X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxA.java;h=d204f5f12bf7131d1de92c56e5eabc7b0e952bdc;hb=9351f2c2e8af0c3bf1280f9696f1459db2819005;hp=837a24bbf57281739c882e50c448d9c36a66c4a6;hpb=a5c10503459aaada602af51a0169b568ada036b4;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java
index 837a24b..d204f5f 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java
@@ -21,7 +21,7 @@
 // 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;
 
@@ -40,17 +40,18 @@ import org.forester.util.ForesterUtil;
 
 public class ArchaeopteryxA extends JApplet {
 
-    private static final long  serialVersionUID    = 2314899014580484146L;
-    private final static Color background_color    = new Color( 0, 0, 0 );
-    private final static Color font_color          = new Color( 0, 255, 0 );
-    private final static Color ex_background_color = new Color( 0, 0, 0 );
-    private final static Color ex_font_color       = new Color( 255, 0, 0 );
-    private final static Font  font                = new Font( Configuration.getDefaultFontFamilyName(), Font.BOLD, 9 );
+    private static final long  serialVersionUID      = 2314899014580484146L;
+    private final static Color background_color      = new Color( 0, 0, 0 );
+    private final static Color font_color            = new Color( 0, 255, 0 );
+    private final static Color ex_background_color   = new Color( 0, 0, 0 );
+    private final static Color ex_font_color         = new Color( 255, 0, 0 );
+    private final static Font  font                  = new Font( Configuration.getDefaultFontFamilyName(), Font.BOLD, 9 );
     private MainFrameApplet    _mainframe_applet;
-    private String             _url_string         = "";
-    private String             _message_1          = "";
-    private String             _message_2          = "";
-    public final static String NAME                = "ArchaeopteryxA";
+    private String             _tree_url_str         = "";
+    private String             _species_tree_url_str = "";
+    private String             _message_1            = "";
+    private String             _message_2            = "";
+    public final static String NAME                  = "ArchaeopteryxA";
 
     @Override
     public void destroy() {
@@ -59,13 +60,15 @@ public class ArchaeopteryxA extends JApplet {
             getMainFrameApplet().close();
         }
     }
+    
+    
 
     /**
      * This method returns the current external node data which
      * has been selected by the user by clicking the "Return ..."
      * menu item. This method is expected to be called from Javascript or
      * something like it.
-     * 
+     *
      * @return current external node data as String
      */
     public String getCurrentExternalNodesDataBuffer() {
@@ -80,16 +83,34 @@ public class ArchaeopteryxA extends JApplet {
         return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
     }
 
-    public String getUrlString() {
-        return _url_string;
+    public String getSpeciesTreeUrlStr() {
+        return _species_tree_url_str;
+    }
+
+    public String getTreeUrlStr() {
+        return _tree_url_str;
     }
 
     @Override
     public void init() {
         boolean has_exception = false;
         setName( NAME );
-        setUrlString( getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ) );
-        AptxUtil.printAppletMessage( NAME, "URL of phylogenies to load: \"" + getUrlString() + "\"" );
+        setTreeUrlStr( getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ) );
+        setSpeciesTreeUrlStr( getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD ) );
+        if ( !ForesterUtil.isEmpty( getTreeUrlStr() ) ) {
+            AptxUtil.printAppletMessage( NAME, "URL of tree(s) to load: " + getTreeUrlStr() );
+        }
+        else {
+            ForesterUtil.printErrorMessage( NAME, "no URL for tree(s) to load!" );
+            setBackground( ex_background_color );
+            setForeground( ex_font_color );
+            has_exception = true;
+            setMessage1( "no URL for tree(s) to load" );
+            repaint();
+        }
+        if ( !ForesterUtil.isEmpty( getSpeciesTreeUrlStr() ) ) {
+            AptxUtil.printAppletMessage( NAME, "URL of species tree to load: " + getSpeciesTreeUrlStr() );
+        }
         setBackground( background_color );
         setForeground( font_color );
         setFont( font );
@@ -116,15 +137,26 @@ public class ArchaeopteryxA extends JApplet {
                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
             }
             setVisible( false );
-            _mainframe_applet = new MainFrameApplet( this, configuration );
-            URL url = null;
-            url = new URL( getUrlString() );
-            final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( url, configuration
+            _mainframe_applet = new MainFrameApplet( this, configuration, getSpeciesTreeUrlStr() );
+            final URL tree_url = new URL( getTreeUrlStr() );
+            final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( tree_url, configuration
                     .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration
-                    .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction() );
+                    .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction(), configuration
+                    .isMidpointReroot() );
+            if ( phys == null ) {
+                ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are null" );
+            }
+            else if ( phys.length < 1 ) {
+                ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are empty" );
+            }
+            else {
+                AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + tree_url );
+            }
+            AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: "
+                    + tree_url );
             AptxUtil.addPhylogeniesToTabs( phys,
-                                           new File( url.getFile() ).getName(),
-                                           getUrlString(),
+                                           new File( tree_url.getFile() ).getName(),
+                                           getTreeUrlStr(),
                                            getMainFrameApplet().getConfiguration(),
                                            getMainFrameApplet().getMainPanel() );
             getMainFrameApplet().getMainPanel().getControlPanel().showWholeAll();
@@ -159,13 +191,13 @@ public class ArchaeopteryxA extends JApplet {
         if ( default_sequence != null ) {
             getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox()
                     .setSelectedItem( default_sequence );
-            /* GUILHEM_END */
         }
+        /* GUILHEM_END */
     }
 
     /**
      * Prints message when initialization is finished. Called automatically.
-     * 
+     *
      * @param g
      *            Graphics
      */
@@ -207,7 +239,11 @@ public class ArchaeopteryxA extends JApplet {
         _message_2 = message_2;
     }
 
-    private void setUrlString( final String url_string ) {
-        _url_string = url_string;
+    private void setSpeciesTreeUrlStr( final String url_string ) {
+        _species_tree_url_str = url_string;
+    }
+
+    private void setTreeUrlStr( final String url_string ) {
+        _tree_url_str = url_string;
     }
 }