From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 17 Nov 2016 11:02:34 +0000 (+0000)
Subject: JAL-2327 add isContactFeature
X-Git-Tag: Release_2_10_1~10^2~1^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4c4998c1524e4d567720c42ca41adbfe74d60d90;p=jalview.git

JAL-2327 add isContactFeature
---

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 0baa78e..15f54b9 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -532,4 +532,20 @@ public class SequenceFeature
     return s.hashCode() + getBegin() + getEnd() + (int) getScore()
             + getStrand();
   }
+
+  /**
+   * Answers true if the feature's start/end values represent two related
+   * positions, rather than ends of a range. Such features may be visualised or
+   * reported differently to features on a range.
+   */
+  public boolean isContactFeature()
+  {
+    // TODO abstract one day to a FeatureType class
+    if ("disulfide bond".equalsIgnoreCase(type)
+            || "disulphide bond".equalsIgnoreCase(type))
+    {
+      return true;
+    }
+    return false;
+  }
 }
diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index 5150337..23812ea 100644
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -197,4 +197,24 @@ public class SequenceFeatureTest
     sf1.setStatus("new");
     assertTrue(sf1.equals(sf2));
   }
+
+  @Test(groups = { "Functional" })
+  public void testIsContactFeature()
+  {
+    SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+            "group");
+    assertFalse(sf.isContactFeature());
+    sf.setType("");
+    assertFalse(sf.isContactFeature());
+    sf.setType(null);
+    assertFalse(sf.isContactFeature());
+    sf.setType("Disulfide Bond");
+    assertTrue(sf.isContactFeature());
+    sf.setType("disulfide bond");
+    assertTrue(sf.isContactFeature());
+    sf.setType("Disulphide Bond");
+    assertTrue(sf.isContactFeature());
+    sf.setType("disulphide bond");
+    assertTrue(sf.isContactFeature());
+  }
 }