X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=f17bd3349604541fd923c9da101bf16e77abea80;hb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;hp=4df57ef5fd2588ff7d5810a1e635d568255eb7b2;hpb=ce4840757da155836d19edb70821fce6d2258d88;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 4df57ef..f17bd33 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -22,6 +22,7 @@ package jalview.datamodel;
 
 import jalview.datamodel.features.FeatureLocationI;
 
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Map.Entry;
@@ -58,9 +59,9 @@ 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, score 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;
 
@@ -70,7 +71,9 @@ public class SequenceFeature implements FeatureLocationI
 
   public final String featureGroup;
 
-  public float score;
+  public final float score;
+
+  private final boolean contactFeature;
 
   public String description;
 
@@ -91,7 +94,8 @@ public class SequenceFeature implements FeatureLocationI
    */
   public SequenceFeature(SequenceFeature cpy)
   {
-    this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup());
+    this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy
+            .getScore());
   }
 
   /**
@@ -106,12 +110,7 @@ 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);
   }
 
   /**
@@ -127,28 +126,39 @@ public class SequenceFeature implements FeatureLocationI
   public SequenceFeature(String theType, String theDesc, int theBegin,
           int theEnd, float theScore, String group)
   {
-    this(theType, theDesc, theBegin, theEnd, group);
+    this.type = theType;
+    this.description = theDesc;
+    this.begin = theBegin;
+    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);
   }
 
   /**
-   * A copy constructor that allows the begin and end positions and group to be
-   * modified
+   * A copy constructor that allows the value of final fields to be 'modified'
    * 
    * @param sf
+   * @param newType
    * @param newBegin
    * @param newEnd
    * @param newGroup
+   * @param newScore
    */
-  public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
-          String newGroup)
+  public SequenceFeature(SequenceFeature sf, String newType, int newBegin,
+          int newEnd, String newGroup, float newScore)
   {
-    this(sf.getType(), newBegin, newEnd, newGroup);
-    score = sf.score;
-    description = sf.description;
+    this(newType, sf.getDescription(), newBegin, newEnd, newScore,
+            newGroup);
+
     if (sf.otherDetails != null)
     {
-      otherDetails = new HashMap<String, Object>();
+      otherDetails = new HashMap<>();
       for (Entry<String, Object> entry : sf.otherDetails.entrySet())
       {
         otherDetails.put(entry.getKey(), entry.getValue());
@@ -156,7 +166,7 @@ public class SequenceFeature implements FeatureLocationI
     }
     if (sf.links != null && sf.links.size() > 0)
     {
-      links = new Vector<String>();
+      links = new Vector<>();
       for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
       {
         links.addElement(sf.links.elementAt(i));
@@ -165,20 +175,18 @@ public class SequenceFeature implements FeatureLocationI
   }
 
   /**
-   * Constructor that sets the final fields type, begin, end, group
+   * A copy constructor that allows the value of final fields to be 'modified'
    * 
-   * @param theType
-   * @param theBegin
-   * @param theEnd
-   * @param theGroup
+   * @param sf
+   * @param newBegin
+   * @param newEnd
+   * @param newGroup
+   * @param newScore
    */
-  private SequenceFeature(String theType, int theBegin, int theEnd,
-          String theGroup)
+  public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
+          String newGroup, float newScore)
   {
-    type = theType;
-    begin = theBegin;
-    end = theEnd;
-    featureGroup = theGroup;
+    this(sf, sf.getType(), newBegin, newEnd, newGroup, newScore);
   }
 
   /**
@@ -226,8 +234,8 @@ public class SequenceFeature implements FeatureLocationI
       return false;
     }
 
-    if (!(type + description + featureGroup + getPhase()).equals(sf.type
-            + sf.description + sf.featureGroup + sf.getPhase()))
+    if (!(type + description + featureGroup + getPhase()).equals(
+            sf.type + sf.description + sf.featureGroup + sf.getPhase()))
     {
       return false;
     }
@@ -325,7 +333,7 @@ public class SequenceFeature implements FeatureLocationI
   {
     if (links == null)
     {
-      links = new Vector<String>();
+      links = new Vector<>();
     }
 
     if (!links.contains(labelLink))
@@ -339,11 +347,6 @@ public class SequenceFeature implements FeatureLocationI
     return score;
   }
 
-  public void setScore(float value)
-  {
-    score = value;
-  }
-
   /**
    * Used for getting values which are not in the basic set. eg STRAND, PHASE
    * for GFF file
@@ -392,7 +395,7 @@ public class SequenceFeature implements FeatureLocationI
     {
       if (otherDetails == null)
       {
-        otherDetails = new HashMap<String, Object>();
+        otherDetails = new HashMap<>();
       }
 
       otherDetails.put(key, value);
@@ -521,13 +524,7 @@ 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;
   }
 
   /**
@@ -540,3 +537,21 @@ public class SequenceFeature implements FeatureLocationI
     return begin == 0 && end == 0;
   }
 }
+
+class SFSortByEnd implements Comparator<SequenceFeature>
+{
+  @Override
+  public int compare(SequenceFeature a, SequenceFeature b)
+  {
+    return a.getEnd() - b.getEnd();
+  }
+}
+
+class SFSortByBegin implements Comparator<SequenceFeature>
+{
+  @Override
+  public int compare(SequenceFeature a, SequenceFeature b)
+  {
+    return a.getBegin() - b.getBegin();
+  }
+}