X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=90438d52622454d4d5fd167e841697ac8c9c1221;hb=ad35f232acd499d9457056ca24b663866a09edd2;hp=497fc2a2e26cbd1eb552be9b772faad77c6abef4;hpb=ae282720c1bba85d9b52ebc2e85c6a9857b2c6db;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 497fc2a..90438d5 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;
 
@@ -279,7 +279,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     public void mousePressed(MouseEvent evt)
     {
 
-
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
         if(aa==null)
           return;
@@ -314,7 +313,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }
 
 
-        if (SwingUtilities.isRightMouseButton(evt))
+        if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)
         {
             if (av.getColumnSelection() == null)
             {
@@ -349,6 +348,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
+        if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
         min = res;
         max = res;
 
@@ -430,6 +432,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
+        if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
         SequenceGroup sg = av.getSelectionGroup();
 
         if (res < min)
@@ -508,12 +513,17 @@ 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 +597,8 @@ 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 +613,12 @@ 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 +661,49 @@ 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))
@@ -667,6 +717,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             return;
         }
 
+
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
         int x = 0, y = 0;
@@ -689,6 +740,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;
             }
 
+
             lastSS = ' ';
             lastSSX = 0;
 
@@ -706,6 +758,45 @@ 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;
@@ -944,7 +1035,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
                 default:
                   g.setColor(Color.gray);
-                  if(!av.wrapAlignment || endRes==av.endRes)
                   g.fillRect(lastSSX, y + 6 + iconOffset,
                              (x*av.charWidth) - lastSSX, 2);
 
@@ -1168,13 +1258,16 @@ 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;
       }
     }