import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.util.ForesterUtil;
//
try {
int filename_index = 0;
if ( args.length == 0 ) {
- conf = new Configuration( null, false, false );
+ conf = new Configuration( null, false, false, true );
}
else if ( args.length > 0 ) {
// check for a config file
if ( args[ 0 ].startsWith( "-open" ) ) {
filename_index += 1;
}
- conf = new Configuration( config_filename, false, false );
+ conf = new Configuration( config_filename, false, false, true );
if ( args.length > filename_index ) {
f = new File( args[ filename_index ] );
final String err = ForesterUtil.isReadableFile( f );
ForesterUtil.fatalError( Constants.PRG_NAME, err );
}
boolean nhx_or_nexus = false;
- final PhylogenyParser p = ForesterUtil.createParserDependingOnFileType( f, conf
+ final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( f, conf
.isValidatePhyloXmlAgainstSchema() );
if ( p instanceof NHXParser ) {
nhx_or_nexus = true;
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
nhx.setIgnoreQuotes( false );
- ForesterUtil.TAXONOMY_EXTRACTION te = ForesterUtil.TAXONOMY_EXTRACTION.NO;
+ PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
if ( conf.isExtractPfamTaxonomyCodesInNhParsing() ) {
- te = ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
+ te = PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
}
nhx.setTaxonomyExtraction( te );
}
else if ( p instanceof PhyloXmlParser ) {
MainFrameApplication.warnIfNotPhyloXmlValidation( conf );
}
- phylogenies = ForesterUtil.readPhylogenies( p, f );
+ phylogenies = PhylogenyMethods.readPhylogenies( p, f );
if ( nhx_or_nexus && conf.isInternalNumberAreConfidenceForNhParsing() ) {
for( final Phylogeny phy : phylogenies ) {
- ForesterUtil.transferInternalNodeNamesToConfidence( phy );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
}
}
}
if ( f != null ) {
title = f.getName();
}
+ File current_dir = null;
+ if ( ( phylogenies != null ) && ( phylogenies.length > 0 ) ) {
+ current_dir = new File( "." );
+ }
try {
- MainFrameApplication.createInstance( phylogenies, conf, title );
+ MainFrameApplication.createInstance( phylogenies, conf, title, current_dir );
}
catch ( final Exception ex ) {
- Util.unexpectedException( ex );
+ AptxUtil.unexpectedException( ex );
}
catch ( final Error err ) {
- Util.unexpectedError( err );
+ AptxUtil.unexpectedError( err );
}
}
}
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