Correct Preferences to check for SEQUENCE_NAME as well as SEQUENCE_ID on

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index b43989a..b57b951 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -21,7 +21,9 @@
 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;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
@@ -126,6 +128,10 @@ public class Preferences extends GPreferences
         String url = st.nextToken();
         // check for '|' within a regex
         int rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+        if (rxstart == -1)
+        {
+          rxstart = url.indexOf("$" + SEQUENCE_NAME + "$");
+        }
         while (rxstart == -1 && url.indexOf("/=$") == -1)
         {
           url = url + "|" + st.nextToken();
@@ -143,6 +149,12 @@ 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);
+      }
     }
 
     /**