From 3dfe7249d7b369536e3e151c7e7b44c0d4d1458e Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 16 Aug 2017 15:51:55 +0100
Subject: [PATCH] JAL-2665 Selecting on wrapped alignments

---
 src/jalview/gui/SeqCanvas.java |   44 ++++++++++++++++++++++++++++------------
 1 file changed, 31 insertions(+), 13 deletions(-)

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 558c1ca..9b6c298 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1034,17 +1034,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    */
   private BufferedImage drawSelectionGroup()
   {
-    int verticalOffset = 0;
-    if (av.getWrapAlignment())
-    {
-      verticalOffset = charHeight;
-      if (av.getScaleAboveWrapped())
-      {
-        verticalOffset += charHeight;
-      }
-    }
-
-    // get a new image of the correct size
+ // get a new image of the correct size
     BufferedImage selectionImage = setupImage();
 
     if (selectionImage == null)
@@ -1058,6 +1048,32 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       // nothing to draw
       return null;
     }
+    
+    // set up values in case the alignment is wrapped
+    int verticalOffset = 0;
+    int horizontalOffset = 0;
+    if (av.getWrapAlignment())
+    {
+      int hgap = charHeight;
+      if (av.getScaleAboveWrapped())
+      {
+        hgap += charHeight;
+      }
+      
+      // get the start res of the group and work out the offsets for it in the wrapped alignment
+      int groupstart = group.getStartRes();
+      int cWidth = (getWidth() - LABEL_EAST - LABEL_WEST) / charWidth;
+      
+      // group is in which slice of alignment? res position / width in residues
+      int slice = groupstart / cWidth;
+      // vertical offset is increased by slice number * number of sequences * height of each sequence
+      verticalOffset = slice * (av.getAlignment().getHeight() * charHeight
+              + getAnnotationHeight() + hgap) + hgap;
+
+      // horizontal offset is number of residues to subtract from group residue
+      // position
+      horizontalOffset = (slice * cWidth);
+    }
 
     // set up drawing colour
     Graphics2D g = (Graphics2D) selectionImage.getGraphics();
@@ -1077,8 +1093,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     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 startx = (group.getStartRes() - startRes - horizontalOffset)
+            * charWidth;
+    int endx = (group.getEndRes() - startRes + 1 - horizontalOffset)
+            * charWidth;
 
     int oldY = -1;
     int i = 0;
-- 
1.7.10.2