From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 13 Nov 2017 18:57:10 +0000 (+0000)
Subject: JAL-2758 remove configurable behaviour - Uniprot sequences are only assigned IDs... 
X-Git-Tag: Release_2_10_3b1~35^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b5fb170aae86089a49a0529dbb4c04bf36e0499b;p=jalview.git

JAL-2758 remove configurable behaviour - Uniprot sequences are only assigned IDs derived from Entry name
---

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 94bc582..73775cf 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -60,11 +60,6 @@ public class Uniprot extends DbSourceProxyImpl
   private static Mapping map;
 
   /**
-   * configurable parameter controlling prefixing of entry names with accessions
-   */
-  private boolean includeAllIds = false;
-
-  /**
    * Constructor
    */
   public Uniprot()
@@ -208,7 +203,7 @@ public class Uniprot extends DbSourceProxyImpl
    */
   public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
   {
-    String id = getUniprotEntryId(entry, includeAllIds);
+    String id = getUniprotEntryId(entry);
     SequenceI sequence = new Sequence(id,
             entry.getUniprotSequence().getContent());
     sequence.setDescription(getUniprotEntryDescription(entry));
@@ -318,21 +313,9 @@ public class Uniprot extends DbSourceProxyImpl
    *          UniprotEntry
    * @return The accession id(s) and name(s) delimited by '|'.
    */
-  public static String getUniprotEntryId(UniprotEntry entry,
-          boolean includeAllIds)
+  public static String getUniprotEntryId(UniprotEntry entry)
   {
     StringBuilder name = new StringBuilder(32);
-    if (includeAllIds)
-    {
-      // // use 'canonicalised' name for optimal id matching
-      name.append(DBRefSource.UNIPROT);
-      for (String accessionId : entry.getAccession())
-      {
-        name.append(BAR_DELIMITER);
-        name.append(accessionId);
-      }
-
-    }
     for (String n : entry.getName())
     {
       if (name.length() > 0)