Merge branch 'develop' into bug/JAL-1608createGroups

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

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 9363c23..da3cb92 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,9 +22,11 @@ package jalview.bin;
 
 import jalview.datamodel.PDBEntry;
 import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
 import jalview.util.ColorUtils;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
@@ -127,6 +129,10 @@ 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>
@@ -184,6 +190,8 @@ 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:
@@ -225,6 +233,9 @@ public class Cache
 
   public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
 
+  /**
+   * Sifts settings
+   */
   public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
           .getProperty("user.home")
           + File.separatorChar
@@ -235,6 +246,12 @@ public class Cache
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
 
   /**
+   * Identifiers.org download settings
+   */
+  private static final String ID_ORG_FILE = System.getProperty("user.home")
+          + File.separatorChar + ".identifiers.org.ids.json";
+
+  /**
    * Allowed values are PDB or mmCIF
    */
   private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
@@ -445,6 +462,10 @@ public class Cache
             "sifts_cache_threshold_in_days",
             DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
+    IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
+            "http://www.jalview.org/services/identifiers"));
+    IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
+
     System.out
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
@@ -1017,7 +1038,7 @@ public class Cache
       String file = st.nextToken();
       try
       {
-        UserColourScheme ucs = ColourSchemes.loadColourScheme(file);
+        UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
         if (ucs != null)
         {
           if (coloursFound.length() > 0)