X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=315b14123b2b3f50a8adc352fcc15e8127ea3520;hb=237972562c84b83dbd287071cdd839d97aaf7d4b;hp=dbc1c926f8343cdbee711700eecdf9a9c87109b4;hpb=82cbe684b0afeb8a6a8c6014b9266cb90439dfe7;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index dbc1c92..315b141 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -49,6 +49,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     AlignmentPanel ap;
     int activeRow = -1;
     BufferedImage image;
+    BufferedImage fadedImage;
     Graphics2D gg;
     FontMetrics fm;
     int imgWidth = 0;
@@ -107,7 +108,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     public int adjustPanelHeight()
     {
         // setHeight of panels
-        image = null;
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
         int height = 0;
 
@@ -508,12 +508,17 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             }
         }
 
+        if(row==-1)
+          return;
+
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
         if(av.hasHiddenColumns)
           res = av.getColumnSelection().adjustForHiddenColumns(res);
 
-        if (row > -1 && res<aa[row].annotations.length)
+        if ( aa[row].annotations!=null
+             && row > -1
+             && res < (int) aa[row].annotations.length)
         {
             if(aa[row].graphGroup>-1)
             {
@@ -587,6 +592,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
         gg.setFont(av.getFont());
         fm = gg.getFontMetrics();
+        gg.setColor(Color.white);
+        gg.fillRect(0, 0, imgWidth, image.getHeight());
       }
 
 
@@ -601,9 +608,12 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */
     public void fastPaint(int horizontal)
     {
-        if ((horizontal == 0) || gg==null ||
-                (av.alignment.getAlignmentAnnotation() == null) ||
-                (av.alignment.getAlignmentAnnotation().length < 1))
+        if ((horizontal == 0)
+            || gg==null
+            || av.alignment.getAlignmentAnnotation()==null
+            || av.alignment.getAlignmentAnnotation().length < 1
+            || av.updatingConsensus
+            || av.updatingConservation)
         {
             repaint();
             return;
@@ -646,14 +656,49 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */
     public void drawComponent(Graphics g, int startRes, int endRes)
     {
-      g.setFont(av.getFont());
+      if(av.updatingConsensus || av.updatingConservation)
+      {
+        if(image==null)
+         {
+           return;
+         }
+        //We'll keep a record of the old image,
+        //and draw a faded image until the calculation
+        //has completed
+        if(fadedImage==null
+           || fadedImage.getWidth()!=imgWidth
+        || fadedImage.getHeight()!=image.getHeight())
+        {
+          fadedImage = new BufferedImage(
+              imgWidth, image.getHeight(),
+              BufferedImage.TYPE_INT_RGB);
+
+          Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
+
+          fadedG.setColor(Color.white);
+        fadedG.fillRect(0, 0, imgWidth, image.getHeight());
+
+          fadedG.setComposite(
+              AlphaComposite.getInstance(
+                  AlphaComposite.SRC_OVER, .3f));
+          fadedG.drawImage(image, 0, 0, this);
+
+        }
+
+      }
+      else
+        fadedImage = null;
+
 
+      g.setColor(Color.white);
+      g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+
+      g.setFont(av.getFont());
       if (fm == null)
         fm = g.getFontMetrics();
 
 
-        g.setColor(Color.white);
-        g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+
 
         if ( (av.alignment.getAlignmentAnnotation() == null) ||
                 (av.alignment.getAlignmentAnnotation().length < 1))
@@ -710,22 +755,39 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
             if (av.updatingConsensus && aa[i].label.equals("Consensus"))
             {
-              g.setColor(Color.darkGray);
-              g.drawString("Recalculating Consensus....", 20, y - 5);
               y += av.charHeight;
+
+              g.drawImage(fadedImage,
+              0,y-row.height,imgWidth, y,
+              0,y-row.height,imgWidth, y, this);
+              g.setColor(Color.black);
+             // g.drawString("Calculating Consensus....",20, y-row.height/2);
+
               continue;
             }
             else if (av.updatingConservation && aa[i].label.equals("Conservation"))
             {
-              g.setColor(Color.darkGray);
-              g.drawString("Recalculating Conservation.....", 20, y - 5);
+
               y += av.charHeight;
+              g.drawImage(fadedImage,
+                          0, y - row.height, imgWidth, y,
+                          0, y - row.height, imgWidth, y, this);
+
+              g.setColor(Color.black);
+            //  g.drawString("Calculating Conservation.....",20, y-row.height/2);
+
               continue;
             }
             else if (av.updatingConservation && aa[i].label.equals("Quality"))
             {
-              g.setColor(Color.darkGray);
-              g.drawString("Recalculating Quality....", 20, y - 5);
+
+              y += av.charHeight;
+              g.drawImage(fadedImage,
+                          0, y - row.height, imgWidth, y,
+                          0, y - row.height, imgWidth, y, this);
+              g.setColor(Color.black);
+             /// g.drawString("Calculating Quality....",20, y-row.height/2);
+
               continue;
             }
 
@@ -1192,13 +1254,16 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       for (int j = sRes; j < eRes; j++)
       {
+        if (aa.annotations[j] != null)
+        {
           g.setColor(aa.annotations[j].colour);
 
-          height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
-          if(height>y)
+          height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
+          if (height > y)
             height = y;
 
           g.fillRect(x, y - height, av.charWidth, height);
+        }
           x += av.charWidth;
       }
     }