X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=844c1abfaa242c082fa7ad624df27783e2bd4421;hb=9f08afb8654d8e19fddfd3c6de0e8702804ea97d;hp=bf1372eeac184092917e29aef24eab281de64ff4;hpb=efbf36f3efcd7a971a6ca33d098f54b204f2cae9;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index bf1372e..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;
@@ -286,7 +287,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
 
         int height = 0;
-        activeRow = 0;
+        activeRow = -1;
 
 
         for (int i = 0; i < aa.length; i++)
@@ -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;
@@ -646,16 +652,45 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */
     public void drawComponent(Graphics g, int startRes, int endRes)
     {
+      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();
 
-      g.setFont(av.getFont());
+          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))
@@ -669,10 +704,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             return;
         }
 
+
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-        int x = 0;
-        int y = 0;
+        int x = 0, y = 0;
+        int column=0;
         char lastSS;
         int lastSSX;
         int iconOffset = av.charHeight / 2;
@@ -691,10 +727,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;
             }
 
+
             lastSS = ' ';
             lastSSX = 0;
 
-
             if (row.graph>0)
             {
                 if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )
@@ -709,27 +745,68 @@ 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;
+                iconOffset = av.charHeight / 2 + 4;
             }
             else
             {
                 iconOffset = 0;
             }
 
-            int column = startRes;
-
-            while (column < endRes)
+            x = 0;
+            while (x < endRes-startRes)
             {
               if (av.hasHiddenColumns)
               {
-                column = av.getColumnSelection().adjustForHiddenColumns(column);
+                column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);
                 if (column > row.annotations.length-1)
                 {
                   break;
                 }
               }
+              else
+                column = startRes+x;
+
 
                 if ((row.annotations.length <= column) ||
                         (row.annotations[column] == null))
@@ -741,7 +818,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     validRes = true;
                 }
 
-                x = (column - startRes) * av.charWidth;
 
                 if (activeRow == i)
                 {
@@ -755,8 +831,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
                             if (v == column)
                             {
-                                g.fillRect((column - startRes) * av.charWidth, y,
-                                    av.charWidth, row.height);
+                                g.fillRect(x * av.charWidth, y,
+                                    av.charWidth, av.charHeight);
                             }
                         }
                     }
@@ -773,8 +849,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
                     if (column == 0 || row.graph>0)
                     {
-                        g.drawString(row.annotations[column].displayCharacter, x+charOffset,
-                            y + iconOffset + 3);
+                        g.drawString(row.annotations[column].displayCharacter,
+                                     (x*av.charWidth)+charOffset,
+                            y + iconOffset );
                     }
                     else if (
                         row.annotations[column - 1] == null
@@ -784,8 +861,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                   (row.annotations[column].displayCharacter.length() <2 &&
                    row.annotations[column].secondaryStructure==' ')))
                     {
-                        g.drawString(row.annotations[column].displayCharacter, x+charOffset,
-                            y + iconOffset + 3);
+                        g.drawString(row.annotations[column].displayCharacter,
+                                     x*av.charWidth+charOffset,
+                                     y + iconOffset );
                     }
                 }
 
@@ -797,47 +875,50 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                         switch (lastSS)
                         {
                         case 'H':
-                            g.setColor(HELIX_COLOUR);
-                            if(MAC)
-                            {
-                              //Off by 1 offset when drawing rects and ovals
-                              //to offscreen image on the MAC
-                              g.fillRoundRect(lastSSX, y + 4 + iconOffset,
-                                              x - lastSSX, 7, 8, 8);
-                              break;
-                            }
-
-                            int sCol = (lastSSX / av.charWidth) + startRes;
-                            int x1 = lastSSX;
-                            int x2 = x;
-
-                           if(sCol==0 ||
-                              row.annotations[sCol-1]==null ||
-                              row.annotations[sCol-1].secondaryStructure!='H')
-                           {
-                             g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ;
-                             x1 += av.charWidth/2;
-                           }
-
-                            if(row.annotations[column]==null ||
-                               row.annotations[column].secondaryStructure!='H')
-                            {
-                              g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180);
-                              x2 -= av.charWidth/2;
-                            }
-
-                            g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);
+                          g.setColor(HELIX_COLOUR);
+                          if (MAC)
+                          {
+                            //Off by 1 offset when drawing rects and ovals
+                            //to offscreen image on the MAC
+                            g.fillRoundRect(lastSSX, y + 4 + iconOffset,
+                                            (x*av.charWidth) - lastSSX, 7, 8, 8);
                             break;
+                          }
+
+                          int sCol = (lastSSX / av.charWidth) + startRes;
+                          int x1 = lastSSX;
+                          int x2 = (x*av.charWidth);
+
+                         if(sCol==0 ||
+                            row.annotations[sCol-1]==null ||
+                            row.annotations[sCol-1].secondaryStructure!='H')
+                         {
+                           g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;
+                           x1 += av.charWidth/2;
+                         }
+
+                          if(row.annotations[column]==null ||
+                             row.annotations[column].secondaryStructure!='H')
+                          {
+                            g.fillArc((x*av.charWidth)-av.charWidth,
+                                      y+4+iconOffset, av.charWidth, 8, 270,180);
+                            x2 -= av.charWidth/2;
+                          }
+
+                          g.fillRect(x1, y+4+iconOffset, x2-x1, 8);
+                              break;
 
                         case 'E':
                             g.setColor(SHEET_COLOUR);
                             g.fillRect(lastSSX, y + 4 + iconOffset,
-                                x - lastSSX - 4, 7);
-                            g.fillPolygon(new int[] { x - 5, x - 5, x },
+                                (x*av.charWidth) - lastSSX - 4, 7);
+                            g.fillPolygon(new int[] { (x*av.charWidth) - 4,
+                                          (x*av.charWidth) - 4,
+                                          (x*av.charWidth) },
                                 new int[]
                                 {
                                     y + iconOffset, y + 14 + iconOffset,
-                                    y + 7 + iconOffset
+                                    y + 8 + iconOffset
                                 }, 3);
 
                             break;
@@ -846,7 +927,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                         default:
                             g.setColor(Color.gray);
                             g.fillRect(lastSSX, y + 6 + iconOffset,
-                                x - lastSSX, 2);
+                                (x*av.charWidth) - lastSSX, 2);
 
                             break;
                         }
@@ -860,22 +941,24 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                             lastSS = ' ';
                         }
 
-                        lastSSX = x;
+                        lastSSX = (x*av.charWidth);
                     }
                 }
 
-                column++;
+
+            column++;
+            x++;
             }
 
             if(column>=row.annotations.length)
-              column = row.annotations.length-1;
+                column = row.annotations.length-1;
 
-            x += av.charWidth;
+          //  x ++;
 
             if (row.hasIcons)
             {
-                switch (lastSS)
-                {
+              switch (lastSS)
+              {
                 case 'H':
                   g.setColor(HELIX_COLOUR);
                   if (MAC)
@@ -883,67 +966,71 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     //Off by 1 offset when drawing rects and ovals
                     //to offscreen image on the MAC
                     g.fillRoundRect(lastSSX, y + 4 + iconOffset,
-                                    x - lastSSX, 7, 8, 8);
+                                    (x*av.charWidth) - lastSSX, 7, 8, 8);
                     break;
                   }
 
-
                   int sCol = (lastSSX / av.charWidth) + startRes;
                   int x1 = lastSSX;
-                  int x2 = x;
-
-                 if(sCol==0 ||
-                    row.annotations[sCol-1]==null ||
-                    row.annotations[sCol-1].secondaryStructure!='H')
-                 {
-                   g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ;
-                   x1 += av.charWidth/2;
-                 }
-
-                  if(row.annotations[column]==null ||
-                     row.annotations[column].secondaryStructure!='H')
+                  int x2 = (x*av.charWidth);
+
+                  if (sCol == 0 ||
+                      row.annotations[sCol - 1] == null ||
+                      row.annotations[sCol - 1].secondaryStructure != 'H')
                   {
-                    g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180);
-                    x2 -= av.charWidth/2;
+                    g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
+                    x1 += av.charWidth / 2;
                   }
 
-                  g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);
-
-                    break;
+                  if (row.annotations[column] == null ||
+                      row.annotations[column].secondaryStructure != 'H')
+                  {
+                    g.fillArc((x*av.charWidth) - av.charWidth,
+                              y + 4 + iconOffset, av.charWidth, 8, 270,
+                              180);
+                    x2 -= av.charWidth / 2;
+                  }
 
-                case 'E':
-                    g.setColor(SHEET_COLOUR);
+                  g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
 
-                    if (row.annotations[endRes] ==null
-                        || row.annotations[endRes].secondaryStructure != 'E')
-                    {
-                      g.fillRect(lastSSX, y + 4 + iconOffset,
-                                 x - lastSSX - 4, 7);
-                      g.fillPolygon(new int[]
-                                    {x - 5, x - 5, x},
-                                    new int[]
-                                    {
-                                    y + iconOffset, y + 14 + iconOffset,
-                                    y + 7 + iconOffset
-                      }, 3);
-                    }
-                    else
-                      g.fillRect(lastSSX, y + 4 + iconOffset,
-                                 x - lastSSX, 7);
+                  break;
 
-                    break;
+                case 'E':
+                  g.setColor(SHEET_COLOUR);
 
+                  if (row.annotations[endRes] == null
+                      || row.annotations[endRes].secondaryStructure != 'E')
+                  {
+                    g.fillRect(lastSSX, y + 4 + iconOffset,
+                               (x*av.charWidth) - lastSSX - 4, 7);
+                    g.fillPolygon(new int[]
+                                  {(x*av.charWidth) - 4,
+                                  (x*av.charWidth) - 4,
+                                 (x*av.charWidth)},
+                                  new int[]
+                                  {
+                                  y + iconOffset, y + 14 + iconOffset,
+                                  y + 7 + iconOffset
+                    }, 3);
+                  }
+                  else
+                   {
+                     g.fillRect(lastSSX, y + 4 + iconOffset,
+                                (x+1) * av.charWidth - lastSSX, 7);
+                   }
+                  break;
 
                 default:
-                    g.setColor(Color.gray);
-                    if(!av.wrapAlignment || endRes==av.endRes)
-                      g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2);
+                  g.setColor(Color.gray);
+                  if(!av.wrapAlignment || endRes==av.endRes)
+                  g.fillRect(lastSSX, y + 6 + iconOffset,
+                             (x*av.charWidth) - lastSSX, 2);
 
-                    break;
-                }
-            }
+                  break;
+              }
+          }
 
-            if (row.graph>0)
+            if (row.graph>0 && row.graphHeight>0)
             {
                 if(row.graph == AlignmentAnnotation.LINE_GRAPH )
                 {
@@ -1017,8 +1104,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       if(sRes==0)
       {
-        sRes++;
-        x+=av.charWidth;
+        x++;
       }
 
       int y1=y, y2=y;
@@ -1033,24 +1119,25 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       eRes = Math.min(eRes, aa.annotations.length);
 
-      int column = sRes;
+      int column;
       int aaMax = aa.annotations.length-1;
 
-      while( column < eRes )
+      while( x < eRes - sRes )
       {
+        column = sRes + x;
         if(av.hasHiddenColumns)
         {
           column = av.getColumnSelection().adjustForHiddenColumns(column);
-          if(column > aaMax)
-          {
-            break;
-          }
+        }
+
+        if (column > aaMax)
+        {
+          break;
         }
 
         if(aa.annotations[column]==null || aa.annotations[column-1]==null)
         {
-          x+=av.charWidth;
-          column ++;
+          x++;
           continue;
         }
 
@@ -1059,12 +1146,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);
           y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);
 
-          g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
-          x += av.charWidth;
-
-          column++;
-
+          g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);
+          x ++;
        }
+
        if(aa.threshold!=null)
        {
            g.setColor(aa.threshold.colour);
@@ -1090,12 +1175,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       eRes = Math.min(eRes, aa.annotations.length);
 
-      int x=0, y1, y2;
+      int x=0, y1=y, y2=y;
 
       float range = max - min;
 
-      y1 = y2 = y;
-
       if(min<0)
         y2 = y - (int)((0-min / (range))*aa.graphHeight);
 
@@ -1103,25 +1186,25 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
 
-
-      int column = sRes;
+      int column;
       int aaMax = aa.annotations.length-1;
 
-      while( column < eRes )
+      while( x < eRes-sRes )
       {
+        column = sRes + x;
         if(av.hasHiddenColumns)
         {
           column = av.getColumnSelection().adjustForHiddenColumns(column);
-          if(column > aaMax)
-          {
+        }
+
+        if(column > aaMax)
+        {
             break;
-          }
         }
 
         if (aa.annotations[column] == null)
         {
-          x += av.charWidth;
-          column ++;
+          x ++;
           continue;
         }
 
@@ -1129,12 +1212,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);
 
           if(y1-y2>0)
-            g.fillRect(x, y2, av.charWidth, y1-y2 );
+            g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );
           else
-            g.fillRect(x, y1, av.charWidth, y2-y1 );
+            g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );
 
-          x += av.charWidth;
-          column ++;
+          x ++ ;
 
       }
       if(aa.threshold!=null)
@@ -1155,6 +1237,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     // used by overview window
     public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
     {
+      eRes = Math.min(eRes, aa.annotations.length);
       g.setColor(Color.white);
       g.fillRect(0, 0, width, y);
       g.setColor(new Color(0, 0, 180));
@@ -1163,13 +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;
       }
     }