JAL-3053

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

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 9c4087e..f17bd33 100755 (executable)
--- 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;
@@ -157,7 +158,7 @@ public class SequenceFeature implements FeatureLocationI
 
     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());
@@ -165,7 +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));
@@ -332,7 +333,7 @@ public class SequenceFeature implements FeatureLocationI
   {
     if (links == null)
     {
-      links = new Vector<String>();
+      links = new Vector<>();
     }
 
     if (!links.contains(labelLink))
@@ -394,7 +395,7 @@ public class SequenceFeature implements FeatureLocationI
     {
       if (otherDetails == null)
       {
-        otherDetails = new HashMap<String, Object>();
+        otherDetails = new HashMap<>();
       }
 
       otherDetails.put(key, value);
@@ -536,3 +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();
+  }
+}