// 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
+// 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
// 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
+// 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.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.util.ParserUtils;
-import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.util.CommandLineArguments;
import org.forester.util.ForesterUtil;
-public class cladinator {
+public final class cladinator {
- final static private String PRG_NAME = "cladinator";
- final static private String PRG_VERSION = "0.100";
- final static private String PRG_DATE = "170721";
- final static private String PRG_DESC = "clades within clades";
- 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 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( ".##" );
public static void main( final String args[] ) {
try {
print_help();
System.exit( 0 );
}
- else if ( ( args.length != 2 ) ) {
+ else if ( ( args.length != 2 && args.length != 3 ) ) {
System.out.println();
System.out.println( "Wrong number of arguments." );
System.out.println();
System.exit( -1 );
}
final List<String> allowed_options = new ArrayList<String>();
+ 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 );
+ 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 Exception e ) {
+ catch ( final IOException e ) {
System.out.println( "\nCould not read \"" + intreefile + "\" [" + e.getMessage() + "]\n" );
System.exit( -1 );
}
- execute( p, query );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
- }
- }
-
- private static void execute( final Phylogeny p, final String query ) {
- final PhylogenyNode qnode = p.getNode( query );
- if ( qnode.isRoot() ) {
- throw new IllegalStateException( "Unexpected error: Query " + query
- + " is root. This should have never happened" );
- }
- if ( qnode.getParent().isRoot() ) {
- throw new IllegalStateException( "Unexpected error: Parent of query " + query
- + " is root. This should have never happened" );
- }
- final PhylogenyNode qnode_pp = qnode.getParent().getParent();
- final List<PhylogenyNode> qnode_ext_nodes = qnode_pp.getAllExternalDescendants();
- final int lec_ext_nodes = qnode_ext_nodes.size() - 1;
- final int p_ext_nodes = p.getNumberOfExternalNodes() - 1;
- final double lec_ratio = ( 100.0 * lec_ext_nodes ) / p_ext_nodes;
- final List<String> qnode_ext_nodes_names = new ArrayList<String>();
- for( final PhylogenyNode qnode_ext_node : qnode_ext_nodes ) {
- String name = qnode_ext_node.getName();
- if ( ForesterUtil.isEmptyTrimmed( name ) ) {
- throw new IllegalArgumentException( "external node(s) with empty names found" );
- }
- name = name.trim();
- if ( !name.equals( query ) ) {
- qnode_ext_nodes_names.add( name );
+ 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();
}
- final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( qnode_ext_nodes_names );
- System.out.println( );
- System.out.println( "Results:");
- if ( greatest_common_prefix.length() < 1 ) {
- System.out.println( "WARNING: No greatest common prefix" );
- }
- else {
- System.out.println( "Greatest common prefix: " + greatest_common_prefix );
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
}
- if ( qnode_pp.isRoot() ) {
- System.out.println( "WARNING: Least Encompassing Clade is entire tree" );
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ ForesterUtil.fatalError( PRG_NAME, "Unexpected errror!" );
}
- System.out.println( "Least Encompassing Clade has " + lec_ext_nodes + " external nodes (" +lec_ratio + "% of a total of "+ p_ext_nodes +")" );
}
private final static void print_help() {
- System.out.println( "Usage: " + PRG_NAME
- + " <gene tree file> <query>" );
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out.println( PRG_NAME + " [options] <gene tree file> <query>" );
+ System.out.println();
+ System.out.println( " options:" );
+ System.out.println( " -" + SEP_OPTION + "=<separator>: 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();
}
}
git://source.jalview.org / jalview.git / blobdiff