From 095f0d92cb343875bd0f76f833c1eaa8614c22cd Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 21 Nov 2016 11:35:44 +0000
Subject: [PATCH] JAL-2333 corrected select columns with 'contact' feature

---
 src/jalview/controller/AlignViewController.java    |   51 ++++++++++++++------
 .../controller/AlignViewControllerTest.java        |   27 +++++++++++
 2 files changed, 63 insertions(+), 15 deletions(-)

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index f508bc3..806e9a5 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -243,10 +243,6 @@ public class AlignViewController implements AlignViewControllerI
         SequenceFeature[] sfs = sq.getSequenceFeatures();
         if (sfs != null)
         {
-          /*
-           * check whether the feature start/end (base 1) 
-           * overlaps the selection start/end
-           */
           int ist = sq.findIndex(sq.getStart());
           int iend = sq.findIndex(sq.getEnd());
           if (iend < startPosition || ist > endPosition)
@@ -264,29 +260,54 @@ public class AlignViewController implements AlignViewControllerI
               // - findIndex wastes time by starting from first character and
               // counting
 
-              int i = sq.findIndex(sf.getBegin());
-              int j = sq.findIndex(sf.getEnd());
-              if (j < startPosition || i > endPosition)
+              int sfStartCol = sq.findIndex(sf.getBegin());
+              int sfEndCol = sq.findIndex(sf.getEnd());
+
+              if (sf.isContactFeature())
+              {
+                /*
+                 * 'contact' feature - check for 'start' or 'end'
+                 * position within the selected region
+                 */
+                if (sfStartCol >= startPosition
+                        && sfStartCol <= endPosition)
+                {
+                  bs.set(sfStartCol - 1);
+                  sequenceHasFeature = true;
+                }
+                if (sfEndCol >= startPosition && sfEndCol <= endPosition)
+                {
+                  bs.set(sfEndCol - 1);
+                  sequenceHasFeature = true;
+                }
+                continue;
+              }
+
+              /*
+               * contiguous feature - select feature positions (if any) 
+               * within the selected region
+               */
+              if (sfStartCol > endPosition || sfEndCol < startPosition)
               {
                 // feature is outside selected region
                 continue;
               }
               sequenceHasFeature = true;
-              if (i < startPosition)
+              if (sfStartCol < startPosition)
               {
-                i = startPosition;
+                sfStartCol = startPosition;
               }
-              if (i < ist)
+              if (sfStartCol < ist)
               {
-                i = ist;
+                sfStartCol = ist;
               }
-              if (j > endPosition)
+              if (sfEndCol > endPosition)
               {
-                j = endPosition;
+                sfEndCol = endPosition;
               }
-              for (; i <= j; i++)
+              for (; sfStartCol <= sfEndCol; sfStartCol++)
               {
-                bs.set(i - 1); // convert to base 0
+                bs.set(sfStartCol - 1); // convert to base 0
               }
             }
           }
diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index 7fd8965..d7f7acb 100644
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -53,6 +53,9 @@ public class AlignViewControllerTest
             null));
     seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
             0f, null));
+    // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
+    seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", 8, 12,
+            0f, null));
 
     /*
      * select the first three columns --> Metal in seq1 2-3
@@ -107,6 +110,30 @@ public class AlignViewControllerTest
     assertEquals(0, bs.cardinality());
 
     /*
+     * columns 9-11 should not match disulfide bond at 8/12
+     */
+    sg.setStartRes(8);
+    sg.setEndRes(10);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
+            sg, bs);
+    assertEquals(0, seqCount);
+    assertEquals(0, bs.cardinality());
+
+    /*
+     * columns 6-14 should match disulfide bond at 8/12
+     */
+    sg.setStartRes(5);
+    sg.setEndRes(13);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
+            sg, bs);
+    assertEquals(1, seqCount);
+    assertEquals(2, bs.cardinality());
+    assertTrue(bs.get(7));
+    assertTrue(bs.get(11));
+
+    /*
      * look for a feature that isn't there
      */
     sg.setStartRes(0);
-- 
1.7.10.2