X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;fp=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=a289dbacf0bd4ef43458f95e1c1ad7357ab6ef41;hb=8f11fde42942229be12283a3b82ac2405dbbdd8f;hp=edb41e6fec14506b051c21a690a027414f25b1a2;hpb=bee4e181ec5e773444de9ac85ef4e9fc6ca99ed6;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index edb41e6..a289dba 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -30,6 +30,7 @@ import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
 
+import java.awt.AlphaComposite;
 import java.awt.BasicStroke;
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -356,16 +357,74 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     // img and call later.
     super.paintComponent(g);
 
+    BufferedImage selectImage = drawSelectionGroup();
+
     if (lcimg != null
             && (fastPaint
                     || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g
                     .getClipBounds().height)))
     {
+      Graphics2D g2 = (Graphics2D) lcimg.getGraphics();
+      g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC));
+      // g.drawImage(lcimg, 0, 0, this);
+
+      // overlay selection group on lcimg
+      if (selectImage != null)
+      {
+        g2.setComposite(
+                AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+        g2.drawImage(selectImage, 0, 0, this);
+      }
       g.drawImage(lcimg, 0, 0, this);
+
       fastPaint = false;
       return;
     }
 
+    lcimg = setupImage(lcimg);
+    // img = lcimg;
+    if (lcimg == null)
+    {
+      return;
+    }
+    
+    if (av.antiAlias)
+    {
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+              RenderingHints.VALUE_ANTIALIAS_ON);
+    }
+    
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
+    
+    ViewportRanges ranges = av.getRanges();
+    if (av.getWrapAlignment())
+    {
+      drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+    }
+    else
+    {
+      drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+              ranges.getStartSeq(), ranges.getEndSeq(), 0);
+    }
+
+    Graphics2D g2 = (Graphics2D) lcimg.getGraphics();
+    // g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC));
+    // g.drawImage(lcimg, 0, 0, this); // scrolling only works with g not g2???
+
+    // overlay selection group on lcimg
+    if (selectImage != null)
+    {
+      g2.setComposite(
+              AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+      g2.drawImage(selectImage, 0, 0, this);
+    }
+    g.drawImage(lcimg, 0, 0, this);
+    // g.drawImage(selectImage, 0, 0, this);
+  }
+
+  private BufferedImage setupImage(BufferedImage lcimg)
+  {
     // this draws the whole of the alignment
     imgWidth = getWidth();
     imgHeight = getHeight();
@@ -375,7 +434,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     if ((imgWidth < 1) || (imgHeight < 1))
     {
-      return;
+      return null;
     }
 
     if (lcimg == null || imgWidth != lcimg.getWidth()
@@ -384,7 +443,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       try
       {
         lcimg = img = new BufferedImage(imgWidth, imgHeight,
-                BufferedImage.TYPE_INT_RGB);
+                BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
         gg = (Graphics2D) img.getGraphics();
         gg.setFont(av.getFont());
       } catch (OutOfMemoryError er)
@@ -393,32 +452,42 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
         new OOMWarning("Creating alignment image for display", er);
 
-        return;
+        return null;
       }
     }
+    return lcimg;
+  }
 
-    if (av.antiAlias)
-    {
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-              RenderingHints.VALUE_ANTIALIAS_ON);
-    }
+  private BufferedImage setupSelectionImage()
+  {
+    BufferedImage lcimg = null;
 
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, imgWidth, imgHeight);
+    int width = getWidth();
+    int height = getHeight();
 
-    ViewportRanges ranges = av.getRanges();
-    if (av.getWrapAlignment())
+    width -= (width % charWidth);
+    height -= (height % charHeight);
+
+    if ((width < 1) || (height < 1))
     {
-      drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+      return null;
     }
-    else
+
+    try
     {
-      drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
-              ranges.getStartSeq(), ranges.getEndSeq(), 0);
-    }
+      lcimg = new BufferedImage(imgWidth, imgHeight,
+              BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+    } catch (OutOfMemoryError er)
+    {
+      System.gc();
+      System.err.println(
+              "Selection Group image OutOfMemory Redraw Error.\n" + er);
+      new OOMWarning("Creating alignment image for display", er);
 
-    g.drawImage(lcimg, 0, 0, this);
+      return null;
+    }
 
+    return lcimg;
   }
 
   /**
@@ -794,7 +863,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     // ///////////////////////////////////
     // Now outline any areas if necessary
     // ///////////////////////////////////
-    SequenceGroup group = av.getSelectionGroup();
+    // SequenceGroup group = av.getSelectionGroup();
+
+    SequenceGroup group = null;
 
     int sx = -1;
     int sy = -1;
@@ -802,7 +873,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int groupIndex = -1;
     int visWidth = (endRes - startRes + 1) * charWidth;
 
-    if ((group == null) && (av.getAlignment().getGroups().size() > 0))
+    // if ((group == null) && (av.getAlignment().getGroups().size() > 0))
+    if (av.getAlignment().getGroups().size() > 0)
     {
       group = av.getAlignment().getGroups().get(0);
       groupIndex = 0;
@@ -854,7 +926,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               oldY = sy;
               inGroup = true;
 
-              if (group == av.getSelectionGroup())
+              /*if (group == av.getSelectionGroup())
               {
                 g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
                         BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f },
@@ -862,10 +934,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
                 g.setColor(Color.RED);
               }
               else
-              {
+              {*/
                 g.setStroke(new BasicStroke());
                 g.setColor(group.getOutlineColour());
-              }
+              // }
             }
           }
           else
@@ -981,6 +1053,156 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
   }
 
+  /*
+   * Draw the selection group as a separate image and overlay
+   */
+  private BufferedImage drawSelectionGroup()
+  {
+    // get a new image of the correct size
+    BufferedImage selectionImage = setupSelectionImage();
+
+    if (selectionImage == null)
+    {
+      return null;
+    }
+
+    SequenceGroup group = av.getSelectionGroup();
+    if (group == null)
+    {
+      // nothing to draw
+      return null;
+    }
+
+    // set up drawing colour
+    Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+    // set background to transparent
+    g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
+    g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
+
+    g.setComposite(AlphaComposite.Src);
+    g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+            BasicStroke.JOIN_ROUND, 3f, new float[]
+    { 5f, 3f }, 0f));
+    g.setColor(Color.RED);
+
+    int visWidth = av.getRanges().getViewportWidth() * charWidth;
+
+    int startRes = av.getRanges().getStartRes();
+
+    // set x start and end positions of group
+    int startx = (group.getStartRes() - startRes) * charWidth;
+    int endx = (group.getEndRes() - startRes + 1) * charWidth;
+
+    int oldY = -1;
+    int i = 0;
+    boolean inGroup = false;
+    int top = -1;
+    int bottom = -1;
+
+    // get sequences to determine y positions of group
+    int startSeq = av.getRanges().getStartSeq();
+    for (i = startSeq; i <= av.getRanges().getEndSeq(); ++i)
+    {
+      int sy = (i - startSeq) * charHeight;
+
+      if (group.getSequences(null)
+              .contains(av.getAlignment().getSequenceAt(i)))
+      {
+        if ((bottom == -1) && !group.getSequences(null)
+                .contains(av.getAlignment().getSequenceAt(i + 1)))
+        {
+          bottom = sy + charHeight;
+        }
+
+        if (!inGroup)
+        {
+          if (((top == -1) && (i == 0)) || !group.getSequences(null)
+                  .contains(av.getAlignment().getSequenceAt(i - 1)))
+          {
+            top = sy;
+          }
+
+          oldY = sy;
+          inGroup = true;
+        }
+      }
+      else
+      {
+        if (inGroup)
+        {
+          // if start position is visible, draw vertical line to left of
+          // group
+          if (startx >= 0 && startx < visWidth * charWidth)
+          {
+            g.drawLine(startx, oldY, startx, sy);
+          }
+
+          // if end position is visible, draw vertical line to right of
+          // group
+          if (endx <= visWidth * charWidth)
+          {
+            g.drawLine(endx, oldY, endx, sy);
+          }
+
+          if (endx > visWidth * charWidth)
+          {
+            endx = visWidth * charWidth;
+          }
+
+          // draw horizontal line at top of group
+          if (top != -1)
+          {
+            g.drawLine(startx, top, endx, top);
+            top = -1;
+          }
+
+          // draw horizontal line at bottom of group
+          if (bottom != -1)
+          {
+            g.drawLine(startx, bottom, endx, bottom);
+            bottom = -1;
+          }
+
+          inGroup = false;
+        }
+      }
+    }
+    if (inGroup)
+    {
+      int sy = (i - startSeq) * charHeight;
+      if (startx >= 0 && startx < visWidth)
+      {
+        g.drawLine(startx, oldY, startx, sy);
+      }
+
+      if (endx < visWidth)
+      {
+        g.drawLine(endx, oldY, endx, sy);
+      }
+
+      if (endx > visWidth)
+      {
+        endx = visWidth;
+      }
+
+      if (top != -1)
+      {
+        g.drawLine(startx, top, endx, top);
+        top = -1;
+      }
+
+      if (bottom != -1)
+      {
+        g.drawLine(startx, bottom - 1, endx, bottom - 1);
+        bottom = -1;
+      }
+
+      inGroup = false;
+    }
+
+    return selectionImage;
+  }
+
   /**
    * DOCUMENT ME!
    *