JAL-1031 allow empty selections to pass through to tree builder, which will ignore...

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 4948613..bcb518f 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -133,6 +133,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     showGroupConservation.setState(viewport.isShowGroupConservation());\r
     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());\r
     showSequenceLogo.setState(viewport.isShowSequenceLogo());\r
+    normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());\r
 \r
     seqLimits.setState(viewport.showJVSuffix);\r
 \r
@@ -719,6 +720,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {\r
       showSequenceLogo_actionPerformed();\r
     }\r
+    else if (evt.getSource() == normSequenceLogo)\r
+    {\r
+      normSequenceLogo_actionPerformed();\r
+    }\r
     else if (evt.getSource() == showConsensusHistogram)\r
     {\r
       showConsensusHistogram_actionPerformed();\r
@@ -929,6 +934,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {\r
       showSequenceLogo_actionPerformed();\r
     }\r
+    else if (source == normSequenceLogo)\r
+    {\r
+      normSequenceLogo_actionPerformed();\r
+    }\r
     else if (source == showConsensusHistogram)\r
     {\r
       showConsensusHistogram_actionPerformed();\r
@@ -1833,6 +1842,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     viewport.setShowSequenceLogo(showSequenceLogo.getState());\r
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
   }\r
+  protected void normSequenceLogo_actionPerformed()\r
+  {\r
+    showSequenceLogo.setState(true);\r
+    viewport.setShowSequenceLogo(true);\r
+    viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());\r
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+  }\r
 \r
   protected void applyAutoAnnotationSettings_actionPerformed()\r
   {\r
@@ -2506,7 +2522,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 \r
     if ((viewport.getSelectionGroup() != null && viewport\r
             .getSelectionGroup().getSize() > 1)\r
-            || (viewport.getSelectionGroup() == null && viewport.getAlignment()\r
+            || (viewport.getAlignment()\r
                     .getHeight() > 1))\r
     {\r
       final TreePanel tp = new TreePanel(alignPanel, type, pwType);\r
@@ -2878,6 +2894,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();\r
   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();\r
   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();\r
+  CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();\r
 \r
   private void jbInit() throws Exception\r
   {\r
@@ -3093,6 +3110,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     showGroupConservation.setLabel("Group Conservation");\r
     showConsensusHistogram.setLabel("Show Consensus Histogram");\r
     showSequenceLogo.setLabel("Show Consensus Logo");\r
+    normSequenceLogo.setLabel("Normalise Consensus Logo");\r
     applyAutoAnnotationSettings.setLabel("Apply to all groups");\r
     applyAutoAnnotationSettings.setState(true);\r
     autoAnnMenu.setLabel("Autocalculated Annotation");\r
@@ -3109,6 +3127,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     showGroupConservation.addItemListener(this);\r
     showConsensusHistogram.addItemListener(this);\r
     showSequenceLogo.addItemListener(this);\r
+    normSequenceLogo.addItemListener(this);\r
+    \r
     applyAutoAnnotationSettings.addItemListener(this);\r
     formatMenu.setLabel("Format");\r
     selectMenu.setLabel("Select");\r
@@ -3162,6 +3182,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     autoAnnMenu.add(applyAutoAnnotationSettings);\r
     autoAnnMenu.add(showConsensusHistogram);\r
     autoAnnMenu.add(showSequenceLogo);\r
+    autoAnnMenu.add(normSequenceLogo);\r
     autoAnnMenu.addSeparator();\r
     autoAnnMenu.add(showGroupConservation);\r
     autoAnnMenu.add(showGroupConsensus);\r