JAL-3121 round trip GFF attributes including map-valued attributes

[jalview.git] / src / jalview / datamodel / SequenceFeature.java

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index c8a7def..2dd9cf0 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -28,7 +28,7 @@ import jalview.datamodel.features.FeatureSources;
 import jalview.util.StringUtils;
 
 import java.util.Comparator;
-import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.SortedMap;
@@ -50,10 +50,10 @@ public class SequenceFeature implements FeatureLocationI
 
   private static final String STATUS = "status";
 
-  private static final String STRAND = "STRAND";
+  public static final String STRAND = "STRAND";
 
-  // private key for Phase designed not to conflict with real GFF data
-  private static final String PHASE = "!Phase";
+  // key for Phase designed not to conflict with real GFF data
+  public static final String PHASE = "!Phase";
 
   // private key for ENA location designed not to conflict with real GFF data
   private static final String LOCATION = "!Location";
@@ -61,12 +61,6 @@ public class SequenceFeature implements FeatureLocationI
   private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td><td>%s</td></tr>";
 
   /*
-   * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
-   * name1=value1;name2=value2,value3;...etc
-   */
-  private static final String ATTRIBUTES = "ATTRIBUTES";
-
-  /*
    * 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
@@ -174,19 +168,13 @@ public class SequenceFeature implements FeatureLocationI
 
     if (sf.otherDetails != null)
     {
-      otherDetails = new HashMap<>();
-      for (Entry<String, Object> entry : sf.otherDetails.entrySet())
-      {
-        otherDetails.put(entry.getKey(), entry.getValue());
-      }
+      otherDetails = new LinkedHashMap<>();
+      otherDetails.putAll(sf.otherDetails);
     }
     if (sf.links != null && sf.links.size() > 0)
     {
       links = new Vector<>();
-      for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
-      {
-        links.addElement(sf.links.elementAt(i));
-      }
+      links.addAll(sf.links);
     }
   }
 
@@ -440,7 +428,10 @@ public class SequenceFeature implements FeatureLocationI
     {
       if (otherDetails == null)
       {
-        otherDetails = new HashMap<>();
+        /*
+         * LinkedHashMap preserves insertion order of attributes
+         */
+        otherDetails = new LinkedHashMap<>();
       }
 
       otherDetails.put(key, value);
@@ -483,16 +474,6 @@ public class SequenceFeature implements FeatureLocationI
     return (String) getValue(STATUS);
   }
 
-  public void setAttributes(String attr)
-  {
-    setValue(ATTRIBUTES, attr);
-  }
-
-  public String getAttributes()
-  {
-    return (String) getValue(ATTRIBUTES);
-  }
-
   /**
    * Return 1 for forward strand ('+' in GFF), -1 for reverse strand ('-' in
    * GFF), and 0 for unknown or not (validly) specified
@@ -643,10 +624,6 @@ public class SequenceFeature implements FeatureLocationI
       for (Entry<String, Object> entry : ordered.entrySet())
       {
         String key = entry.getKey();
-        if (ATTRIBUTES.equals(key))
-        {
-          continue; // to avoid double reporting
-        }
 
         Object value = entry.getValue();
         if (value instanceof Map<?, ?>)