From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 31 May 2017 08:00:46 +0000 (+0100)
Subject: JAL-2547 handle contact features 'around' a gap correctly
X-Git-Tag: Release_2_10_3b1~222^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=dec3f30e62e66366d1f697157201c95b50a5e395

JAL-2547 handle contact features 'around' a gap correctly
---

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index f0ec51c..4aa205e 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -909,7 +909,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   /**
    * Removes from the list of features any that start after, or end before, the
    * given column position. This allows us to retain only those features
-   * adjacent to a gapped position that straddle the position.
+   * adjacent to a gapped position that straddle the position. Contact features
+   * that 'straddle' the position are also removed, since they are not 'at' the
+   * position.
    * 
    * @param features
    * @param column
@@ -924,7 +926,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     while (it.hasNext())
     {
       SequenceFeature sf = it.next();
-      if (sequence.findIndex(sf.getBegin()) > column
+      if (sf.isContactFeature()
+              || sequence.findIndex(sf.getBegin()) > column
               || sequence.findIndex(sf.getEnd()) < column)
       {
         it.remove();
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 6773611..ef9d8b3 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -804,7 +804,9 @@ public class SeqPanel extends JPanel implements MouseListener,
   /**
    * Removes from the list of features any that start after, or end before, the
    * given column position. This allows us to retain only those features
-   * adjacent to a gapped position that straddle the position.
+   * adjacent to a gapped position that straddle the position. Contact features
+   * that 'straddle' the position are also removed, since they are not 'at' the
+   * position.
    * 
    * @param features
    * @param column
@@ -819,7 +821,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     while (it.hasNext())
     {
       SequenceFeature sf = it.next();
-      if (sequence.findIndex(sf.getBegin()) > column
+      if (sf.isContactFeature()
+              || sequence.findIndex(sf.getBegin()) > column
               || sequence.findIndex(sf.getEnd()) < column)
       {
         it.remove();