From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 31 Oct 2016 08:14:49 +0000 (+0000)
Subject: Use ACCESSION_ID for database accession id, and SEQUENCE_ID for sequence
X-Git-Tag: Release_2_10_1^2~18^2~2^2~14
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=8abc6bc1d2dac87289bc2658e7c1be352f1deb9f

Use ACCESSION_ID for database accession id, and SEQUENCE_ID for sequence
name.
---

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index b57b951..be0ac05 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -21,7 +21,6 @@
 package jalview.gui;
 
 import static jalview.util.UrlConstants.EMBLEBI_STRING;
-import static jalview.util.UrlConstants.OLD_EMBLEBI_STRING;
 import static jalview.util.UrlConstants.SEQUENCE_ID;
 import static jalview.util.UrlConstants.SEQUENCE_NAME;
 import static jalview.util.UrlConstants.SRS_STRING;
@@ -149,12 +148,6 @@ public class Preferences extends GPreferences
       {
         sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
       }
-      // upgrade old EMBL-EBI link
-      int emblPos = sequenceURLLinks.indexOf(OLD_EMBLEBI_STRING);
-      if (emblPos > -1)
-      {
-        sequenceURLLinks.setElementAt(EMBLEBI_STRING, emblPos);
-      }
     }
 
     /**
diff --git a/src/jalview/util/UrlConstants.java b/src/jalview/util/UrlConstants.java
index ce6d980..b511b8c 100644
--- a/src/jalview/util/UrlConstants.java
+++ b/src/jalview/util/UrlConstants.java
@@ -29,22 +29,17 @@ public class UrlConstants
   /*
    * Sequence ID string
    */
-  public static final String SEQUENCE_ID = "SEQUENCE_ID";
+  public static final String SEQUENCE_ID = "ACCESSION_ID";
 
   /*
    * Sequence Name string
    */
-  public static final String SEQUENCE_NAME = "SEQUENCE_NAME";
+  public static final String SEQUENCE_NAME = "SEQUENCE_ID";
 
   /*
    * Default sequence URL link string for EMBL-EBI search
    */
-  public static final String EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_NAME$";
-
-  /*
-   * Default sequence URL link string for EMBL-EBI search
-   */
-  public static final String OLD_EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
+  public static final String EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
 
   /*
    * Default sequence URL link string for SRS 
diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index b4e8629..9e49828 100644
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+import static jalview.util.UrlConstants.SEQUENCE_NAME;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
@@ -458,11 +460,15 @@ public class PopupMenuTest
     List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
 
     // links as might be added into Preferences | Connections dialog
-    links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_NAME$");
-    links.add("UNIPROT | http://www.uniprot.org/uniprot/$SEQUENCE_ID$");
-    links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$SEQUENCE_ID$");
+    links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+            + SEQUENCE_NAME + "$");
+    links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + SEQUENCE_ID
+            + "$");
+    links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
+            + SEQUENCE_ID + "$");
     // Gene3D entry tests for case (in)sensitivity
-    links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$SEQUENCE_ID$&mode=protein");
+    links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
+            + SEQUENCE_ID + "$&mode=protein");
 
     // make seq0 dbrefs
     refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));