X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=1658f0f88d1263ad47442d82317914ef9abac389;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=4c2b8b643a7cec6b5af4d6495f44ab760c310c3a;hpb=e327ac5df98f528afeb347ac9a79085ad0d0975b;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 4c2b8b6..1658f0f88 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -32,6 +32,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
@@ -882,48 +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)
@@ -2988,12 +2984,11 @@ public class Jalview2XML
           Features[] features = jseqs[i].getFeatures();
           for (int f = 0; f < features.length; f++)
           {
-            jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
-                    features[f].getType(), features[f].getDescription(),
-                    features[f].getStatus(), features[f].getBegin(),
-                    features[f].getEnd(), features[f].getFeatureGroup());
-
-            sf.setScore(features[f].getScore());
+            SequenceFeature sf = new SequenceFeature(features[f].getType(),
+                    features[f].getDescription(), features[f].getBegin(),
+                    features[f].getEnd(), features[f].getScore(),
+                    features[f].getFeatureGroup());
+            sf.setStatus(features[f].getStatus());
             for (int od = 0; od < features[f].getOtherDataCount(); od++)
             {
               OtherData keyValue = features[f].getOtherData(od);