+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2012 Christian M. Zmasek
+// Copyright (C) 2012 Sanford Burnham Medical Research Institute
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
package org.forester.application;
import java.io.File;
import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
import org.forester.io.parsers.GeneralMsaParser;
import org.forester.msa.Msa;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.CommandLineArguments;
import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterUtil;
public class msa_quality {
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String FROM_OPTION = "f";
+ final static private String TO_OPTION = "t";
+ final static private String STEP_OPTION = "s";
+ final static private String WINDOW_OPTION = "w";
+ final static private String PRG_NAME = "msa_quality";
+ final static private String PRG_VERSION = "1.00";
+ final static private String PRG_DATE = "2012.05.18";
+ final static private String E_MAIL = "phylosoft@gmail.com";
+ final static private String WWW = "www.phylosoft.org/forester/";
+
public static void main( final String args[] ) {
- CommandLineArguments cla = null;
try {
- cla = new CommandLineArguments( args );
+ final CommandLineArguments cla = new CommandLineArguments( args );
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length != 3 ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ final File in = cla.getFile( 0 );
+ int from = 0;
+ int to = 0;
+ int window = 0;
+ int step = 0;
+ if ( cla.isOptionSet( FROM_OPTION ) && cla.isOptionSet( TO_OPTION ) ) {
+ from = cla.getOptionValueAsInt( FROM_OPTION );
+ to = cla.getOptionValueAsInt( TO_OPTION );
+ }
+ else if ( cla.isOptionSet( STEP_OPTION ) && cla.isOptionSet( WINDOW_OPTION ) ) {
+ step = cla.getOptionValueAsInt( STEP_OPTION );
+ window = cla.getOptionValueAsInt( WINDOW_OPTION );
+ }
+ else {
+ printHelp();
+ System.exit( 0 );
+ }
+ Msa msa = null;
+ msa = GeneralMsaParser.parse( new FileInputStream( in ) );
+ if ( cla.isOptionSet( FROM_OPTION ) ) {
+ singleCalc( in, from, to, msa );
+ }
+ else {
+ windowedCalcs( window, step, msa );
+ }
}
catch ( final Exception e ) {
- // ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
- }
- // if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
- // printHelp();
- // System.exit( 0 );
- // }
- final File in = cla.getFile( 0 );
- Msa msa = null;
- try {
- msa = GeneralMsaParser.parse( new FileInputStream( in ) );
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ }
+
+ private static void printHelp() {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out.println( PRG_NAME + " <options> <msa input file>" );
+ System.out.println();
+ System.out.println( " options: " );
+ System.out.println();
+ System.out.println( " -" + FROM_OPTION + "=<integer>: from (msa column)" );
+ System.out.println( " -" + TO_OPTION + "=<integer>: to (msa column)" );
+ System.out.println( " or" );
+ System.out.println( " -" + WINDOW_OPTION + "=<integer>: window size (msa columns)" );
+ System.out.println( " -" + STEP_OPTION + "=<integer>: step size (msa columns)" );
+ System.out.println();
+ System.out.println();
+ System.out.println();
+ }
+
+ private static void windowedCalcs( int window, int step, final Msa msa ) {
+ if ( window < 1 ) {
+ window = 1;
+ }
+ if ( step < 1 ) {
+ step = 1;
}
- catch ( final FileNotFoundException e ) {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ final double id_ratios[] = new double[ msa.getLength() ];
+ for( int i = 0; i <= msa.getLength() - 1; ++i ) {
+ id_ratios[ i ] = MsaMethods.calculateIdentityRatio( msa, i );
}
- catch ( final IOException e ) {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ String min_pos = "";
+ String max_pos = "";
+ double min = 1;
+ double max = 0;
+ for( int i = 0; i <= msa.getLength() - 1; i += step ) {
+ int to = i + window - 1;
+ if ( to > ( msa.getLength() - 1 ) ) {
+ to = msa.getLength() - 1;
+ }
+ final DescriptiveStatistics stats = calc( i, to, id_ratios );
+ final double mean = stats.arithmeticMean();
+ final String pos = i + "-" + to;
+ System.out.print( pos );
+ System.out.print( ":\t" );
+ System.out.print( mean );
+ if ( stats.getN() > 2 ) {
+ System.out.print( "\t" );
+ System.out.print( stats.median() );
+ System.out.print( "\t" );
+ System.out.print( stats.sampleStandardDeviation() );
+ }
+ System.out.println();
+ if ( mean > max ) {
+ max = mean;
+ max_pos = pos;
+ }
+ if ( mean < min ) {
+ min = mean;
+ min_pos = pos;
+ }
}
- final int end = 2;
- final int start = 6;
+ System.out.println( "Min: " + min_pos + ": " + min );
+ System.out.println( "Max: " + max_pos + ": " + max );
+ }
+
+ private static void singleCalc( final File in, int from, int to, final Msa msa ) {
+ if ( from < 0 ) {
+ from = 0;
+ }
+ if ( to > ( msa.getLength() - 1 ) ) {
+ to = msa.getLength() - 1;
+ }
+ final DescriptiveStatistics stats = calc( from, to, msa );
+ System.out.println( in.toString() + ": " + from + "-" + to + ":" );
+ System.out.println();
+ System.out.println( stats.toString() );
+ }
+
+ private static DescriptiveStatistics calc( final int from, final int to, final Msa msa ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( int c = start; c <= end; ++c ) {
+ for( int c = from; c <= to; ++c ) {
stats.addValue( MsaMethods.calculateIdentityRatio( msa, c ) );
}
+ return stats;
+ }
+
+ private static DescriptiveStatistics calc( final int from, final int to, final double id_ratios[] ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( int c = from; c <= to; ++c ) {
+ stats.addValue( id_ratios[ c ] );
+ }
+ return stats;
}
}
git://source.jalview.org / jalview.git / blobdiff