From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 10 Apr 2006 11:10:06 +0000 (+0000)
Subject: Fixed protein desc bug
X-Git-Tag: Release_2_08~32
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e651bfd6da43bae19e157d6fdf1efbb484acda76;p=jalview.git

Fixed protein desc bug
---

diff --git a/src/jalview/datamodel/UniprotEntry.java b/src/jalview/datamodel/UniprotEntry.java
index d2f4dcf..dcdaee9 100755
--- a/src/jalview/datamodel/UniprotEntry.java
+++ b/src/jalview/datamodel/UniprotEntry.java
@@ -28,7 +28,7 @@ public class UniprotEntry
   Vector accession;
   Vector feature;
   Vector dbrefs;
-  Vector proteinName;
+  UniprotProteinName protName;
 
   public void setAccession(Vector items)
   {
@@ -50,14 +50,15 @@ public class UniprotEntry
      return accession;
    }
 
-   public void setProteinName(Vector items)
+   public void setProtein(UniprotProteinName names)
    {
-     proteinName = items;
+     protName = names;
    }
 
-   public Vector getProteinName()
+
+   public UniprotProteinName getProtein()
    {
-     return proteinName;
+     return protName;
    }
 
   public void setName(Vector na)
diff --git a/src/jalview/datamodel/UniprotProteinName.java b/src/jalview/datamodel/UniprotProteinName.java
new file mode 100755
index 0000000..5146ab1
--- /dev/null
+++ b/src/jalview/datamodel/UniprotProteinName.java
@@ -0,0 +1,38 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class UniprotProteinName
+{
+    /**
+   * internal content storage
+   */
+  private java.util.Vector names;
+
+  public void setName(java.util.Vector names)
+  {
+    this.names = names;
+  }
+
+  public java.util.Vector getName()
+  {
+    return names;
+  }
+
+}
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 67a3eff..fc8f042 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -239,6 +239,7 @@ public class SequenceFetcher
   {
     EBIFetchClient ebi = new EBIFetchClient();
     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
+   // File file = new File("H:/jalview/classes/fer1.xml");
     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
     Vector entries = sff.getUniprotEntries(file);
 
@@ -249,6 +250,7 @@ public class SequenceFetcher
       while (en.hasMoreElements())
       {
         UniprotEntry entry = (UniprotEntry) en.nextElement();
+
         StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
         Enumeration en2 = entry.getAccession().elements();
         while (en2.hasMoreElements())
@@ -263,8 +265,10 @@ public class SequenceFetcher
           name.append(en2.nextElement());
         }
 
-        if (entry.getProteinName() != null)
-          name.append(" " + entry.getProteinName().elementAt(0));
+        if (entry.getProtein() != null)
+        {
+           name.append(" " + entry.getProtein().getName().elementAt(0));
+        }
 
         result.append(name + "\n" + entry.getUniprotSequence().getContent() +
                       "\n");
@@ -293,8 +297,9 @@ public class SequenceFetcher
           e = entry.getFeature().elements();
           while (e.hasMoreElements())
           {
-            sequence[i].getDatasetSequence().addSequenceFeature( (
-                SequenceFeature) e.nextElement());
+            SequenceFeature sf = (SequenceFeature) e.nextElement();
+            sf.setFeatureGroup("Uniprot");
+            sequence[i].getDatasetSequence().addSequenceFeature( sf );
           }
         }
       }
diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 61b25f9..9bc214f 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -65,16 +65,19 @@ public class SequenceFeatureFetcher implements Runnable
       map.loadMapping(url);
 
       // 2. Unmarshal the data
-      Unmarshaller unmar = new Unmarshaller();
+      Unmarshaller unmar = new Unmarshaller(uni);
       unmar.setIgnoreExtraElements(true);
       unmar.setMapping(map);
-      uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
+   //   unmar.setDebug(true);
 
+      uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
     }
     catch (Exception e)
     {
       System.out.println("Error getUniprotEntries() "+e);
     }
+
+
     return uni.getUniprotEntries();
   }