From: cmzmasek Date: Sun, 3 Sep 2017 02:14:56 +0000 (-0700) Subject: old version... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=33f9886c3683a4e63aec04be8f33fdd74e2410b4;p=jalview.git old version... --- diff --git a/forester/java/src/org/forester/application/cladinatorOLD.java b/forester/java/src/org/forester/application/cladinatorOLD.java new file mode 100644 index 0000000..23fe98a --- /dev/null +++ b/forester/java/src/org/forester/application/cladinatorOLD.java @@ -0,0 +1,181 @@ +// $Id: +// FORESTER -- software libraries and applications +// for evolutionary biology research and applications. +// +// Copyright (C) 2017 Christian M. Zmasek +// Copyright (C) 2017 J. Craig Venter 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: phyloxml @ gmail . com +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester + +package org.forester.application; + +import java.io.File; +import java.io.IOException; +import java.text.DecimalFormat; +import java.util.ArrayList; +import java.util.List; + +import org.forester.clade_analysis.AnalysisSingle; +import org.forester.clade_analysis.ResultSingle; +import org.forester.io.parsers.PhylogenyParser; +import org.forester.io.parsers.util.ParserUtils; +import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; +import org.forester.phylogeny.factories.PhylogenyFactory; +import org.forester.util.CommandLineArguments; +import org.forester.util.ForesterUtil; + +public final class cladinatorOLD { + + final static private String PRG_NAME = "cladinator"; + final static private String PRG_VERSION = "0.101"; + final static private String PRG_DATE = "170810"; + final static private String PRG_DESC = "clades within clades -- analysis of pplacer type outputs"; + final static private String E_MAIL = "phyloxml@gmail.com"; + final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String SEP_OPTION = "s"; + private final static DecimalFormat df2 = new DecimalFormat( "0.0#" ); + + public static void main( final String args[] ) { + try { + ForesterUtil.printProgramInformation( PRG_NAME, + PRG_DESC, + PRG_VERSION, + PRG_DATE, + E_MAIL, + WWW, + ForesterUtil.getForesterLibraryInformation() ); + CommandLineArguments cla = null; + try { + cla = new CommandLineArguments( args ); + } + catch ( final Exception e ) { + ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); + } + if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) { + System.out.println(); + print_help(); + System.exit( 0 ); + } + else if ( ( args.length != 2 && args.length != 3 ) ) { + System.out.println(); + System.out.println( "Wrong number of arguments." ); + System.out.println(); + print_help(); + System.exit( -1 ); + } + final List allowed_options = new ArrayList(); + allowed_options.add( SEP_OPTION ); + final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); + if ( dissallowed_options.length() > 0 ) { + ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); + } + final String separator; + if ( cla.isOptionSet( SEP_OPTION ) ) { + separator = cla.getOptionValue( SEP_OPTION ); + } + else { + separator = null; + } + final File intreefile = cla.getFile( 0 ); + final String query = cla.getName( 1 ); + System.out.println( "Input tree: " + intreefile ); + System.out.println( "Query : " + query ); + if ( !ForesterUtil.isEmpty( separator ) ) { + System.out.println( "Separator : " + separator ); + } + else { + System.out.println( "Separator : none" ); + } + Phylogeny p = null; + try { + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile, true ); + p = factory.create( intreefile, pp )[ 0 ]; + } + catch ( final IOException e ) { + System.out.println( "\nCould not read \"" + intreefile + "\" [" + e.getMessage() + "]\n" ); + System.exit( -1 ); + } + final ResultSingle res = AnalysisSingle.execute( p, query, separator ); + System.out.println(); + System.out.println( "Result:" ); + System.out.println( "Query : " + query ); + System.out.print( "Greatest Common Prefix : " + res.getGreatestCommonPrefix() ); + if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefix() ) + && !ForesterUtil.isEmpty( res.getGreatestCommonCladeSubtreeConfidence() ) ) { + System.out.println( "\t(" + res.getGreatestCommonCladeSubtreeConfidence() + ")" ); + } + else { + System.out.println(); + } + System.out.print( "Greatest Common Prefix Up : " + res.getGreatestCommonPrefixUp() ); + if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixUp() ) + && !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpSubtreeConfidence() ) ) { + System.out.println( "\t(" + res.getGreatestCommonCladeUpSubtreeConfidence() + ")" ); + } + else { + System.out.println(); + } + System.out.print( "Greatest Common Prefix Down : " + res.getGreatestCommonPrefixDown() ); + if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixDown() ) + && !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownSubtreeConfidence() ) ) { + System.out.println( "\t(" + res.getGreatestCommonCladeDownSubtreeConfidence() + ")" ); + } + else { + System.out.println(); + } + System.out.println( "Least Encompassing Clade size: " + res.getLeastEncompassingCladeSize() + + " external nodes" ); + final double lec_ratio = ( 100.0 * res.getLeastEncompassingCladeSize() ) / res.getTreeSize(); + System.out.println( "Least Encompassing Clade size: " + df2.format( lec_ratio ) + "%" ); + System.out.println( "Total tree size : " + res.getTreeSize() + " external nodes" ); + if ( res.getWarnings().size() > 0 ) { + System.out.println( "Warnings:" ); + for( final String s : res.getWarnings() ) { + System.out.println( s ); + } + } + System.out.println(); + } + catch ( final IllegalArgumentException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); + } + catch ( final Exception e ) { + e.printStackTrace(); + ForesterUtil.fatalError( PRG_NAME, "Unexpected errror!" ); + } + } + + private final static void print_help() { + System.out.println( "Usage:" ); + System.out.println(); + System.out.println( PRG_NAME + " [options] " ); + System.out.println(); + System.out.println( " options:" ); + System.out.println( " -" + SEP_OPTION + "=: the separator to be used" ); + System.out.println(); + System.out.println( "Example:" ); + System.out.println(); + System.out.println( " " + PRG_NAME + " -s=. my_tree.xml A.1.1.1" ); + System.out.println(); + } +}