From ce4840757da155836d19edb70821fce6d2258d88 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 25 May 2017 10:35:08 +0100
Subject: [PATCH] JAL-2505 simplifying number of SequenceFeature constructors
 JAL-2060 constant for NO_SCORE defined in SequenceFeature

---
 src/jalview/datamodel/SequenceFeature.java |  109 ++++++++++++----------------
 1 file changed, 48 insertions(+), 61 deletions(-)

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 627e1ae..4df57ef 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";
@@ -85,81 +92,43 @@ 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);
   }
 
   /**
    * 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.type = theType;
+    this.description = theDesc;
+    this.begin = theBegin;
+    this.end = theEnd;
+    this.featureGroup = group;
+    this.score = NO_SCORE;
   }
 
   /**
    * 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(theType, theDesc, theBegin, theEnd, group);
+    this.score = theScore;
   }
 
   /**
@@ -175,6 +144,24 @@ public class SequenceFeature implements FeatureLocationI
           String newGroup)
   {
     this(sf.getType(), newBegin, newEnd, newGroup);
+    score = sf.score;
+    description = sf.description;
+    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));
+      }
+    }
   }
 
   /**
-- 
1.7.10.2