From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 28 Aug 2017 10:56:33 +0000 (+0100)
Subject: JAL-2665 Changes for review comments; printing with selgroup working
X-Git-Tag: Release_2_10_3b1~140^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fbug%2FJAL-2665;p=jalview.git

JAL-2665 Changes for review comments; printing with selgroup working
---

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 8ece1e5..c060ef0 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -712,7 +712,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
-      List<SequenceI> before = sequences;
       sequences.remove(s);
       changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
               sequences.size() + 1, sequences.size());
@@ -1375,10 +1374,10 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
-      List<SequenceI> before = sequences;
+      int before = sequences.size();
       sequences.clear();
       changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
-              sequences);
+              sequences.size());
     }
   }
 
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index e62707f..c4eb26a 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1107,8 +1107,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * single graphics context), then reset to (0, scale height)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
-    getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
-            startSeq, endSeq, 0);
+    getSeqPanel().seqCanvas.drawPanelForPrint(alignmentGraphics, startRes,
+            endRes, startSeq, endSeq);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index b6153a8..955a9e6 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -371,8 +371,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
             ranges.getStartRes(), ranges.getEndRes(),
             ranges.getStartSeq(), ranges.getEndSeq());
 
-    if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
-            || (getVisibleRect().height != g.getClipBounds().height))
+    if ((img != null) && (fastPaint
+            || (getVisibleRect().width != g.getClipBounds().width)
+            || (getVisibleRect().height != g.getClipBounds().height)))
     {
       BufferedImage lcimg = buildLocalImage(selectImage);
       g.drawImage(lcimg, 0, 0, this);
@@ -419,6 +420,31 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     }
   }
 
+  /**
+   * Draw an alignment panel for printing
+   * 
+   * @param g1
+   *          Graphics object to draw with
+   * @param startRes
+   *          start residue of print area
+   * @param endRes
+   *          end residue of print area
+   * @param startSeq
+   *          start sequence of print area
+   * @param endSeq
+   *          end sequence of print area
+   */
+  public void drawPanelForPrint(Graphics g1, int startRes, int endRes,
+          int startSeq, int endSeq)
+  {
+    BufferedImage selectImage = drawSelectionGroup(startRes, endRes,
+            startSeq, endSeq);
+    drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
+    ((Graphics2D) g1).setComposite(
+            AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+    g1.drawImage(selectImage, 0, 0, this);
+  }
+
   /*
    * Make a local image by combining the cached image img
    * with any selection
@@ -752,23 +778,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     return annotations.adjustPanelHeight();
   }
 
-  /**
-   * DOCUMENT ME!
+  /*
+   * Draw an alignment panel for printing
    * 
    * @param g1
-   *          DOCUMENT ME!
+   *          Graphics object to draw with
    * @param startRes
-   *          DOCUMENT ME!
+   *          start residue of print area
    * @param endRes
-   *          DOCUMENT ME!
+   *          end residue of print area
    * @param startSeq
-   *          DOCUMENT ME!
+   *          start sequence of print area
    * @param endSeq
-   *          DOCUMENT ME!
+   *          end sequence of print area
    * @param offset
-   *          DOCUMENT ME!
+   *          vertical offset
    */
-  public void drawPanel(Graphics g1, int startRes, int endRes,
+  private void drawPanel(Graphics g1, int startRes, int endRes,
           int startSeq, int endSeq, int offset)
   {
     updateViewport();
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 5dbd778..c863117 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1710,40 +1710,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (stretchGroup == null)
     {
-      // Only if left mouse button do we want to change group sizes
-
-      // define a new group here
-      SequenceGroup sg = new SequenceGroup();
-      sg.setStartRes(res);
-      sg.setEndRes(res);
-      sg.addSequence(sequence, false);
-      av.setSelectionGroup(sg);
-      stretchGroup = sg;
-
-      if (av.getConservationSelected())
-      {
-        SliderPanel.setConservationSlider(ap, av.getResidueShading(),
-                ap.getViewName());
-      }
-
-      if (av.getAbovePIDThreshold())
-      {
-        SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
-                ap.getViewName());
-      }
-      // TODO: stretchGroup will always be not null. Is this a merge error ?
-      if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
-      {
-        // Edit end res position of selected group
-        changeEndRes = true;
-      }
-      else if ((stretchGroup != null)
-              && (stretchGroup.getStartRes() == res))
-      {
-        // Edit end res position of selected group
-        changeStartRes = true;
-      }
-      stretchGroup.getWidth();
+      createStretchGroup(res, sequence);
     }
 
     if (stretchGroup != null)
@@ -1754,6 +1721,44 @@ public class SeqPanel extends JPanel implements MouseListener,
     seqCanvas.repaint();
   }
 
+  private void createStretchGroup(int res, SequenceI sequence)
+  {
+    // Only if left mouse button do we want to change group sizes
+    // define a new group here
+    SequenceGroup sg = new SequenceGroup();
+    sg.setStartRes(res);
+    sg.setEndRes(res);
+    sg.addSequence(sequence, false);
+    av.setSelectionGroup(sg);
+    stretchGroup = sg;
+
+    if (av.getConservationSelected())
+    {
+      SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+              ap.getViewName());
+    }
+
+    if (av.getAbovePIDThreshold())
+    {
+      SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+              ap.getViewName());
+    }
+    // TODO: stretchGroup will always be not null. Is this a merge error ?
+    // or is there a threading issue here?
+    if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
+    {
+      // Edit end res position of selected group
+      changeEndRes = true;
+    }
+    else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
+    {
+      // Edit end res position of selected group
+      changeStartRes = true;
+    }
+    stretchGroup.getWidth();
+
+  }
+
   /**
    * Build and show a pop-up menu at the right-click mouse position
    *