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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
archaeopteryx
/
Archaeopteryx.java
diff --git
a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
index
46ac48c
..
c23dcca
100644
(file)
--- a/
forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
+++ b/
forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
@@
-21,7
+21,7
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
package org.forester.archaeopteryx;
@@
-36,12
+36,6
@@
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.util.ForesterUtil;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.util.ForesterUtil;
-//
-// java -javaagent:shiftone-jrat.jar -cp
-// $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/java/forester.jar:.
-// org.forester.archaeopteryx.Archaeopteryx
-// -c $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/_aptx_configuration_file
-//
public final class Archaeopteryx {
public static MainFrame createApplication( final Phylogeny phylogeny ) {
public final class Archaeopteryx {
public static MainFrame createApplication( final Phylogeny phylogeny ) {
@@
-94,11
+88,7
@@
public final class Archaeopteryx {
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
nhx.setIgnoreQuotes( false );
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
nhx.setIgnoreQuotes( false );
- PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
- if ( conf.isExtractPfamTaxonomyCodesInNhParsing() ) {
- te = PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
- }
- nhx.setTaxonomyExtraction( te );
+ nhx.setTaxonomyExtraction( conf.getTaxonomyExtraction() );
}
else if ( p instanceof NexusPhylogeniesParser ) {
nhx_or_nexus = true;
}
else if ( p instanceof NexusPhylogeniesParser ) {
nhx_or_nexus = true;
@@
-125,14
+115,21
@@
public final class Archaeopteryx {
if ( f != null ) {
title = f.getName();
}
if ( f != null ) {
title = f.getName();
}
+ File current_dir = null;
+ if ( ( phylogenies != null ) && ( phylogenies.length > 0 ) ) {
+ current_dir = new File( "." );
+ }
try {
try {
- MainFrameApplication.createInstance( phylogenies, conf, title );
+ MainFrameApplication.createInstance( phylogenies, conf, title, current_dir );
+ }
+ catch ( final OutOfMemoryError e ) {
+ AptxUtil.outOfMemoryError( e );
}
}
- catch ( final Exception ex ) {
- AptxUtil.unexpectedException( ex );
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
}
}
- catch ( final Error err ) {
- AptxUtil.unexpectedError( err );
+ catch ( final Error e ) {
+ AptxUtil.unexpectedError( e );
}
}
}
\ No newline at end of file
}
}
}
\ No newline at end of file