From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 13 Jun 2005 11:34:15 +0000 (+0000)
Subject: PaintRefresh changed
X-Git-Tag: Release_2_0~63
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;p=jalview.git

PaintRefresh changed
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 25b74b6..b314854 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -749,10 +749,6 @@ public class AlignFrame
       {
         ( (ResidueColourScheme) cs).setThreshold(threshold);
       }
-      else if (cs instanceof ScoreColourScheme)
-      {
-        ( (ScoreColourScheme) cs).setThreshold(threshold);
-      }
 
       viewport.setGlobalColourScheme(cs);
     }
@@ -760,10 +756,6 @@ public class AlignFrame
     {
       ( (ResidueColourScheme) cs).setThreshold(0);
     }
-    else if (cs instanceof ScoreColourScheme)
-    {
-      ( (ScoreColourScheme) cs).setThreshold(0);
-    }
 
     if (viewport.getConservationSelected())
     {
@@ -804,9 +796,16 @@ public class AlignFrame
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
+        if(cs==null)
+        {
+          sg.cs = null;
+          continue;
+        }
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
+          cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
+          sg.cs = cxs;
         }
         else
         {
@@ -827,10 +826,6 @@ public class AlignFrame
           {
             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
           }
-          else if (sg.cs instanceof ScoreColourScheme)
-          {
-            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-          }
 
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
         }
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 3c3c52c..8b6939e 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -44,7 +44,7 @@ public class IdCanvas
   {
     setLayout(null);
     this.av = av;
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.alignment);
   }
 
   public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 33463d4..d548936 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -238,7 +238,7 @@ public class IdPanel
       av.getSelectionGroup().recalcConservation();
 
     mouseDragging = false;
-    PaintRefresher.Refresh(this);
+    PaintRefresher.Refresh(this, av.alignment);
   }
 
   public void highlightSearchResults(java.util.Vector found)
diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 670af70..2da1db6 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -17,44 +17,51 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 
-package jalview.appletgui;
 
-import java.util.*;
+
+package jalview.appletgui;
 
 import java.awt.*;
+import java.util.*;
+import jalview.datamodel.*;
 
 public class PaintRefresher
 {
-  static Vector components = new Vector();
+  static Hashtable components = new Hashtable();
 
-  public static void Register(Component c)
+  public static void Register(Component comp, AlignmentI al)
   {
-    if (!components.contains(c))
+    if(components.containsKey(al))
     {
-      components.addElement(c);
+      Vector comps = (Vector)components.get(al);
+      comps.addElement(comp);
     }
     else
     {
-      components.removeElement(c);
+      Vector vcoms = new Vector();
+      vcoms.addElement(comp);
+      components.put(al, vcoms);
     }
   }
 
-  public static void Refresh(Component c)
+  public static void Refresh(AlignmentI al)
+  {
+    Refresh(null, al);
+  }
+
+  public static void Refresh(Component c, AlignmentI al)
   {
     Component temp;
-    Enumeration e = components.elements();
-    while (e.hasMoreElements())
+    Vector coms = (Vector)components.get(al);
+    Enumeration e = coms.elements();
+    while( e.hasMoreElements() )
     {
-      temp = (Component) e.nextElement();
+      temp = (Component)e.nextElement();
 
-      if (!temp.isValid())
-      {
-        components.removeElement(temp);
-      }
-      else if (temp == c)
-      {
+      if(!temp.isValid())
+        coms.removeElement( temp );
+      else if( temp == c )
         continue;
-      }
 
       temp.repaint();
     }
@@ -62,3 +69,4 @@ public class PaintRefresher
   }
 
 }
+
diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 8d22f37..88b6251 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -91,7 +91,7 @@ public class RotatableCanvas
     this.points = points;
     this.npoint = npoint;
     this.av = av;
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.alignment);
 //
     prefsize = getPreferredSize();
     orig = new float[npoint][3];
@@ -471,7 +471,7 @@ public class RotatableCanvas
       if (av.getSelectionGroup() != null)
       {
         av.getSelectionGroup().addOrRemove(found, true);
-        PaintRefresher.Refresh(this);
+        PaintRefresher.Refresh(this, av.alignment);
       }
       else
       {
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 438d7ad..5aa5d66 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -50,7 +50,7 @@ public class SeqCanvas
     this.av = av;
     fr = new FeatureRenderer(av);
     sr = new SequenceRenderer(av);
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.alignment);
 
   }
 
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 9d14b26..6e2a544 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -593,28 +593,23 @@ public class SeqPanel
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
-    mouseDragging = false;
+    if(mouseDragging)
+     {
+       stretchGroup.recalcConservation();
+       mouseDragging = false;
+     }
 
     if (stretchGroup == null)
     {
       return;
     }
 
-    stretchGroup.recalcConservation();
-
-    if (stretchGroup.cs instanceof ClustalxColourScheme)
-    {
-      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences,
-                                                 av.alignment.getWidth());
-    }
-
-    else if (stretchGroup.cs instanceof ConservationColourScheme)
+    if (stretchGroup.cs instanceof ConservationColourScheme)
     {
       ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
       stretchGroup.cs = ccs;
       SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                                         stretchGroup.getName());
-
     }
     else
     {
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index b00d6cc..136be52 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -70,7 +70,7 @@ public class TreeCanvas
     longestName = label;
     setLayout(null);
 
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.alignment);
   }
 
   public void TreeSelectionChanged(Sequence sequence)
@@ -85,7 +85,8 @@ public class TreeCanvas
     selected.setEndRes(av.alignment.getWidth());
     selected.addOrRemove(sequence, true);
 
-    PaintRefresher.Refresh(this);
+System.out.println("called here");
+    PaintRefresher.Refresh(this, av.alignment);
     repaint();
   }
 
@@ -424,7 +425,6 @@ public class TreeCanvas
 
   public void mousePressed(MouseEvent e)
   {
-
     av.setCurrentTree(tree);
 
     int x = e.getX();
@@ -472,14 +472,22 @@ public class TreeCanvas
 
           Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(
               i), new Vector());
-          SequenceGroup sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true, false,
-                                     0, av.alignment.getWidth());
+
+          Vector sequences = new Vector();
           for (int j = 0; j < l.size(); j++)
           {
-            SequenceNode sn = (SequenceNode) l.elementAt(j);
-            sg.addSequence( (Sequence) sn.element(), false);
+            sequences.addElement( (Sequence) ( (SequenceNode) l.elementAt(j)).element());
           }
 
+          ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),
+              ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));
+
+
+          SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",
+                                               cs, true, true,
+                                               false, 0, av.alignment.getWidth());
+
+
           if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
           {
             ConservationColourScheme ccs = (ConservationColourScheme) av.
@@ -503,7 +511,7 @@ public class TreeCanvas
       }
     }
 
-    PaintRefresher.Refresh(this);
+    PaintRefresher.Refresh(this, av.alignment);
     repaint();
 
   }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 068d605..1a48af6 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -47,7 +47,7 @@ public class AlignmentPanel
   AnnotationLabels alabels;
 
   // this value is set false when selection area being dragged
-  boolean fastPaint = false;
+  boolean fastPaint = true;
   int hextent = 0;
   int vextent = 0;
 
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index c14da85..b38fd21 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -42,7 +42,7 @@ public class IdCanvas
   {
     setLayout(new BorderLayout());
     this.av = av;
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.alignment);
   }
 
   public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
@@ -177,9 +177,6 @@ public class IdCanvas
 
   void drawIds(int starty, int endy)
   {
-    if(gg==null)
-      return;
-
 
     Color currentColor = Color.white;
     Color currentTextColor = Color.black;
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 00fe35f..db24821 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -247,7 +247,7 @@ public class IdPanel
     }
 
     mouseDragging = false;
-    PaintRefresher.Refresh(this);
+    PaintRefresher.Refresh(av.alignment);
   }
 
   public void highlightSearchResults(java.util.Vector found)
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 6bec8fd..e59ecd9 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -16,47 +16,53 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-package jalview.gui;
-
-import java.util.*;
 
+package jalview.gui;
 import java.awt.*;
+import java.util.*;
+import jalview.datamodel.*;
 
 public class PaintRefresher
 {
-  static Vector components = new Vector();
+  static Hashtable components = new Hashtable();
 
-  public static void Register(Component c)
+  public static void Register(Component comp, AlignmentI al)
   {
-    if (!components.contains(c))
+    if(components.containsKey(al))
     {
-      components.add(c);
+      Vector comps = (Vector)components.get(al);
+      comps.addElement(comp);
     }
     else
     {
-      components.remove(c);
+      Vector vcoms = new Vector();
+      vcoms.addElement(comp);
+      components.put(al, vcoms);
     }
   }
 
-  public static void Refresh(Component c)
+  public static void Refresh(AlignmentI al)
   {
-    Component temp;
-    Enumeration e = components.elements();
+    Refresh(null, al);
+  }
 
-    while (e.hasMoreElements())
+  public static void Refresh(Component c, AlignmentI al)
+  {
+    Component temp;
+    Vector coms = (Vector)components.get(al);
+    Enumeration e = coms.elements();
+    while( e.hasMoreElements() )
     {
-      temp = (Component) e.nextElement();
-
-      if (!temp.isValid())
-      {
-        components.removeElement(temp);
-      }
-      else if (temp == c)
-      {
+      temp = (Component)e.nextElement();
+
+      if(!temp.isValid())
+        coms.removeElement( temp );
+      else if( temp == c )
         continue;
-      }
 
       temp.repaint();
     }
+
   }
+
 }
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 7576173..d563e09 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -634,7 +634,7 @@ public class PopupMenu
     SequenceGroup sg = ap.av.getSelectionGroup();
     ap.av.alignment.deleteGroup(sg);
     ap.av.setSelectionGroup(null);
-    ap.repaint();
+    refresh();
   }
 
   void pdbMenuItem_actionPerformed(ActionEvent e)
@@ -676,7 +676,7 @@ public class PopupMenu
       sg.setOutlineColour(col);
     }
 
-    ap.repaint();
+    refresh();
   }
 
   public void showBoxes_actionPerformed(ActionEvent e)
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index c89cd59..6ae66a2 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -75,7 +75,7 @@ public class RotatableCanvas
     this.npoint = npoint;
     this.av = av;
     ToolTipManager.sharedInstance().registerComponent(this);
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.alignment);
 
     //
     prefsize = getPreferredSize();
@@ -475,7 +475,7 @@ public class RotatableCanvas
       if (av.getSelectionGroup() != null)
       {
         av.getSelectionGroup().addOrRemove(found, true);
-        PaintRefresher.Refresh(this);
+        PaintRefresher.Refresh(this, av.alignment);
       }
       else
       {
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 1194d08..789fb3f 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -44,13 +44,15 @@ public class SeqCanvas
   int LABEL_WEST;
   int LABEL_EAST;
 
+
   public SeqCanvas(AlignViewport av)
   {
     this.av = av;
     fr = new FeatureRenderer(av);
     sr = new SequenceRenderer(av);
     setLayout(new BorderLayout());
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.alignment);
+    setBackground(Color.white);
   }
 
   void drawNorthScale(Graphics g, int startx, int endx, int ypos)
@@ -212,16 +214,16 @@ public class SeqCanvas
    * NOTE 1: The av limits are set in setFont in this class and
    * in the adjustment listener in SeqPanel when the scrollbars move.
    */
+
+
+  // Set this to false to force a full panel paint
   public void paintComponent(Graphics g)
   {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-
-    if (fastPaint)
+    if (fastPaint  ||  getWidth() !=  g.getClipBounds().width
+                   ||  getHeight() != g.getClipBounds().height)
     {
       g.drawImage(img, 0, 0, this);
       fastPaint = false;
-
       return;
     }
 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 52d137b..a643ab8 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -60,6 +60,7 @@ public class SeqPanel
   public SeqPanel(AlignViewport avp, AlignmentPanel p)
   {
     this.av = avp;
+    setBackground(Color.white);
 
     seqCanvas = new SeqCanvas(avp);
     setLayout(new BorderLayout());
@@ -160,9 +161,9 @@ public class SeqPanel
         doMouseEnteredDefineMode(evt);
       }
     });
-    repaint();
   }
 
+
   public void doMouseReleased(MouseEvent evt)
   {
     if (seqEditOccurred > -1)
@@ -176,7 +177,7 @@ public class SeqPanel
     editingSeqs = false;
     groupEditing = false;
 
-    ap.repaint();
+    seqCanvas.repaint();
   }
 
   public void doMousePressed(MouseEvent evt)
@@ -443,14 +444,14 @@ public class SeqPanel
 
     endEdit = res;
     lastres = res;
-    repaint();
+    seqCanvas.repaint();
   }
 
   public void drawChars(int seqstart, int seqend, int start)
   {
     seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
                         seqend, av.getStartRes(), av.getStartSeq(), 0);
-    repaint();
+    seqCanvas.repaint();
   }
 
   public void insertChar(int j, int seq)
@@ -465,7 +466,7 @@ public class SeqPanel
     seqEditOccurred = seq;
 
     av.alignment.getWidth();
-    repaint();
+    seqCanvas.repaint();
   }
 
   void editOccurred(int i)
@@ -608,24 +609,26 @@ public class SeqPanel
 
     stretchGroup.getWidth();
 
-    repaint();
+    seqCanvas.repaint();
   }
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
-    mouseDragging = false;
+    if(mouseDragging)
+    {
+      stretchGroup.recalcConservation();
+      mouseDragging = false;
+    }
 
     if (stretchGroup == null)
     {
       return;
     }
 
-    stretchGroup.recalcConservation();
-
     if (stretchGroup.cs instanceof ClustalxColourScheme)
     {
-      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences,
-                                                 av.alignment.getWidth());
+      ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.sequences,
+                                                     stretchGroup.getWidth());
     }
     else if (stretchGroup.cs instanceof ConservationColourScheme)
     {
@@ -644,7 +647,7 @@ public class SeqPanel
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-    repaint();
+    seqCanvas.repaint();
     ap.idPanel.repaint();
   }
 
@@ -743,7 +746,7 @@ public class SeqPanel
       scrollThread.setEvent(evt);
     }
 
-    repaint();
+    seqCanvas.repaint();
   }
 
   public void doMouseEnteredDefineMode(MouseEvent e)
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 0f74faf..2864eb4 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -65,7 +65,7 @@ public class TreeCanvas
     tree.findHeight(tree.getTopNode());
     longestName = label;
 
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.alignment);
   }
 
   public void TreeSelectionChanged(Sequence sequence)
@@ -81,7 +81,7 @@ public class TreeCanvas
     selected.setEndRes(av.alignment.getWidth());
     selected.addOrRemove(sequence, true);
 
-    PaintRefresher.Refresh(this);
+    PaintRefresher.Refresh(this, av.alignment);
     repaint();
   }
 
@@ -568,11 +568,19 @@ public class TreeCanvas
             sequences.add( (Sequence)((SequenceNode) l.elementAt(j)).element());
           }
 
+          ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),
+              ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));
+
           SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",
-                           av.getGlobalColourScheme(), true, true,
+                           cs, true, true,
                            false, 0, av.alignment.getWidth());
 
 
+           ( (ResidueColourScheme) sg.cs).setThreshold(25);
+
+
+
+
           if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
           {
             ConservationColourScheme ccs = (ConservationColourScheme) av.
@@ -594,7 +602,7 @@ public class TreeCanvas
       }
     }
 
-    PaintRefresher.Refresh(this);
+    PaintRefresher.Refresh(this, av.alignment);
     repaint();
   }