// $Id: support_statistics.java,v 1.12 2009/11/20 22:22:09 cmzmasek Exp $
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// 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: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.application;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.CommandLineArguments;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
public final class support_statistics {
final static private int PLACES = 2;
final static private String HELP_OPTION = "help";
final static private String OUTPUTFILE_OPTION = "o";
final static private String PRG_NAME = "support_statistics";
final static private String PRG_VERSION = "1.0";
final static private String PRG_DATE = "2008.08.29";
private static StringBuffer analyze( final File[] phylogenies_infiles, final Phylogeny[] phylogenies ) {
final DescriptiveStatistics[] dss = new DescriptiveStatistics[ phylogenies.length ];
for( int i = 0; i < phylogenies.length; i++ ) {
dss[ i ] = new BasicDescriptiveStatistics();
final Phylogeny p = phylogenies[ i ];
for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
if ( !node.isRoot() && !node.isExternal() ) {
double s = PhylogenyMethods.getConfidenceValue( node );
if ( s < 0.0 ) {
s = 0.0;
}
dss[ i ].addValue( s );
}
}
}
DescriptiveStatistics dss_comp = null;
if ( dss.length > 2 ) {
dss_comp = new BasicDescriptiveStatistics();
for( final DescriptiveStatistics element : dss ) {
dss_comp.addValue( element.arithmeticMean() );
}
}
int max_length = 30;
for( int i = 0; i < phylogenies.length; i++ ) {
final int l = phylogenies_infiles[ i ].getName().length();
if ( l > max_length ) {
max_length = l;
}
}
final StringBuffer sb = new StringBuffer();
sb.append( "\t" + ForesterUtil.normalizeString( "name:", max_length, true, ' ' ) + "\t" );
sb.append( "median:" + "\t" );
sb.append( "mean:" + "\t" );
sb.append( "sd:" + "\t" );
sb.append( "min:" + "\t" );
sb.append( "max:" + "\t" );
sb.append( "n:" + "\t" );
if ( dss_comp != null ) {
sb.append( "\"z-score\":" );
}
sb.append( ForesterUtil.getLineSeparator() );
for( int i = 0; i < phylogenies.length; i++ ) {
sb.append( i + 1 + ":\t"
+ ForesterUtil.normalizeString( phylogenies_infiles[ i ].getName(), max_length, true, ' ' ) + "\t" );
sb.append( ForesterUtil.round( dss[ i ].median(), support_statistics.PLACES ) + "\t" );
sb.append( ForesterUtil.round( dss[ i ].arithmeticMean(), support_statistics.PLACES ) + "\t" );
try {
sb.append( ForesterUtil.round( dss[ i ].sampleStandardDeviation(), support_statistics.PLACES ) + "\t" );
}
catch ( final ArithmeticException ex ) {
sb.append( "n/a\t" );
}
sb.append( ForesterUtil.round( dss[ i ].getMin(), support_statistics.PLACES ) + "\t" );
sb.append( ForesterUtil.round( dss[ i ].getMax(), support_statistics.PLACES ) + "\t" );
sb.append( dss[ i ].getN() + "\t" );
if ( dss_comp != null ) {
final double z_score = dss_comp.sampleStandardUnit( dss[ i ].arithmeticMean() );
sb.append( ForesterUtil.round( z_score, support_statistics.PLACES ) + "\t" );
}
sb.append( ForesterUtil.getLineSeparator() );
}
if ( dss_comp != null ) {
sb.append( ForesterUtil.getLineSeparator() );
sb.append( "\t" + ForesterUtil.normalizeString( "values for support means:", max_length, true, ' ' )
+ "\t\t" );
sb.append( ForesterUtil.round( dss_comp.arithmeticMean(), support_statistics.PLACES ) + "\t" );
sb.append( ForesterUtil.round( dss_comp.sampleStandardDeviation(), support_statistics.PLACES ) + "\t" );
sb.append( ForesterUtil.round( dss_comp.getMin(), support_statistics.PLACES ) + "\t" );
sb.append( ForesterUtil.round( dss_comp.getMax(), support_statistics.PLACES ) + "\t" );
}
return sb;
}
public static void main( final String args[] ) {
ForesterUtil.printProgramInformation( support_statistics.PRG_NAME,
support_statistics.PRG_VERSION,
support_statistics.PRG_DATE );
if ( ( args.length < 1 ) ) {
System.out.println();
System.out.println( "wrong number of arguments" );
System.out.println();
support_statistics.printHelp();
System.exit( -1 );
}
CommandLineArguments cla = null;
try {
cla = new CommandLineArguments( args );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
}
if ( cla.isOptionSet( support_statistics.HELP_OPTION ) ) {
System.out.println();
support_statistics.printHelp();
System.exit( 0 );
}
final List<String> allowed_options = new ArrayList<String>();
allowed_options.add( support_statistics.OUTPUTFILE_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( support_statistics.PRG_NAME, "unknown option(s): " + dissallowed_options );
}
final File[] phylogenies_infiles = new File[ cla.getNumberOfNames() ];
for( int i = 0; i < phylogenies_infiles.length; ++i ) {
phylogenies_infiles[ i ] = cla.getFile( i );
}
File outfile = null;
if ( cla.isOptionSet( support_statistics.OUTPUTFILE_OPTION ) ) {
try {
outfile = new File( cla.getOptionValue( support_statistics.OUTPUTFILE_OPTION ) );
}
catch ( final IllegalArgumentException e ) {
ForesterUtil.fatalError( support_statistics.PRG_NAME, "error in command line: " + e.getMessage() );
}
final String error = ForesterUtil.isWritableFile( outfile );
if ( error != null ) {
ForesterUtil.fatalError( support_statistics.PRG_NAME, error );
}
}
final Phylogeny[] phylogenies = new Phylogeny[ phylogenies_infiles.length ];
for( int i = 0; i < phylogenies_infiles.length; i++ ) {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser pp = ForesterUtil
.createParserDependingOnFileType( phylogenies_infiles[ i ], true );
phylogenies[ i ] = factory.create( phylogenies_infiles[ i ], pp )[ 0 ];
}
catch ( final IOException e ) {
ForesterUtil.fatalError( support_statistics.PRG_NAME, "could not read \"" + phylogenies_infiles[ i ]
+ "\": " + e.getMessage() );
}
}
final StringBuffer sb = support_statistics.analyze( phylogenies_infiles, phylogenies );
System.out.println();
System.out.println( sb );
System.out.println();
if ( outfile != null ) {
try {
final PrintWriter out = new PrintWriter( outfile );
out.println( sb );
out.flush();
out.close();
System.out.println( "wrote file: " + outfile );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( support_statistics.PRG_NAME, "failed to write output: " + e.getMessage() );
}
}
System.out.println( support_statistics.PRG_NAME + ": successfully completed" );
System.out.println();
}
private static void printHelp() {
System.out.println( "usage:" );
System.out.println();
System.out.println( support_statistics.PRG_NAME + " [-o=<outfile>] <phylogeny infile 1> "
+ "<phylogeny infile 2> <phylogeny infile 3> ..." );
System.out.println();
System.out.println( " options: " );
System.out.println();
System.out.println( " -o=<outfile> : write output to file" );
System.out.println();
}
}