X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=fd426d3effe0243ff0610c8d848679a765185c66;hb=8d2724b83aca38ef75d68787cc5939d950467e63;hp=865f0d485bb4daf71879902d5d134169367a8178;hpb=21c29b20790ac555b2e2a124a034f6c6b4486270;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 865f0d4..fd426d3 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,11 +14,14 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.Conservation;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
@@ -50,6 +53,7 @@ import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.RNAInteractionColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
@@ -91,8 +95,9 @@ import java.util.StringTokenizer;
 import java.util.Vector;
 
 public class AlignFrame extends EmbmenuFrame implements ActionListener,
-        ItemListener, KeyListener
+        ItemListener, KeyListener, AlignViewControllerGuiI
 {
+  public AlignViewControllerI avc;
   public AlignmentPanel alignPanel;
 
   public AlignViewport viewport;
@@ -121,7 +126,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     viewport = new AlignViewport(al, applet);
     alignPanel = new AlignmentPanel(this, viewport);
-
+    avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
 
@@ -542,6 +547,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       break;
 
+    case KeyEvent.VK_G:
+      if (evt.isControlDown())
+      {
+        if (evt.isShiftDown())
+        {
+          this.unGroup_actionPerformed();
+        }
+        else
+        {
+          this.createGroup_actionPerformed();
+        }
+      }
+      break;
+      
     case KeyEvent.VK_U:
       if (evt.isControlDown())
       {
@@ -1022,6 +1041,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       changeColour(new PurinePyrimidineColourScheme());
     }
+    else if (source == RNAInteractionColour)
+    {
+      changeColour(new RNAInteractionColourScheme());
+    }
     else if (source == RNAHelixColour)
     {
       new RNAHelicesColourChooser(viewport, alignPanel);
@@ -1887,41 +1910,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   protected void makeGrpsFromSelection_actionPerformed()
   {
-    if (viewport.getSelectionGroup() != null)
-    {
-      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
-              viewport.getSequenceSelection(),
-              viewport.getAlignmentView(true).getSequenceStrings(
-                      viewport.getGapCharacter()), viewport.getAlignment()
-                      .getGroups());
-      viewport.getAlignment().deleteAllGroups();
-      viewport.sequenceColours = null;
-      viewport.setSelectionGroup(null);
-      // set view properties for each group
-      for (int g = 0; g < gps.length; g++)
-      {
-        // gps[g].setShowunconserved(viewport.getShowUnconserved());
-        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
-        viewport.getAlignment().addGroup(gps[g]);
-        Color col = new Color((int) (Math.random() * 255),
-                (int) (Math.random() * 255), (int) (Math.random() * 255));
-        col = col.brighter();
-        for (SequenceI sq : gps[g].getSequences(null))
-          viewport.setSequenceColour(sq, col);
-      }
+    if (avc.makeGroupsFromSelection()) {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
       alignPanel.paintAlignment(true);
     }
   }
 
+  protected void createGroup_actionPerformed()
+  {
+    avc.createGroup();
+  }
+  protected void unGroup_actionPerformed()
+  {
+    if (avc.unGroup())
+    {
+      alignPanel.alignmentChanged();
+    }
+  }
   protected void deleteGroups_actionPerformed()
   {
-    viewport.getAlignment().deleteAllGroups();
-    viewport.sequenceColours = null;
-    viewport.setSelectionGroup(null);
-
-    alignPanel.paintAlignment(true);
+    if (avc.deleteGroups())
+    {
+      alignPanel.alignmentChanged();
+    }
   }
 
   public void selectAllSequenceMenuItem_actionPerformed()
@@ -2820,6 +2832,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem purinePyrimidineColour = new MenuItem();
 
+  MenuItem RNAInteractionColour = new MenuItem();
+
   MenuItem RNAHelixColour = new MenuItem();
 
   MenuItem userDefinedColour = new MenuItem();
@@ -2866,6 +2880,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem grpsFromSelection = new MenuItem();
 
+  MenuItem createGroup = new MenuItem();
+
+  MenuItem unGroup = new MenuItem();
+
   MenuItem delete = new MenuItem();
 
   MenuItem copy = new MenuItem();
@@ -3023,6 +3041,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     buriedColour.addActionListener(this);
     purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
     purinePyrimidineColour.addActionListener(this);
+    RNAInteractionColour.setLabel(MessageManager.getString("label.rna_interaction"));
+    RNAInteractionColour.addActionListener(this);
     RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
     RNAHelixColour.addActionListener(this);
     userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
@@ -3074,6 +3094,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     deleteGroups.addActionListener(this);
     grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(this);
+    createGroup.setLabel(MessageManager.getString("action.create_group"));
+    unGroup.setLabel(MessageManager.getString("action.remove_group"));
     copy.setLabel(MessageManager.getString("action.copy"));
     copy.addActionListener(this);
     cut.setLabel(MessageManager.getString("action.cut"));
@@ -3247,6 +3269,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
     colourMenu.add(purinePyrimidineColour);
+    //    colourMenu.add(RNAInteractionColour);
     colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
@@ -3302,11 +3325,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     selectMenu.add(deselectAllSequenceMenuItem);
     selectMenu.add(invertSequenceMenuItem);
     selectMenu.add(invertColSel);
+    selectMenu.add(createGroup);
+    selectMenu.add(unGroup);
     selectMenu.add(grpsFromSelection);
     selectMenu.add(deleteGroups);
 
   }
 
+  
+  public void setStatus(String string) {
+    statusBar.setText(string);
+  };
+
   MenuItem featureSettings = new MenuItem();
 
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();