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88 lines
2.8 KiB
C++
88 lines
2.8 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 STATISTICSGAPS_H
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#define STATISTICSGAPS_H
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#include <iostream>
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#include <iomanip>
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#include "utils.h"
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#include "defines.h"
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using namespace std;
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/* ***************************************************************************************************************** */
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/* Header Class File: StatisticsGaps. */
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/* ***************************************************************************************************************** */
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class statisticsGaps {
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int columns;
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int columnLength;
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int maxGaps;
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int halfWindow;
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int dataType;
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int *gapsInColumn;
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int *numColumnsWithGaps;
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int *aminosXInColumn;
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int *gapsWindow;
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public:
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/* Class constructor without parameters. */
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statisticsGaps(void);
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/* Class destroyer. */
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~statisticsGaps(void);
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/* Class constructor with parameters. */
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statisticsGaps(string *, int, int, int);
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/* Methods allows us compute the gapWindows' values. */
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bool applyWindow(int);
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/* This methods returns a gaps' vector reference. */
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int *getGapsWindow(void);
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/* Allows compute and select the cut point value. */
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double calcCutPoint(float, float);
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/* Automatic method to find a cut point value using the first and the second slopes. */
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int calcCutPointMixSlope(void);
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/* Automatic method to compute a cut point valur using the second slope approach. */
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int calcCutPoint2ndSlope(void);
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/* This methods print the gaps' percentage of each column in the alignment. */
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void printGapsColumns(void);
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/* This methods prints the statistics for the alignment relates to gaps. */
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void printGapsAcl(void);
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};
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#endif
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