quick fix for the new uniprot name schema - description line for retrieved uniprot...

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index a889ac9..26e9737 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -40,7 +40,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
     super();\r
     addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);\r
     addDbSourceProperty(DBRefSource.PROTSEQDB);\r
-    addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));\r
+//    addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));\r
   }\r
 \r
   /*\r
@@ -50,7 +50,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    */\r
   public String getAccessionSeparator()\r
   {\r
-    return ";";\r
+    return null; // ";";\r
   }\r
 \r
   /*\r
@@ -123,6 +123,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
       Alignment al=null;\r
       ebi = new EBIFetchClient();\r
       StringBuffer result=new StringBuffer();\r
+      // uniprotxml parameter required since december 2007\r
       File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml", null);\r
       Vector entries = getUniprotEntries(file);\r
 \r
@@ -148,9 +149,12 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
             name.append(en2.nextElement());\r
           }\r
 \r
-          if (entry.getProtein() != null)\r
+          if (entry.getProtein()!=null && entry.getProtein().getName()!=null)\r
           {\r
-            name.append(" " + entry.getProtein().getName().elementAt(0));\r
+              for (int nm=0,nmSize=entry.getProtein().getName().size(); nm<nmSize;nm++)\r
+              {\r
+                name.append(" " + entry.getProtein().getName().elementAt(nm));\r
+              }\r
           }\r
 \r
           result.append(name + "\n"\r