X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=844c1abfaa242c082fa7ad624df27783e2bd4421;hb=b3b59df08fc4183bb35e4ed5a54841a990b71346;hp=8bed8e2aacf707880781b13d6ef8c5c17a40bbf4;hpb=38fac06c61046ef7eac2c362148e9d1df7d49ec0;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 8bed8e2..844c1ab 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -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;
@@ -314,7 +315,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }
 
 
-        if (SwingUtilities.isRightMouseButton(evt))
+        if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)
         {
             if (av.getColumnSelection() == null)
             {
@@ -418,8 +419,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       if(graphStretch>-1)
       {
         av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();
-        if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)
-          av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;
+        if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0)
+          av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
         graphStretchY = evt.getY();
         adjustPanelHeight();
         ap.repaint();
@@ -587,6 +588,8 @@ 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 +604,12 @@ 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 +652,45 @@ 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)
+      {
+        //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))
@@ -667,6 +704,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             return;
         }
 
+
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
         int x = 0, y = 0;
@@ -689,6 +727,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;
             }
 
+
             lastSS = ' ';
             lastSSX = 0;
 
@@ -706,6 +745,45 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 }
             }
 
+            if (av.updatingConsensus && aa[i].label.equals("Consensus"))
+            {
+              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"))
+            {
+
+              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"))
+            {
+
+              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;
+            }
+
+
             if (row.hasText)
             {
                 iconOffset = av.charHeight / 2 + 4;
@@ -952,7 +1030,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
               }
           }
 
-            if (row.graph>0)
+            if (row.graph>0 && row.graphHeight>0)
             {
                 if(row.graph == AlignmentAnnotation.LINE_GRAPH )
                 {
@@ -1168,13 +1246,16 @@ 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;
       }
     }