2.08, not 2.07

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 67a3eff..fc8f042 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -239,6 +239,7 @@ public class SequenceFetcher
   {\r
     EBIFetchClient ebi = new EBIFetchClient();\r
     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
+   // File file = new File("H:/jalview/classes/fer1.xml");\r
     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
     Vector entries = sff.getUniprotEntries(file);\r
 \r
@@ -249,6 +250,7 @@ public class SequenceFetcher
       while (en.hasMoreElements())\r
       {\r
         UniprotEntry entry = (UniprotEntry) en.nextElement();\r
+\r
         StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
         Enumeration en2 = entry.getAccession().elements();\r
         while (en2.hasMoreElements())\r
@@ -263,8 +265,10 @@ public class SequenceFetcher
           name.append(en2.nextElement());\r
         }\r
 \r
-        if (entry.getProteinName() != null)\r
-          name.append(" " + entry.getProteinName().elementAt(0));\r
+        if (entry.getProtein() != null)\r
+        {\r
+           name.append(" " + entry.getProtein().getName().elementAt(0));\r
+        }\r
 \r
         result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
                       "\n");\r
@@ -293,8 +297,9 @@ public class SequenceFetcher
           e = entry.getFeature().elements();\r
           while (e.hasMoreElements())\r
           {\r
-            sequence[i].getDatasetSequence().addSequenceFeature( (\r
-                SequenceFeature) e.nextElement());\r
+            SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+            sf.setFeatureGroup("Uniprot");\r
+            sequence[i].getDatasetSequence().addSequenceFeature( sf );\r
           }\r
         }\r
       }\r