Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0fd0945..63ba101 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());
@@ -576,8 +577,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     case KeyEvent.VK_F2:
       viewport.cursorMode = !viewport.cursorMode;
-      setStatus(MessageManager
-              .formatMessage("label.keyboard_editing_mode", new String[]
+      setStatus(MessageManager.formatMessage("label.keyboard_editing_mode",
+              new String[]
               { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
       {
@@ -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();
@@ -1453,9 +1462,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else
     {
-      features = formatter.printGffFormat(viewport.getAlignment()
-              .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
-              false);
+      features = formatter.printGffFormat(
+              viewport.getAlignment().getSequencesArray(),
+              alignPanel.getFeatureRenderer(), true, false);
     }
 
     if (displayTextbox)
@@ -1584,8 +1593,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     catch (java.net.MalformedURLException ex)
     {
       url = viewport.applet.getCodeBase() + url;
-    }
-    catch (UnsupportedEncodingException ex)
+    } catch (UnsupportedEncodingException ex)
     {
       System.err.println(
               "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
@@ -1701,8 +1709,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                                           // viewport.getColumnSelection().getHiddenColumns()
                                           // != null;
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.getAlignment().getSequences());
+    originalSource.notifyAlignment();
   }
 
   /**
@@ -1734,8 +1741,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                                           // != null;
 
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.getAlignment().getSequences());
+    originalSource.notifyAlignment();
   }
 
   AlignmentViewport getOriginatingSource(CommandI command)
@@ -2084,8 +2090,7 @@ 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 +2164,7 @@ 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)
     {
@@ -2358,8 +2362,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                 column, al);
       }
 
-      setStatus(MessageManager
-              .formatMessage("label.removed_columns", new String[]
+      setStatus(MessageManager.formatMessage("label.removed_columns",
+              new String[]
               { Integer.valueOf(trimRegion.getSize()).toString() }));
       addHistoryItem(trimRegion);
 
@@ -2372,7 +2376,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         }
       }
 
-      viewport.firePropertyChange("alignment", null, al.getSequences());
+      viewport.notifyAlignment();
     }
   }
 
@@ -2402,8 +2406,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     addHistoryItem(removeGapCols);
 
-    setStatus(MessageManager
-            .formatMessage("label.removed_empty_columns", new String[]
+    setStatus(MessageManager.formatMessage("label.removed_empty_columns",
+            new String[]
             { Integer.valueOf(removeGapCols.getSize()).toString() }));
 
     // This is to maintain viewport position on first residue
@@ -2416,7 +2420,7 @@ 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 +2454,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     ranges.setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null, al.getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2774,6 +2778,26 @@ 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 +3148,10 @@ 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();
@@ -3521,17 +3549,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     hydrophobicityColour.setLabel(
             MessageManager.getString("label.colourScheme_hydrophobic"));
     hydrophobicityColour.addActionListener(this);
-    helixColour.setLabel(MessageManager
-            .getString("label.colourScheme_helix_propensity"));
+    helixColour.setLabel(
+            MessageManager.getString("label.colourScheme_helixpropensity"));
     helixColour.addActionListener(this);
     strandColour.setLabel(MessageManager
-            .getString("label.colourScheme_strand_propensity"));
+            .getString("label.colourScheme_strandpropensity"));
     strandColour.addActionListener(this);
     turnColour.setLabel(
-            MessageManager.getString("label.colourScheme_turn_propensity"));
+            MessageManager.getString("label.colourScheme_turnpropensity"));
     turnColour.addActionListener(this);
     buriedColour.setLabel(
-            MessageManager.getString("label.colourScheme_buried_index"));
+            MessageManager.getString("label.colourScheme_buriedindex"));
     buriedColour.addActionListener(this);
     purinePyrimidineColour.setLabel(MessageManager
             .getString("label.colourScheme_purine/pyrimidine"));
@@ -3540,19 +3568,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // .getString("label.rna_interaction"));
     // RNAInteractionColour.addActionListener(this);
     RNAHelixColour.setLabel(
-            MessageManager.getString("label.colourScheme_rna_helices"));
+            MessageManager.getString("label.colourScheme_rnahelices"));
     RNAHelixColour.addActionListener(this);
     userDefinedColour
             .setLabel(MessageManager.getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
     PIDColour.setLabel(
-            MessageManager.getString("label.colourScheme_%_identity"));
+            MessageManager.getString("label.colourScheme_%identity"));
     PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel(
             MessageManager.getString("label.colourScheme_blosum62"));
     BLOSUM62Colour.addActionListener(this);
     tcoffeeColour.setLabel(
-            MessageManager.getString("label.colourScheme_t-coffee_scores"));
+            MessageManager.getString("label.colourScheme_t-coffeescores"));
     // it will be enabled only if a score file is provided
     tcoffeeColour.setEnabled(false);
     tcoffeeColour.addActionListener(this);
@@ -4152,7 +4180,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       // register the association(s) and quit, don't create any windows.
       if (StructureSelectionManager.getStructureSelectionManager(applet)
-              .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
+              .setMapping(seqs, chains, pdb.getFile(), protocol,
+                      null) == null)
       {
         System.err.println("Failed to map " + pdb.getFile() + " ("
                 + protocol + ") to any sequences");