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 e3282d8..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
@@ -249,7 +250,8 @@ public class SequenceFetcher
       while (en.hasMoreElements())\r
       {\r
         UniprotEntry entry = (UniprotEntry) en.nextElement();\r
-        StringBuffer name = new StringBuffer(">Uniprot/Swiss-Prot");\r
+\r
+        StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
         Enumeration en2 = entry.getAccession().elements();\r
         while (en2.hasMoreElements())\r
         {\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
@@ -288,10 +292,15 @@ public class SequenceFetcher
         }\r
 \r
         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
-        e = entry.getFeature().elements();\r
-        while(e.hasMoreElements())\r
+        if (entry.getFeature() != null)\r
         {\r
-          sequence[i].getDatasetSequence().addSequenceFeature((SequenceFeature)e.nextElement());\r
+          e = entry.getFeature().elements();\r
+          while (e.hasMoreElements())\r
+          {\r
+            SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+            sf.setFeatureGroup("Uniprot");\r
+            sequence[i].getDatasetSequence().addSequenceFeature( sf );\r
+          }\r
         }\r
       }\r
     }\r
@@ -341,7 +350,7 @@ public class SequenceFetcher
 \r
   SequenceI[] parseResult(String result, String title)\r
   {\r
-    String format = IdentifyFile.Identify(result, "Paste");\r
+    String format = new IdentifyFile().Identify(result, "Paste");\r
     SequenceI[] sequences = null;\r
 \r
     if (FormatAdapter.formats.contains(format))\r