--- /dev/null
+// $Id:
+// 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: phylosoft @ 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.util.ArrayList;
+import java.util.List;
+
+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 {
+
+ 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";
+
+ 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 ) ) {
+ System.out.println();
+ System.out.println( "Wrong number of arguments." );
+ System.out.println();
+ print_help();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ final File intreefile = cla.getFile( 0 );
+ final String query = cla.getName( 1 );
+ System.out.println( "Input tree: " + intreefile );
+ System.out.println( "Query: " + query );
+ 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 ) {
+ 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 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 );
+ }
+ if ( qnode_pp.isRoot() ) {
+ System.out.println( "WARNING: Least Encompassing Clade is entire tree" );
+ }
+ 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();
+ }
+}
ann.append( n.getName() );
ann.append( separator );
}
+ if ( n.getNodeData().isHasTaxonomy() ) {
+ if ( getControlPanel().isShowTaxonomyCode()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ ann.append( separator );
+ }
+ if ( getControlPanel().isShowTaxonomyScientificNames()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ ann.append( n.getNodeData().getTaxonomy().getScientificName() );
+ ann.append( separator );
+ }
+ if ( getControlPanel().isShowTaxonomyCommonNames()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+ ann.append( n.getNodeData().getTaxonomy().getCommonName() );
+ ann.append( separator );
+ }
+ }
if ( getControlPanel().isShowSeqSymbols()
&& !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
ann.append( n.getNodeData().getSequence().getSymbol() );
ann.append( n.getNodeData().getSequence().getAccession().asText() );
ann.append( separator );
}
- if ( n.getNodeData().isHasTaxonomy() ) {
- if ( getControlPanel().isShowTaxonomyCode()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
- ann.append( separator );
- }
- if ( getControlPanel().isShowTaxonomyScientificNames()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- ann.append( n.getNodeData().getTaxonomy().getScientificName() );
- ann.append( separator );
- }
- if ( getControlPanel().isShowTaxonomyCommonNames()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
- ann.append( n.getNodeData().getTaxonomy().getCommonName() );
- ann.append( separator );
- }
- }
- String ann_str;
+
+ final String ann_str;
if ( ann.length() > 0 && ann.charAt( ann.length() - 1 ) == separator ) {
ann_str = ann.substring( 0, ann.length() - 1 );
}
succeeded++;
}
System.out.println( "OK." );
+
+ System.out.print( "Common prefix: " );
+ if ( !testCommonPrefix() ) {
+ System.out.println( "failed." );
+ failed++;
+ }
+ else {
+ succeeded++;
+ }
+ System.out.println( "OK." );
+
System.out.print( "Sequence writer: " );
if ( testSequenceWriter() ) {
System.out.println( "OK." );
}
}
+
private static boolean testEngulfingOverlapRemoval() {
try {
final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
return true;
}
+
+ private static boolean testCommonPrefix() {
+ final List<String> l0 = new ArrayList<String>();
+ l0.add( "abc" );
+ if ( !ForesterUtil.greatestCommonPrefix( l0 ).equals( "abc" ) ) {
+ return false;
+ }
+
+ final List<String> l1 = new ArrayList<String>();
+ l1.add( "abc" );
+ l1.add( "abX" );
+ if ( !ForesterUtil.greatestCommonPrefix( l1 ).equals( "ab" ) ) {
+ return false;
+ }
+
+ final List<String> l2 = new ArrayList<String>();
+ l2.add( "abc" );
+ l2.add( "abX" );
+ l2.add( "axy" );
+ if ( !ForesterUtil.greatestCommonPrefix( l2 ).equals( "a" ) ) {
+ return false;
+ }
+
+ final List<String> l3 = new ArrayList<String>();
+ l3.add( "abXsdfsdfsdfsdfsdfsd" );
+ l3.add( "abXsdfsdfsdfsdfsdfsd" );
+ l3.add( "abc" );
+ l3.add( "abXsdfsdfsdfsdfsdfsd" );
+ l3.add( "ab" );
+ l3.add( "abc" );
+ l3.add( "ab" );
+ if ( !ForesterUtil.greatestCommonPrefix( l3 ).equals( "ab" ) ) {
+ return false;
+ }
+
+ final List<String> l4 = new ArrayList<String>();
+ l4.add( "abXsdfsdfsdfsdfsdfsd" );
+ l4.add( "abXsdfsdfsdfsdfsdfsd" );
+ l4.add( "abc" );
+ l4.add( "Xsdfsdfsdfsdfsdfsd" );
+ l4.add( "ab" );
+ l4.add( "abc" );
+ if ( !ForesterUtil.greatestCommonPrefix( l4 ).equals( "" ) ) {
+ return false;
+ }
+
+ final List<String> l5 = new ArrayList<String>();
+ l5.add( "" );
+ if ( !ForesterUtil.greatestCommonPrefix( l5 ).equals( "" ) ) {
+ return false;
+ }
+
+ final List<String> l6 = new ArrayList<String>();
+ l6.add( "abc" );
+ l6.add( "abX" );
+ l6.add( "" );
+ if ( !ForesterUtil.greatestCommonPrefix( l6 ).equals( "" ) ) {
+ return false;
+ }
+ return true;
+ }
+
+
private static boolean testUTF8ParsingFromFile() {
try {
final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
final public static boolean isEmpty( final String s ) {
return ( ( s == null ) || ( s.length() < 1 ) );
}
+
+ final public static boolean isEmptyTrimmed( final String s ) {
+ if ( s == null ) {
+ return true;
+ }
+ return ( ( s.trim().length() < 1 ) );
+ }
/**
* Returns true is Domain domain falls in an uninterrupted stretch of
return the_one;
}
+ public final static String greatestCommonPrefix( final String a, final String b ) {
+ final int min_length = Math.min( a.length(), b.length() );
+ for( int i = 0; i < min_length; ++i ) {
+ if ( a.charAt( i ) != b.charAt( i ) ) {
+ return a.substring( 0, i );
+ }
+ }
+ return a.substring( 0, min_length );
+ }
+
+ public final static String greatestCommonPrefix( final List<String> strings ) {
+ if ( strings == null ) {
+ throw new IllegalArgumentException( "list is null" );
+ }
+ if ( strings.isEmpty() ) {
+ throw new IllegalArgumentException( "list is empty" );
+ }
+ String common = strings.get( 0 );
+ for( int i = 1; i < strings.size(); ++i ) {
+ common = greatestCommonPrefix( common, strings.get( i ) );
+ }
+ return common;
+ }
+
private ForesterUtil() {
}
}
git://source.jalview.org / jalview.git / commitdiff