool isDefinedWindow(void);
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/* This methods returns a pointer to conservationWindow's vector */
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float *getMdkwVector(void);
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/* Associates a pointer to similarity matrix. This matrix is needed to compute the conservation's values. */
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bool setSimilarityMatrix(similarityMatrix *);
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/* Returns if a similarity matrix is being used or not. */
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bool isSimMatrixDef(void);
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/* Computes and selects the cut point values based on conservation's values. */
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double calcCutPoint(float, float);
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/* Prints the conservation's value for each alignment's column. */
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void printConservationColumns(void);
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/* Computes and prints the accumulative statistics associated to the alignment. */
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void printConservationAcl(void);
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};
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#endif
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