in progress

[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 8bd8df5..7f96bdd 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
+++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
@@ -31,7 +31,9 @@ import org.forester.io.parsers.PhylogenyParser;
 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;
 
 //
@@ -66,7 +68,7 @@ public final class Archaeopteryx {
         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
@@ -77,7 +79,7 @@ public final class Archaeopteryx {
                 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 );
@@ -85,16 +87,16 @@ public final class Archaeopteryx {
                         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 );
                     }
@@ -107,10 +109,10 @@ public final class Archaeopteryx {
                     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 );
                         }
                     }
                 }
@@ -123,14 +125,18 @@ public final class Archaeopteryx {
         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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