JAL-2665 Added hidden columns group selection - almost working

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 06cdec4..8ece1e5 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -517,10 +517,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       if (s != null && !sequences.contains(s))
       {
-        List<SequenceI> before = sequences;
         sequences.add(s);
-        changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
-                sequences);
+        changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+                sequences.size() - 1, sequences.size());
       }
 
       if (recalc)
@@ -715,8 +714,8 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       List<SequenceI> before = sequences;
       sequences.remove(s);
-      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
-              sequences);
+      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+              sequences.size() + 1, sequences.size());
 
       if (recalc)
       {

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 9b6c298..318d74d 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -357,7 +357,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     // selectImage will hold any selection we have
     // lcimg is a local *copy* of img which we'll draw selectImage on top of
 
-    BufferedImage selectImage = drawSelectionGroup();
+    ViewportRanges ranges = av.getRanges();
+    BufferedImage selectImage = drawSelectionGroup(
+            av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+            ranges.getStartSeq(), ranges.getEndSeq());
 
     if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
             || (getVisibleRect().height != g.getClipBounds().height))
@@ -401,7 +404,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     gg.setColor(Color.white);
     gg.fillRect(0, 0, img.getWidth(), img.getHeight());
     
-    ViewportRanges ranges = av.getRanges();
     if (av.getWrapAlignment())
     {
       drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
@@ -1029,12 +1031,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
   }
 
+
   /*
    * Draw the selection group as a separate image and overlay
    */
-  private BufferedImage drawSelectionGroup()
+  private BufferedImage drawSelectionGroup(int startRes, int endRes,
+          int startSeq, int endSeq)
   {
- // get a new image of the correct size
+    // get a new image of the correct size
     BufferedImage selectionImage = setupImage();
 
     if (selectionImage == null)
@@ -1049,6 +1053,84 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       return null;
     }
     
+    // set up drawing colour
+    Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+    g.translate(LABEL_WEST, 0);
+    // 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);
+
+    if (!av.hasHiddenColumns())
+    {
+      drawSelectionGroupPart(g, group, startRes, endRes, startSeq, endSeq);
+    }
+    else
+    {
+      // package into blocks of visible columns
+      // Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+      // Graphics g1 = selectionImage.getGraphics();
+
+      int screenY = 0;
+      int blockStart = startRes;
+      int blockEnd = endRes;
+
+      for (int[] region : av.getAlignment().getHiddenColumns()
+              .getHiddenColumnsCopy())
+      {
+        int hideStart = region[0];
+        int hideEnd = region[1];
+
+        if (hideStart <= blockStart)
+        {
+          blockStart += (hideEnd - hideStart) + 1;
+          continue;
+        }
+
+        blockEnd = hideStart - 1;
+
+        g.translate(screenY * charWidth, 0);
+
+        drawSelectionGroupPart(g, group,
+                blockStart, blockEnd, startSeq, endSeq);
+
+        g.translate(-screenY * charWidth, 0);
+        screenY += blockEnd - blockStart + 1;
+        blockStart = hideEnd + 1;
+
+        if (screenY > (endRes - startRes))
+        {
+          // already rendered last block
+          break;
+        }
+      }
+
+      if (screenY <= (endRes - startRes))
+      {
+        // remaining visible region to render
+        blockEnd = blockStart + (endRes - startRes) - screenY;
+        g.translate(screenY * charWidth, 0);
+        drawSelectionGroupPart(g, group,
+                blockStart, blockEnd, startSeq, endSeq);
+
+        g.translate(-screenY * charWidth, 0);
+      }
+    }
+    g.translate(-LABEL_WEST, 0);
+    return selectionImage;
+  }
+
+  /*
+   * Draw the selection group as a separate image and overlay
+   */
+  private void drawSelectionGroupPart(Graphics2D g, SequenceGroup group,
+          int startRes, int endRes, int startSeq, int endSeq)
+  {
     // set up values in case the alignment is wrapped
     int verticalOffset = 0;
     int horizontalOffset = 0;
@@ -1075,23 +1157,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       horizontalOffset = (slice * cWidth);
     }
 
-    // set up drawing colour
-    Graphics2D g = (Graphics2D) selectionImage.getGraphics();
-    g.translate(LABEL_WEST, 0);
-    // 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 - horizontalOffset)
             * charWidth;
@@ -1105,8 +1172,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int bottom = -1;
 
     // get sequences to determine y positions of group
-    int startSeq = av.getRanges().getStartSeq();
-    for (i = startSeq; i <= av.getRanges().getEndSeq(); ++i)
+    for (i = startSeq; i <= endSeq; ++i)
     {
       int sy = verticalOffset + (i - startSeq) * charHeight;
 
@@ -1204,8 +1270,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       inGroup = false;
     }
-    g.translate(-LABEL_WEST, 0);
-    return selectionImage;
   }
 
   /**