From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 5 Jun 2017 08:41:02 +0000 (+0100)
Subject: JAL-2505 explicit (and final) contactFeature property
X-Git-Tag: Release_2_10_3b1~213
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4e77a2d1581819e35ba9e186324c522f1e4b0a25;p=jalview.git

JAL-2505 explicit (and final) contactFeature property
---

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 045bbbd..25dfc40 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -58,9 +58,9 @@ public class SequenceFeature implements FeatureLocationI
   private static final String ATTRIBUTES = "ATTRIBUTES";
 
   /*
-   * type, begin, end, featureGroup are final to ensure that
-   * the integrity of SequenceFeatures data store can't be
-   * broken by direct update of these fields
+   * type, begin, end, featureGroup and contactFeature are final 
+   * to ensure that the integrity of SequenceFeatures data store 
+   * can't be broken by direct update of these fields
    */
   public final String type;
 
@@ -72,6 +72,8 @@ public class SequenceFeature implements FeatureLocationI
 
   public final float score;
 
+  private final boolean contactFeature;
+
   public String description;
 
   /*
@@ -107,12 +109,7 @@ public class SequenceFeature implements FeatureLocationI
   public SequenceFeature(String theType, String theDesc, int theBegin,
           int theEnd, String group)
   {
-    this.type = theType;
-    this.description = theDesc;
-    this.begin = theBegin;
-    this.end = theEnd;
-    this.featureGroup = group;
-    this.score = NO_SCORE;
+    this(theType, theDesc, theBegin, theEnd, NO_SCORE, group);
   }
 
   /**
@@ -134,6 +131,12 @@ public class SequenceFeature implements FeatureLocationI
     this.end = theEnd;
     this.featureGroup = group;
     this.score = theScore;
+
+    /*
+     * for now, only "Disulfide/disulphide bond" is treated as a contact feature
+     */
+    this.contactFeature = "disulfide bond".equalsIgnoreCase(type)
+            || "disulphide bond".equalsIgnoreCase(type);
   }
 
   /**
@@ -504,13 +507,7 @@ public class SequenceFeature implements FeatureLocationI
   @Override
   public boolean isContactFeature()
   {
-    // TODO abstract one day to a FeatureType class
-    if ("disulfide bond".equalsIgnoreCase(type)
-            || "disulphide bond".equalsIgnoreCase(type))
-    {
-      return true;
-    }
-    return false;
+    return contactFeature;
   }
 
   /**