JAL-1385 refactor logic to AlignmentViewController

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0f0ba4e..2cf7602 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -19,6 +19,7 @@ package jalview.appletgui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.Conservation;
+import jalview.api.AlignViewControllerI;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
@@ -92,6 +93,7 @@ import java.util.Vector;
 public class AlignFrame extends EmbmenuFrame implements ActionListener,
         ItemListener, KeyListener
 {
+  public AlignViewControllerI avc;
   public AlignmentPanel alignPanel;
 
   public AlignViewport viewport;
@@ -120,7 +122,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     viewport = new AlignViewport(al, applet);
     alignPanel = new AlignmentPanel(this, viewport);
-
+    avc = new jalview.controller.AlignViewController(viewport, alignPanel);
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
 
@@ -1887,28 +1889,7 @@ 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);
@@ -1917,11 +1898,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   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()

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 829b9ab..382ccda 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -24,6 +24,7 @@ import jalview.analysis.CrossRef;
 import jalview.analysis.NJTree;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewControllerI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
@@ -145,6 +146,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public AlignmentPanel alignPanel;
 
   AlignViewport viewport;
+ 
+  public AlignViewControllerI avc;
+ 
 
   Vector alignPanels = new Vector();
 
@@ -288,6 +292,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
+    avc = new jalview.controller.AlignViewController(viewport, alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
     {
       BLOSUM62Colour.setEnabled(false);
@@ -330,7 +335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     addKeyListener();
-
+    
   }
 
   /**
@@ -558,6 +563,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
   {
     ap.alignFrame = this;
+    avc = new jalview.controller.AlignViewController(viewport, alignPanel);
 
     alignPanels.addElement(ap);
 
@@ -735,7 +741,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     rnahelicesColour
             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
     setShowProductsEnabled();
-
     updateEditMenuBar();
   }
 
@@ -2136,12 +2141,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
-    viewport.getAlignment().deleteAllGroups();
-    viewport.sequenceColours = null;
-    viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(this, viewport.getSequenceSetId());
-    alignPanel.updateAnnotation();
-    alignPanel.paintAlignment(true);
+    if (avc.deleteGroups()) {
+      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+      alignPanel.updateAnnotation();
+      alignPanel.paintAlignment(true);
+    }
   }
 
   /**
@@ -5015,6 +5019,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
       viewport = alignPanel.av;
+      avc.setViewportAndAlignmentPanel(viewport, alignPanel);
       setMenusFromViewport(viewport);
     }
   }
@@ -5455,28 +5460,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
   {
-    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].setShowNonconserved(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 s : gps[g].getSequences())
-          viewport.setSequenceColour(s, col);
-      }
+    if (avc.makeGroupsFromSelection()) {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
       alignPanel.paintAlignment(true);