Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b6f8929..e519f00 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -236,6 +236,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             alignPanel);
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
+    viewport.initInformationWorker(alignPanel);
 
     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
     followMouseOverFlag.setState(viewport.isFollowHighlight());
@@ -882,7 +883,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == autoCalculate)
     {
-      viewport.autoCalculateConsensus = autoCalculate.getState();
+      viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
     }
     else if (source == sortByTree)
     {
@@ -1324,6 +1325,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       sortGroupMenuItem_actionPerformed();
     }
+    else if (source == sortEValueMenuItem)
+    {
+      sortEValueMenuItem_actionPerformed();
+    }
+    else if (source == sortBitScoreMenuItem)
+    {
+      sortBitScoreMenuItem_actionPerformed();
+    }
     else if (source == removeRedundancyMenuItem)
     {
       removeRedundancyMenuItem_actionPerformed();
@@ -1701,8 +1710,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                                           // viewport.getColumnSelection().getHiddenColumns()
                                           // != null;
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.getAlignment().getSequences());
+    originalSource.notifyAlignment();
   }
 
   /**
@@ -1734,8 +1742,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                                           // != null;
 
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.getAlignment().getSequences());
+    originalSource.notifyAlignment();
   }
 
   AlignmentViewport getOriginatingSource(CommandI command)
@@ -2084,8 +2091,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
                                                                              // 2019.04.18
     viewport.getAlignment().getWidth();
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2159,8 +2165,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.setSelectionGroup(null);
     viewport.getAlignment().deleteGroup(sg);
 
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -2372,7 +2377,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         }
       }
 
-      viewport.firePropertyChange("alignment", null, al.getSequences());
+      viewport.notifyAlignment();
     }
   }
 
@@ -2416,7 +2421,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
     ranges.setStartRes(seq.findIndex(startRes) - 1);
-    viewport.firePropertyChange("alignment", null, al.getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2450,7 +2455,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     ranges.setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null, al.getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2774,6 +2779,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   }
 
+  public void sortEValueMenuItem_actionPerformed()
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByEValue(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
+  public void sortBitScoreMenuItem_actionPerformed()
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByBitScore(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
   public void removeRedundancyMenuItem_actionPerformed()
   {
     new RedundancyPanel(alignPanel);
@@ -3124,6 +3149,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem sortGroupMenuItem = new MenuItem();
 
+  MenuItem sortEValueMenuItem = new MenuItem();
+
+  MenuItem sortBitScoreMenuItem = new MenuItem();
+
   MenuItem removeRedundancyMenuItem = new MenuItem();
 
   MenuItem pairwiseAlignmentMenuItem = new MenuItem();