inprogress

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

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index fc6bb32..0866f1c 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -65,8 +65,8 @@ import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Annotation;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
 import org.forester.sdi.GSDI;
 import org.forester.sdi.GSDIR;
 import org.forester.sdi.SDIException;
@@ -140,7 +140,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _lineage_inference;
     // file menu:
     JMenuItem                   _open_item;
-    JMenuItem                   _open_url_item;
     JMenuItem                   _save_item;
     JMenuItem                   _save_all_item;
     JMenuItem                   _close_item;
@@ -208,6 +207,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;
     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;
     JCheckBoxMenuItem           _replace_underscores_cbmi;
+    JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;
     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;
     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;
     // _  search
@@ -268,10 +268,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 applet = getCurrentTreePanel().obtainApplet();
             }
         }
-        if ( o == _open_url_item ) {
-            readPhylogeniesFromURL();
-        }
-        else if ( o == _exit_item ) {
+        if ( o == _exit_item ) {
             close();
         }
         else if ( o == _gsdi_item ) {
@@ -593,10 +590,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
 
     void buildFileMenu() {
         _file_jmenu = createMenu( "File", getConfiguration() );
-        _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
-        _file_jmenu.addSeparator();
         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
-        customizeJMenuItem( _open_url_item );
         customizeJMenuItem( _exit_item );
         _jmenubar.add( _file_jmenu );
     }
@@ -1146,8 +1140,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
     }
 
-    abstract void readPhylogeniesFromURL();
-
     void readPhylogeniesFromWebservice( final int i ) {
         final UrlTreeReader reader = new UrlTreeReader( this, i );
         new Thread( reader ).start();
@@ -1344,6 +1336,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
                 && _replace_underscores_cbmi.isSelected() );
+        options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
+                && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
                 && _search_whole_words_only_cbmi.isSelected() );
         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )