From 743075ad19dc11ae8456491c51a0c8808b996dc1 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 9 Feb 2010 17:36:37 +0000
Subject: [PATCH] groupURL link preference variables

---
 src/jalview/bin/Cache.java       |    2 ++
 src/jalview/gui/Preferences.java |   18 +++++++++++++++++-
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index caf6bc1..621ded0 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -98,6 +98,8 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
  * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
  * $SEQUENCE_ID$</li>
+ *  <li>GROUP_LINKS list of name|URL[|&lt;separator&gt;] tuples - see jalview.utils.GroupURLLink for more info
+ *  </li>
  * <li>DAS_REGISTRY_URL the registry to query</li>
  * <li>DEFAULT_BROWSER for unix</li>
  * <li>DAS_ACTIVE_SOURCE list of active sources</li>
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index b96fb71..8868832 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -44,6 +44,14 @@ public class Preferences extends GPreferences
    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
    */
   public static Vector sequenceURLLinks;
+  /**
+   * Holds name and link separated with | character. Sequence IDS and Sequences must be
+   * $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$
+   * and separation character for first and second token specified after a pipe character at end |,|.
+   * (TODO: proper escape for using | to separate ids or sequences
+   */
+
+  public static Vector groupURLLinks;
   static
   {
     String string = Cache
@@ -51,7 +59,7 @@ public class Preferences extends GPreferences
                     "SEQUENCE_LINKS",
                     "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
     sequenceURLLinks = new Vector();
-
+    
     try
     {
       StringTokenizer st = new StringTokenizer(string, "|");
@@ -71,6 +79,14 @@ public class Preferences extends GPreferences
     {
       System.out.println(ex + "\nError parsing sequence links");
     }
+    /**
+     * TODO: reformulate groupURL encoding so two or more can be stored in the .properties file as '|' separated strings 
+     */
+    
+    groupURLLinks = new Vector();
+    groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
+    groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
+    
   }
 
   Vector nameLinks, urlLinks;
-- 
1.7.10.2