Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 4f4dcd0..c45feb9 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -20,6 +20,11 @@
  */
 package jalview.gui;
 
+import static jalview.util.UrlConstants.DB_ACCESSION;
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+import static jalview.util.UrlConstants.SRS_STRING;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
@@ -111,10 +116,7 @@ public class Preferences extends GPreferences
   public static List<String> groupURLLinks;
   static
   {
-    String string = Cache
-            .getDefault(
-                    "SEQUENCE_LINKS",
-                    "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+    String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
     sequenceURLLinks = new Vector<String>();
 
     try
@@ -125,7 +127,11 @@ public class Preferences extends GPreferences
         String name = st.nextToken();
         String url = st.nextToken();
         // check for '|' within a regex
-        int rxstart = url.indexOf("$SEQUENCE_ID$");
+        int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
+        if (rxstart == -1)
+        {
+          rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+        }
         while (rxstart == -1 && url.indexOf("/=$") == -1)
         {
           url = url + "|" + st.nextToken();
@@ -138,14 +144,10 @@ public class Preferences extends GPreferences
     }
     {
       // upgrade old SRS link
-      int srsPos = sequenceURLLinks
-              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
       if (srsPos > -1)
       {
-        sequenceURLLinks
-                .setElementAt(
-                        "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                        srsPos);
+        sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
       }
     }
 
@@ -537,8 +539,8 @@ public class Preferences extends GPreferences
     /*
      * Save Output settings
      */
-      Cache.applicationProperties.setProperty("EPS_RENDERING",
-              ((OptionsParam) epsRendering.getSelectedItem()).getCode());
+    Cache.applicationProperties.setProperty("EPS_RENDERING",
+            ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 
     /*
      * Save Connections settings
@@ -566,6 +568,7 @@ public class Preferences extends GPreferences
     else
     {
       Cache.applicationProperties.remove("SEQUENCE_LINKS");
+      sequenceURLLinks.clear();
     }
 
     Cache.applicationProperties.setProperty("USE_PROXY",
@@ -1053,7 +1056,8 @@ public class Preferences extends GPreferences
     }
 
     @Override
-    public int hashCode(){
+    public int hashCode()
+    {
       return name.hashCode() + code.hashCode();
     }
   }