final URLConnection url_connection = url.openConnection();

[jalview.git] / forester / java / src / org / forester / archaeopteryx / AptxUtil.java

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index d26127a..1a6b0a5 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -35,10 +35,12 @@ import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.InputStream;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.net.URI;
 import java.net.URL;
+import java.net.URLConnection;
 import java.text.ParseException;
 import java.util.Arrays;
 import java.util.HashSet;
@@ -48,8 +50,6 @@ import java.util.Locale;
 import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import javax.imageio.IIOImage;
 import javax.imageio.ImageIO;
@@ -71,7 +71,6 @@ import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Accession;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
@@ -84,10 +83,6 @@ public final class AptxUtil {
 
     private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
                                                                          .getAvailableFontFamilyNames();
-    private final static Pattern  seq_identifier_pattern_1       = Pattern
-                                                                         .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
-    private final static Pattern  seq_identifier_pattern_2       = Pattern
-                                                                         .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" );
     static {
         Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
     }
@@ -191,28 +186,6 @@ public final class AptxUtil {
         return tax_set;
     }
 
-    public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) {
-        final String n = sequence_name.trim();
-        final Matcher matcher1 = seq_identifier_pattern_1.matcher( n );
-        String group1 = "";
-        String group2 = "";
-        if ( matcher1.matches() ) {
-            group1 = matcher1.group( 1 );
-            group2 = matcher1.group( 2 );
-        }
-        else {
-            final Matcher matcher2 = seq_identifier_pattern_2.matcher( n );
-            if ( matcher2.matches() ) {
-                group1 = matcher2.group( 1 );
-                group2 = matcher2.group( 2 );
-            }
-        }
-        if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) {
-            return null;
-        }
-        return new Accession( group2, group1 );
-    }
-
     public final static void printWarningMessage( final String name, final String message ) {
         System.out.println( "[" + name + "] > " + message );
     }
@@ -678,13 +651,13 @@ public final class AptxUtil {
         System.out.println( "[" + applet_name + "] > " + message );
     }
 
-    final static Phylogeny[] readPhylogeniesFromUrl( final URL url,
-                                                     final boolean phyloxml_validate_against_xsd,
-                                                     final boolean replace_underscores,
-                                                     final boolean internal_numbers_are_confidences,
-                                                     final TAXONOMY_EXTRACTION taxonomy_extraction,
-                                                     final boolean midpoint_reroot ) throws FileNotFoundException,
-            IOException {
+    final public static Phylogeny[] readPhylogeniesFromUrl( final URL url,
+                                                            final boolean phyloxml_validate_against_xsd,
+                                                            final boolean replace_underscores,
+                                                            final boolean internal_numbers_are_confidences,
+                                                            final TAXONOMY_EXTRACTION taxonomy_extraction,
+                                                            final boolean midpoint_reroot )
+            throws FileNotFoundException, IOException {
         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
         final PhylogenyParser parser;
         boolean nhx_or_nexus = false;
@@ -707,16 +680,23 @@ public final class AptxUtil {
                 nex.setIgnoreQuotes( false );
             }
         }
-        final Phylogeny[] phys = factory.create( url.openStream(), parser );
-        if ( nhx_or_nexus && internal_numbers_are_confidences ) {
-            for( final Phylogeny phy : phys ) {
-                PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
+        AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
+        final URLConnection url_connection = url.openConnection();
+        url_connection.setDefaultUseCaches( false );
+        final InputStream i = url_connection.getInputStream();
+        final Phylogeny[] phys = factory.create( i, parser );
+        i.close();
+        if ( phys != null ) {
+            if ( nhx_or_nexus && internal_numbers_are_confidences ) {
+                for( final Phylogeny phy : phys ) {
+                    PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
+                }
             }
-        }
-        if ( midpoint_reroot ) {
-            for( final Phylogeny phy : phys ) {
-                PhylogenyMethods.midpointRoot( phy );
-                PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+            if ( midpoint_reroot ) {
+                for( final Phylogeny phy : phys ) {
+                    PhylogenyMethods.midpointRoot( phy );
+                    PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+                }
             }
         }
         return phys;
@@ -728,6 +708,12 @@ public final class AptxUtil {
         }
     }
 
+    final static void removeVisualStyles( final Phylogeny phy ) {
+        for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+            it.next().getNodeData().setNodeVisualData( null );
+        }
+    }
+
     final static void unexpectedError( final Error e ) {
         System.err.println();
         e.printStackTrace( System.err );