in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
index b9bdcb8..3593218 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
+++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
@@ -110,7 +110,7 @@ public final class Archaeopteryx {
                     else if ( p instanceof PhyloXmlParser ) {
                         MainFrameApplication.warnIfNotPhyloXmlValidation( conf );
                     }
-                    phylogenies = Util.readPhylogenies( p, f );
+                    phylogenies = ForesterUtil.readPhylogenies( p, f );
                     if ( nhx_or_nexus && conf.isInternalNumberAreConfidenceForNhParsing() ) {
                         for( final Phylogeny phy : phylogenies ) {
                             ForesterUtil.transferInternalNodeNamesToConfidence( phy );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 9d3fab4..b1dda81 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -1630,7 +1630,7 @@ public final class MainFrameApplication extends MainFrame {
                         try {
                             final NHXParser nhx = new NHXParser();
                             setSpecialOptionsForNhxParser( nhx );
-                            phys = Util.readPhylogenies( nhx, file );
+                            phys = ForesterUtil.readPhylogenies( nhx, file );
                             nhx_or_nexus = true;
                         }
                         catch ( final Exception e ) {
@@ -1642,7 +1642,7 @@ public final class MainFrameApplication extends MainFrame {
                         warnIfNotPhyloXmlValidation( getConfiguration() );
                         try {
                             final PhyloXmlParser xml_parser = createPhyloXmlParser();
-                            phys = Util.readPhylogenies( xml_parser, file );
+                            phys = ForesterUtil.readPhylogenies( xml_parser, file );
                         }
                         catch ( final Exception e ) {
                             exception = true;
@@ -1651,7 +1651,7 @@ public final class MainFrameApplication extends MainFrame {
                     }
                     else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
                         try {
-                            phys = Util.readPhylogenies( new TolParser(), file );
+                            phys = ForesterUtil.readPhylogenies( new TolParser(), file );
                         }
                         catch ( final Exception e ) {
                             exception = true;
@@ -1662,7 +1662,7 @@ public final class MainFrameApplication extends MainFrame {
                         try {
                             final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
                             setSpecialOptionsForNexParser( nex );
-                            phys = Util.readPhylogenies( nex, file );
+                            phys = ForesterUtil.readPhylogenies( nex, file );
                             nhx_or_nexus = true;
                         }
                         catch ( final Exception e ) {
@@ -1689,7 +1689,7 @@ public final class MainFrameApplication extends MainFrame {
                             else if ( parser instanceof PhyloXmlParser ) {
                                 warnIfNotPhyloXmlValidation( getConfiguration() );
                             }
-                            phys = Util.readPhylogenies( parser, file );
+                            phys = ForesterUtil.readPhylogenies( parser, file );
                         }
                         catch ( final Exception e ) {
                             exception = true;
@@ -2044,7 +2044,7 @@ public final class MainFrameApplication extends MainFrame {
         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
             if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
                 try {
-                    final Phylogeny[] trees = Util.readPhylogenies( new PhyloXmlParser(), file );
+                    final Phylogeny[] trees = ForesterUtil.readPhylogenies( new PhyloXmlParser(), file );
                     t = trees[ 0 ];
                 }
                 catch ( final Exception e ) {
@@ -2054,7 +2054,7 @@ public final class MainFrameApplication extends MainFrame {
             }
             else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
                 try {
-                    final Phylogeny[] trees = Util.readPhylogenies( new TolParser(), file );
+                    final Phylogeny[] trees = ForesterUtil.readPhylogenies( new TolParser(), file );
                     t = trees[ 0 ];
                 }
                 catch ( final Exception e ) {
@@ -2065,7 +2065,7 @@ public final class MainFrameApplication extends MainFrame {
             // "*.*":
             else {
                 try {
-                    final Phylogeny[] trees = Util.readPhylogenies( new PhyloXmlParser(), file );
+                    final Phylogeny[] trees = ForesterUtil.readPhylogenies( new PhyloXmlParser(), file );
                     t = trees[ 0 ];
                 }
                 catch ( final Exception e ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/Util.java b/forester/java/src/org/forester/archaeopteryx/Util.java
index 408a3d7..198dc1a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Util.java
+++ b/forester/java/src/org/forester/archaeopteryx/Util.java
@@ -57,7 +57,6 @@ import javax.swing.text.MaskFormatter;
 
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.tol.TolParser;
-import org.forester.io.parsers.util.PhylogenyParserException;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
@@ -618,15 +617,6 @@ public final class Util {
         System.out.println( "[" + name + "] > " + message );
     }
 
-    final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {
-        final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-        final Phylogeny[] trees = factory.create( file, parser );
-        if ( ( trees == null ) || ( trees.length == 0 ) ) {
-            throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
-        }
-        return trees;
-    }
-
     final static Phylogeny[] readPhylogeniesFromUrl( final URL url, final boolean phyloxml_validate_against_xsd )
             throws FileNotFoundException, IOException {
         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();

diff --git a/forester/java/src/org/forester/surfacing/SurfacingConstants.java b/forester/java/src/org/forester/surfacing/SurfacingConstants.java
index ac29712..c78f157 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingConstants.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingConstants.java
@@ -40,7 +40,7 @@ public class SurfacingConstants {
     static final boolean       SECONDARY_FEATURES_ARE_SCOP  = true;
     static final String        SECONDARY_FEATURES_SCOP_LINK = "http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=";
     public static final String NONE                         = "[none]";
-    public static final String UNIPROT_LINK                 = "http://beta.uniprot.org/taxonomy/?query=";
+    public static final String UNIPROT_LINK                 = "http://www.uniprot.org/taxonomy/?query=";
     public static final String GO_LINK                      = "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&query=";
     public static final String EOL_LINK                     = "http://www.eol.org/search?q=";
     public static final String TOL_LINK                     = "http://www.googlesyndicatedsearch.com/u/TreeofLife?q=";

diff --git a/forester/java/src/org/forester/test/examples/Example1.java b/forester/java/src/org/forester/test/examples/Example1.java
new file mode 100644 (file)
index 0000000..045ee6b
--- /dev/null
+++ b/forester/java/src/org/forester/test/examples/Example1.java
@@ -0,0 +1,59 @@
+// $Id:
+//
+// forester -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2011 Christian M. Zmasek
+// Copyright (C) 2008-2011 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: www.phylosoft.org/forester
+
+package org.forester.test.examples;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.util.ForesterUtil;
+
+public class Example1 {
+
+    public static void main( final String[] args ) {
+        // Reads in (a) tree(s) from a file.
+        final File treefile = new File( "/home/czmasek/tol_117_TEST.xml" );
+        PhylogenyParser parser = null;
+        try {
+            parser = ForesterUtil.createParserDependingOnFileType( treefile, true );
+        }
+        catch ( final IOException e ) {
+            e.printStackTrace();
+        }
+        Phylogeny[] phys = null;
+        try {
+            phys = ForesterUtil.readPhylogenies( parser, treefile );
+        }
+        catch ( final IOException e ) {
+            e.printStackTrace();
+        }
+        // Display of the tree(s) with Archaeopteryx.
+        Archaeopteryx.createApplication( phys );
+    }
+}

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 9aba8cc..11eb2e4 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -66,6 +66,7 @@ import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.io.parsers.tol.TolParser;
+import org.forester.io.parsers.util.PhylogenyParserException;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
@@ -74,6 +75,8 @@ import org.forester.phylogeny.data.Distribution;
 import org.forester.phylogeny.data.Identifier;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.Taxonomy;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 
 public final class ForesterUtil {
@@ -105,6 +108,15 @@ public final class ForesterUtil {
     private ForesterUtil() {
     }
 
+    public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {
+        final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+        final Phylogeny[] trees = factory.create( file, parser );
+        if ( ( trees == null ) || ( trees.length == 0 ) ) {
+            throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+        }
+        return trees;
+    }
+
     final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) {
         if ( sb.length() > 0 ) {
             sb.append( separator );