JAL-2366 updated default URL to www.jalview.org/services/identifiers

[jalview.git] / src / jalview / bin / Cache.java

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index fe21406..9edd712 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -123,6 +123,10 @@ import org.apache.log4j.SimpleLayout;
  * <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>STORED_LINKS list of name|url pairs which user has entered but are not
+ * currently used
+ * <li>DEFAULT_LINK name of single url to be used when user double clicks a
+ * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
  * <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>
@@ -180,6 +184,8 @@ import org.apache.log4j.SimpleLayout;
  * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
  * display</li>
  * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
+ * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
+ * </li>
  * 
  * </ul>
  * Deprecated settings:
@@ -237,9 +243,7 @@ public class Cache
    * Identifiers.org download settings
    */
   private static final String ID_ORG_FILE = System.getProperty("user.home")
-          + File.separatorChar + ".jalview_identifiers";
-
-  private static final String ID_ORG_URL = "http://identifiers.org/rest/collections/";
+          + File.separatorChar + ".identifiers.org.ids.json";
 
   /**
    * Allowed values are PDB or mmCIF
@@ -452,7 +456,8 @@ public class Cache
             "sifts_cache_threshold_in_days",
             DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
-    IdOrgSettings.setUrl(ID_ORG_URL);
+    IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
+            "http://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
     System.out