in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index ece59e5..71e58a5 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -822,6 +822,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+        customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
+        customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
         _jmenubar.add( _options_jmenu );
     }
 

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 5debb52..5df336a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -93,7 +93,7 @@ public final class Configuration {
             { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
             { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
             { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
-            { "Branch Widths", "display", "no" }, { "Protein Domains", "display", "no" },
+            { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
             { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
             { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
             { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index ef2ebcb..b64958b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -126,7 +126,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
     static final String         RIGHT_LINE_UP_DOMAINS                   = "Right-align Domain Architectures";\r
-    static final String         LINE_UP_RENDERABLE_DATA                 = "Line Up Node Diagrams";\r
+    static final String         LINE_UP_RENDERABLE_DATA                 = "Line Up Diagrams (such as Domain Architectures)";\r
     JMenuBar                    _jmenubar;\r
     JMenu                       _file_jmenu;\r
     JMenu                       _tools_menu;\r

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index 6e6db91..389b626 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -282,6 +282,8 @@ public final class MainFrameApplet extends MainFrame {
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+        customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
+        customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
         _jmenubar.add( _options_jmenu );
     }
 

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index a4c7821..b94b97b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -4778,7 +4778,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             return;
         }
         if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
-                && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+                && ( node.getNodeData().getSequence().getDomainArchitecture() != null )
+                && ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
             RenderableDomainArchitecture rds = null;
             try {
                 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();