From daf0320a63cf578d009076b2c3c3c788f7c153af Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 29 Aug 2017 09:40:08 +0100
Subject: [PATCH] JAL-2665 ported fix to 2.10.3. Doesn't work.

---
 src/jalview/gui/AlignmentPanel.java |    5 +--
 src/jalview/gui/SeqCanvas.java      |   64 ++++++++++++++++++++++++++++-------
 2 files changed, 55 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index b45ddef..49750a8 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1100,7 +1100,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * single graphics context), then reset to (0, scale height)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
-    getSeqPanel().seqCanvas.drawPanelForPrint(alignmentGraphics, startRes,
+    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
             endRes, startSeq, endSeq);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
@@ -1228,7 +1228,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pg.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg,
+            pwidth - idWidth,
             totalHeight, 0);
 
     if ((pi * pheight) < totalHeight)
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 04ffc09..8004cac 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -426,7 +426,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    * @param endSeq
    *          end sequence of print area
    */
-  public void drawPanelForPrint(Graphics g1, int startRes, int endRes,
+  public void drawPanelForPrinting(Graphics g1, int startRes, int endRes,
           int startSeq, int endSeq)
   {
     BufferedImage selectImage = drawSelectionGroup(startRes, endRes,
@@ -437,6 +437,37 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     g1.drawImage(selectImage, 0, 0, this);
   }
 
+  /**
+   * Draw a wrapped alignment panel for printing
+   * 
+   * @param g
+   *          Graphics object to draw with
+   * @param canvasWidth
+   *          width of drawing area
+   * @param canvasHeight
+   *          height of drawing area
+   * @param startRes
+   *          start residue of print area
+   */
+  public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
+          int canvasHeight, int startRes)
+  {
+    SequenceGroup group = av.getSelectionGroup();
+    BufferedImage selectImage = new BufferedImage(canvasWidth, canvasHeight,
+            BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+
+    if (group != null)
+    {
+      Graphics2D g2 = selectImage.createGraphics();
+      setupSelectionGroup(g2, selectImage);
+      drawWrappedSelection(g2, group, canvasWidth, canvasHeight, startRes);
+      drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
+      g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+      g.drawImage(selectImage, 0, 0, this);
+      g2.dispose();
+    }
+  }
+
   /*
    * Make a local image by combining the cached image img
    * with any selection
@@ -568,7 +599,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    * @param startRes
    *          DOCUMENT ME!
    */
-  public void drawWrappedPanel(Graphics g, int canvasWidth,
+  private void drawWrappedPanel(Graphics g, int canvasWidth,
           int canvasHeight, int startRes)
   {
     updateViewport();
@@ -1022,16 +1053,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     // 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());
-
-    // set up foreground to draw red dashed line
-    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);
+    setupSelectionGroup(g, selectionImage);
 
     if (!av.getWrapAlignment())
     {
@@ -1049,6 +1071,24 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   }
 
   /*
+   * Set up graphics for selection group
+   */
+  private void setupSelectionGroup(Graphics2D g,
+          BufferedImage selectionImage)
+  {
+    // set background to transparent
+    g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
+    g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
+
+    // set up foreground to draw red dashed line
+    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);
+  }
+
+  /*
    * Draw a selection group over an unwrapped alignment
    * @param g graphics object to draw with
    * @param group selection group
-- 
1.7.10.2