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.Analysis;
-import org.forester.clade_analysis.Result;
+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;
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_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[] ) {
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();
print_help();
System.exit( -1 );
}
- //final List<String> allowed_options = new ArrayList<>();
+ 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 );
}
- final Result res = Analysis.execute( p, query );
+ final ResultSingle res = AnalysisSingle.execute( p, query, separator );
System.out.println();
System.out.println( "Result:" );
- System.out.println( "Greatest common prefix a : " + res.getGreatestCommonPrefix() );
- System.out.println( "Greatest common prefix a (up) : " + res.getGreatestCommonPrefixUp() );
- System.out.println( "Greatest common prefix b (down): " + res.getGreatestCommonPrefixDown() );
+ 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 has " + res.getLeastEncompassingCladeSize()
- + " external nodes (" + df2.format( lec_ratio ) + "% of a total of " + 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 Exception e ) {
+ 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: " + 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