patched for JAL-531 - only display full symbol distribution stats on tooltip/annotati...

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 954648e..0aefe9b 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -85,6 +85,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         {
           sortPairwiseMenuItem_actionPerformed();
         }
+        else if (param.equalsIgnoreCase("Length"))
+        {
+          sortLengthMenuItem_actionPerformed();
+        }
       }
 
       param = applet.getParameter("wrap");
@@ -905,6 +909,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       sortIDMenuItem_actionPerformed();
     }
+    else if (source == sortLengthMenuItem)
+    {
+      sortLengthMenuItem_actionPerformed();
+    }
     else if (source == sortGroupMenuItem)
     {
       sortGroupMenuItem_actionPerformed();
@@ -1675,8 +1683,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       for (int g = 0; g < gps.length; g++)
       {
         // gps[g].setShowunconserved(viewport.getShowUnconserved());
-        gps[g].setIncludeAllConsSymbols(viewport
-                .isIncludeAllConsensusSymbols());
+        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
         viewport.alignment.addGroup(gps[g]);
         Color col = new Color((int) (Math.random() * 255), (int) (Math
                 .random() * 255), (int) (Math.random() * 255));
@@ -2268,6 +2275,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.paintAlignment(true);
   }
 
+  public void sortLengthMenuItem_actionPerformed()
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByLength(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.alignment));
+    alignPanel.paintAlignment(true);
+  }
+
   public void sortGroupMenuItem_actionPerformed()
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -2620,6 +2635,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem sortIDMenuItem = new MenuItem();
 
+  MenuItem sortLengthMenuItem = new MenuItem();
+
   MenuItem sortGroupMenuItem = new MenuItem();
 
   MenuItem removeRedundancyMenuItem = new MenuItem();
@@ -2797,6 +2814,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     sortPairwiseMenuItem.addActionListener(this);
     sortIDMenuItem.setLabel("by ID");
     sortIDMenuItem.addActionListener(this);
+    sortLengthMenuItem.setLabel("by Length");
+    sortLengthMenuItem.addActionListener(this);
     sortGroupMenuItem.setLabel("by Group");
     sortGroupMenuItem.addActionListener(this);
     removeRedundancyMenuItem.setLabel("Remove Redundancy...");
@@ -2846,7 +2865,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     annotationPanelMenuItem.addItemListener(this);
     colourTextMenuItem.setLabel("Colour Text");
     colourTextMenuItem.addItemListener(this);
-    displayNonconservedMenuItem.setLabel("Show non-conserved");
+    displayNonconservedMenuItem.setLabel("Show nonconserved");
     displayNonconservedMenuItem.addItemListener(this);
     alProperties.addActionListener(this);
     overviewMenuItem.setLabel("Overview Window");
@@ -3040,6 +3059,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
     sort.add(sortIDMenuItem);
+    sort.add(sortLengthMenuItem);
     sort.add(sortByTreeMenu);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);