JAL-2557 removal of Sequence.sequenceFeatures

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d6e0123..877d3c0 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -883,48 +883,43 @@ public class Jalview2XML
 
       // TODO: omit sequence features from each alignment view's XML dump if we
       // are storing dataset
-      if (jds.getSequenceFeatures() != null)
+      List<jalview.datamodel.SequenceFeature> sfs = jds
+              .getSequenceFeatures();
+      for (SequenceFeature sf : sfs)
       {
-        jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
-        int index = 0;
-        while (index < sf.length)
-        {
-          Features features = new Features();
+        Features features = new Features();
 
-          features.setBegin(sf[index].getBegin());
-          features.setEnd(sf[index].getEnd());
-          features.setDescription(sf[index].getDescription());
-          features.setType(sf[index].getType());
-          features.setFeatureGroup(sf[index].getFeatureGroup());
-          features.setScore(sf[index].getScore());
-          if (sf[index].links != null)
+        features.setBegin(sf.getBegin());
+        features.setEnd(sf.getEnd());
+        features.setDescription(sf.getDescription());
+        features.setType(sf.getType());
+        features.setFeatureGroup(sf.getFeatureGroup());
+        features.setScore(sf.getScore());
+        if (sf.links != null)
+        {
+          for (int l = 0; l < sf.links.size(); l++)
           {
-            for (int l = 0; l < sf[index].links.size(); l++)
-            {
-              OtherData keyValue = new OtherData();
-              keyValue.setKey("LINK_" + l);
-              keyValue.setValue(sf[index].links.elementAt(l).toString());
-              features.addOtherData(keyValue);
-            }
+            OtherData keyValue = new OtherData();
+            keyValue.setKey("LINK_" + l);
+            keyValue.setValue(sf.links.elementAt(l).toString());
+            features.addOtherData(keyValue);
           }
-          if (sf[index].otherDetails != null)
+        }
+        if (sf.otherDetails != null)
+        {
+          String key;
+          Iterator<String> keys = sf.otherDetails.keySet().iterator();
+          while (keys.hasNext())
           {
-            String key;
-            Iterator<String> keys = sf[index].otherDetails.keySet()
-                    .iterator();
-            while (keys.hasNext())
-            {
-              key = keys.next();
-              OtherData keyValue = new OtherData();
-              keyValue.setKey(key);
-              keyValue.setValue(sf[index].otherDetails.get(key).toString());
-              features.addOtherData(keyValue);
-            }
+            key = keys.next();
+            OtherData keyValue = new OtherData();
+            keyValue.setKey(key);
+            keyValue.setValue(sf.otherDetails.get(key).toString());
+            features.addOtherData(keyValue);
           }
-
-          jseq.addFeatures(features);
-          index++;
         }
+
+        jseq.addFeatures(features);
       }
 
       if (jdatasq.getAllPDBEntries() != null)