X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=ba7412c7f132045e9c01c20687d37e58d69c45be;hb=6ec47c00025dbeb48dba5f5db77754ec50b7a6b5;hp=627e1ae35b3f533860f056e828bf1514eb364ff5;hpb=398491c5f9629ead21e1d1bf975c8372a84c6ebf;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 627e1ae..ba7412c 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -24,6 +24,7 @@ import jalview.datamodel.features.FeatureLocationI;
 
 import java.util.HashMap;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Vector;
 
 /**
@@ -34,6 +35,12 @@ import java.util.Vector;
  */
 public class SequenceFeature implements FeatureLocationI
 {
+  /*
+   * score value if none is set; preferably Float.Nan, but see
+   * JAL-2060 and JAL-2554 for a couple of blockers to that
+   */
+  private static final float NO_SCORE = 0f;
+
   private static final String STATUS = "status";
 
   private static final String STRAND = "STRAND";
@@ -51,9 +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, 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;
 
@@ -63,7 +70,9 @@ public class SequenceFeature implements FeatureLocationI
 
   public final String featureGroup;
 
-  public float score;
+  public final float score;
+
+  private final boolean contactFeature;
 
   public String description;
 
@@ -84,114 +93,99 @@ public class SequenceFeature implements FeatureLocationI
    */
   public SequenceFeature(SequenceFeature cpy)
   {
-    this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup());
-
-    score = cpy.score;
-    description = cpy.description;
-    if (cpy.otherDetails != null)
-    {
-      try
-      {
-        otherDetails = (Map<String, Object>) ((HashMap<String, Object>) cpy.otherDetails)
-                .clone();
-      } catch (Exception e)
-      {
-        // ignore
-      }
-    }
-    if (cpy.links != null && cpy.links.size() > 0)
-    {
-      links = new Vector<String>();
-      for (int i = 0, iSize = cpy.links.size(); i < iSize; i++)
-      {
-        links.addElement(cpy.links.elementAt(i));
-      }
-    }
-  }
-
-  /**
-   * Constructor including a Status value
-   * 
-   * @param type
-   * @param desc
-   * @param status
-   * @param begin
-   * @param end
-   * @param featureGroup
-   */
-  public SequenceFeature(String type, String desc, String status,
-          int begin, int end, String featureGroup)
-  {
-    this(type, desc, begin, end, featureGroup);
-    setStatus(status);
+    this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy
+            .getScore());
   }
 
   /**
    * Constructor
    * 
-   * @param type
-   * @param desc
-   * @param begin
-   * @param end
-   * @param featureGroup
+   * @param theType
+   * @param theDesc
+   * @param theBegin
+   * @param theEnd
+   * @param group
    */
-  SequenceFeature(String type, String desc, int begin, int end,
-          String featureGroup)
+  public SequenceFeature(String theType, String theDesc, int theBegin,
+          int theEnd, String group)
   {
-    this.type = type;
-    this.description = desc;
-    this.begin = begin;
-    this.end = end;
-    this.featureGroup = featureGroup;
+    this(theType, theDesc, theBegin, theEnd, NO_SCORE, group);
   }
 
   /**
    * Constructor including a score value
    * 
-   * @param type
-   * @param desc
-   * @param begin
-   * @param end
-   * @param score
-   * @param featureGroup
+   * @param theType
+   * @param theDesc
+   * @param theBegin
+   * @param theEnd
+   * @param theScore
+   * @param group
    */
-  public SequenceFeature(String type, String desc, int begin, int end,
-          float score, String featureGroup)
+  public SequenceFeature(String theType, String theDesc, int theBegin,
+          int theEnd, float theScore, String group)
   {
-    this(type, desc, begin, end, featureGroup);
-    this.score = score;
+    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);
+    this(newType, sf.getDescription(), newBegin, newEnd, newScore,
+            newGroup);
+
+    if (sf.otherDetails != null)
+    {
+      otherDetails = new HashMap<String, Object>();
+      for (Entry<String, Object> entry : sf.otherDetails.entrySet())
+      {
+        otherDetails.put(entry.getKey(), entry.getValue());
+      }
+    }
+    if (sf.links != null && sf.links.size() > 0)
+    {
+      links = new Vector<String>();
+      for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
+      {
+        links.addElement(sf.links.elementAt(i));
+      }
+    }
   }
 
   /**
-   * 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);
   }
 
   /**
@@ -352,11 +346,6 @@ 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
@@ -534,13 +523,7 @@ 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;
   }
 
   /**