X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=e5bb03f8a6819c15cde4d5769d5790d4fe3f646e;hb=7359853f540f8d2704930c90e0ea9b6969bde51b;hp=da77e228f61e2fcff8145350046f1929ef2498a9;hpb=b4d39d202d7162aed8a41f2e1c42ac81f91c9341;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index da77e22..e5bb03f 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -125,7 +125,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JMenuItem                   _cycle_node_shape_mi;
     private JMenuItem                   _cycle_node_fill_mi;
     private JMenuItem                   _choose_node_size_mi;
-    private JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
     private JMenu                       _analysis_menu;
@@ -242,15 +241,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         }
         else if ( o == _search_case_senstive_cbmi ) {
             updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
+            getMainPanel().getControlPanel().search0();
+            getMainPanel().getControlPanel().search1();
         }
         else if ( o == _search_whole_words_only_cbmi ) {
             updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
+            getMainPanel().getControlPanel().search0();
+            getMainPanel().getControlPanel().search1();
         }
         else if ( o == _inverse_search_result_cbmi ) {
             updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
+            getMainPanel().getControlPanel().search0();
+            getMainPanel().getControlPanel().search1();
         }
         else if ( o == _show_scale_cbmi ) {
             updateOptions( getOptions() );
@@ -297,9 +299,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         else if ( o == _show_default_node_shapes_external_cbmi ) {
             updateOptions( getOptions() );
         }
-        else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
-            updateOptions( getOptions() );
-        }
         else if ( o == _about_item ) {
             MainFrame.about();
         }
@@ -447,45 +446,65 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         setConfiguration( configuration );
         setOptions( Options.createInstance( configuration ) );
         setupUI();
-        URL phys_url = null;
-        Phylogeny[] phys = null;
         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+        if ( ForesterUtil.isEmpty( tree_url_str ) ) {
+            ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
+                    + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+            JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
+                    + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
+            return;
+        }
         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
         // Get URL to tree file
-        if ( tree_url_str != null ) {
-            try {
-                phys_url = new URL( tree_url_str );
-            }
-            catch ( final Exception e ) {
-                ForesterUtil.printErrorMessage( NAME, "error: " + e );
-                e.printStackTrace();
-                JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
-                        + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
-            }
+        URL phys_url = null;
+        try {
+            phys_url = new URL( tree_url_str );
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.printErrorMessage( NAME, "error: " + e );
+            e.printStackTrace();
+            JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
+                    + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
+        }
+        if ( phys_url == null ) {
+            ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
+                    + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+            JOptionPane.showMessageDialog( this,
+                                           NAME + ": Could not create URL from: \"" + tree_url_str,
+                                           "Failed to create URL",
+                                           JOptionPane.ERROR_MESSAGE );
+            return;
         }
         // Load the tree from URL
-        if ( phys_url != null ) {
-            try {
-                phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
-                                                        getConfiguration().isValidatePhyloXmlAgainstSchema(),
-                                                        getConfiguration().isReplaceUnderscoresInNhParsing(),
-                                                        getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
-                                                        getConfiguration().getTaxonomyExtraction(),
-                                                        getConfiguration().isMidpointReroot() );
-            }
-            catch ( final Exception e ) {
-                ForesterUtil.printErrorMessage( NAME, e.toString() );
-                e.printStackTrace();
-                JOptionPane.showMessageDialog( this,
-                                               NAME + ": Failed to read phylogenies: " + "\nException: " + e,
-                                               "Failed to read phylogenies",
-                                               JOptionPane.ERROR_MESSAGE );
-            }
+        Phylogeny[] phys = null;
+        try {
+            phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
+                                                    getConfiguration().isValidatePhyloXmlAgainstSchema(),
+                                                    getConfiguration().isReplaceUnderscoresInNhParsing(),
+                                                    getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
+                                                    getConfiguration().getTaxonomyExtraction(),
+                                                    getConfiguration().isMidpointReroot() );
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.printErrorMessage( NAME, e.toString() );
+            e.printStackTrace();
+            JOptionPane.showMessageDialog( this,
+                                           NAME + ": Failed to read phylogenies: " + "\nException: " + e,
+                                           "Failed to read phylogenies",
+                                           JOptionPane.ERROR_MESSAGE );
+        }
+        if ( phys == null ) {
+            ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
+            JOptionPane.showMessageDialog( this,
+                                           NAME + ": phylogenies from [" + phys_url + "] are null",
+                                           "Failed to read phylogenies",
+                                           JOptionPane.ERROR_MESSAGE );
+            return;
         }
-        if ( ( phys == null ) || ( phys.length < 1 ) ) {
-            ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
+        else if ( phys.length < 1 ) {
+            ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
             JOptionPane.showMessageDialog( this,
-                                           NAME + ": phylogenies from [" + phys_url + "] are null or empty",
+                                           NAME + ": phylogenies from [" + phys_url + "] are empty",
                                            "Failed to read phylogenies",
                                            JOptionPane.ERROR_MESSAGE );
             return;
@@ -585,8 +604,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         setName( NAME );
         getMainPanel().getControlPanel().showWholeAll();
         getMainPanel().getControlPanel().showWhole();
-        System.gc();
-        AptxUtil.printAppletMessage( NAME, "successfully initialized" );
         /* GUILHEM_BEG */
         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
@@ -602,6 +619,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
         }
         /* GUILHEM_END */
+        System.gc();
+        AptxUtil.printAppletMessage( NAME, "successfully initialized" );
         setVisible( true );
     }
 
@@ -721,8 +740,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _options_jmenu
                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
         _options_jmenu
-                .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
-        _options_jmenu
                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
@@ -762,7 +779,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 .isShowDefaultNodeShapesExternal() );
         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
                 .isShowDefaultNodeShapesInternal() );
-        customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
         customizeJMenuItem( _choose_node_size_mi );
@@ -1302,8 +1318,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 && _show_default_node_shapes_internal_cbmi.isSelected() );
         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
                 && _show_default_node_shapes_external_cbmi.isSelected() );
-        options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
-                && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
         }