From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 7 Oct 2013 16:33:16 +0000 (+0100)
Subject: JAL-1385 JAL-535 refactor sequence colour settings to abstract alignment view model
X-Git-Tag: Jalview_2_9~200^2~18^2~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=7c581704d0ce30ffad302f199e0f44f689cd32fb;p=jalview.git

JAL-1385 JAL-535 refactor sequence colour settings to abstract alignment view model
---

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 15e5f1d..5f759b8 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -159,11 +159,17 @@ public interface AlignViewportI
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);
 
+  void setSequenceColour(SequenceI seq, Color col);
+
+  Color getSequenceColour(SequenceI seq);
+
+  void updateSequenceIdColours();
 
   SequenceGroup getSelectionGroup();
 
   SequenceI[] getSequenceSelection();
 
+  void clearSequenceColours();
 
   CigarArray getViewAsCigars(boolean selectedRegionOnly);
 
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index cc04b58..9e4f071 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -91,8 +91,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   public jalview.bin.JalviewLite applet;
 
-  Hashtable sequenceColours;
-
   boolean MAC = false;
 
   Stack historyList = new Stack();
@@ -592,35 +590,6 @@ public class AlignViewport extends AlignmentViewport implements
     showHiddenMarkers = show;
   }
 
-  public Color getSequenceColour(SequenceI seq)
-  {
-    if (sequenceColours == null || !sequenceColours.containsKey(seq))
-    {
-      return Color.white;
-    }
-    else
-    {
-      return (Color) sequenceColours.get(seq);
-    }
-  }
-
-  public void setSequenceColour(SequenceI seq, Color col)
-  {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-
-    if (col == null)
-    {
-      sequenceColours.remove(seq);
-    }
-    else
-    {
-      sequenceColours.put(seq, col);
-    }
-  }
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -628,21 +597,6 @@ public class AlignViewport extends AlignmentViewport implements
     return centreColumnLabels;
   }
 
-  public void updateSequenceIdColours()
-  {
-
-    for (SequenceGroup sg : alignment.getGroups())
-    {
-      if (sg.idColour != null)
-      {
-        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
-        {
-          this.setSequenceColour(s, sg.idColour);
-        }
-      }
-    }
-  }
-
   public boolean followHighlight = true;
 
   public boolean getFollowHighlight()
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 5c62234..68ffd7a 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -578,7 +578,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
         av.setSelectionGroup(null);
         av.getAlignment().deleteAllGroups();
-        av.sequenceColours = null;
+        av.clearSequenceColours();
 
         colourGroups();
 
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7a01b27..407fa94 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -138,8 +138,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   Stack redoList = new Stack();
 
-  Hashtable sequenceColours;
-
   int thresholdTextColour = 0;
 
   Color textColour = Color.black;
@@ -934,35 +932,6 @@ public class AlignViewport extends AlignmentViewport implements
     showHiddenMarkers = show;
   }
 
-  public Color getSequenceColour(SequenceI seq)
-  {
-    if (sequenceColours == null || !sequenceColours.containsKey(seq))
-    {
-      return Color.white;
-    }
-    else
-    {
-      return (Color) sequenceColours.get(seq);
-    }
-  }
-
-  public void setSequenceColour(SequenceI seq, Color col)
-  {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-
-    if (col == null)
-    {
-      sequenceColours.remove(seq);
-    }
-    else
-    {
-      sequenceColours.put(seq, col);
-    }
-  }
-
   /**
    * returns the visible column regions of the alignment
    * 
@@ -1044,23 +1013,6 @@ public class AlignViewport extends AlignmentViewport implements
     centreColumnLabels = centrecolumnlabels;
   }
 
-  public void updateSequenceIdColours()
-  {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-    for (SequenceGroup sg : alignment.getGroups())
-    {
-      if (sg.idColour != null)
-      {
-        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
-        {
-          sequenceColours.put(s, sg.idColour);
-        }
-      }
-    }
-  }
 
   /**
    * enable or disable the display of Database Cross References in the sequence
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index d1003e5..22c89ea 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -852,7 +852,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         {
           aps[a].av.setSelectionGroup(null);
           aps[a].av.getAlignment().deleteAllGroups();
-          aps[a].av.sequenceColours = null;
+          aps[a].av.clearSequenceColours();
         }
         colourGroups();
       }
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index dc352f4..cceff86 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -40,6 +40,7 @@ import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
@@ -783,6 +784,8 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   protected boolean showConsensus = true;
 
+  Hashtable sequenceColours;
+
   /**
    * Property change listener for changes in alignment
    * 
@@ -1542,4 +1545,60 @@ public abstract class AlignmentViewport implements AlignViewportI
     oldrfs.clear();
   }
 
+  @Override
+  public Color getSequenceColour(SequenceI seq)
+  {
+    Color sqc=Color.white;
+    if (sequenceColours != null)
+    {
+      sqc = (Color) sequenceColours.get(seq);
+      if (sqc == null) {
+        sqc = Color.white;
+      }
+    }
+    return sqc;
+  }
+
+  @Override
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+
+    if (col == null)
+    {
+      sequenceColours.remove(seq);
+    }
+    else
+    {
+      sequenceColours.put(seq, col);
+    }
+  }
+
+  @Override
+  public void updateSequenceIdColours()
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+    for (SequenceGroup sg : alignment.getGroups())
+    {
+      if (sg.idColour != null)
+      {
+        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
+        {
+          sequenceColours.put(s, sg.idColour);
+        }
+      }
+    }
+  }
+
+  @Override
+  public void clearSequenceColours()
+  {
+    sequenceColours = null;
+  };
 }