Merge branch 'patch/JAL-3874_newJmolAndGradleDedup' into develop

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

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 353f449..29f0d84 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -182,8 +182,8 @@ import jalview.ws.sifts.SiftsSettings;
  * when shading by annotation</li>
  * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
  * when shading by annotation</li>
- * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org</li>
  * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
  * alignment figure to accommodate even the longest sequence ID or annotation
  * label.</li>
@@ -370,8 +370,8 @@ public class Cache
   }
 
   /**
-   * Loads properties from the given properties file. Any existing properties
-   * are first cleared.
+   * Loads properties from the given properties file. Any existing properties are
+   * first cleared.
    */
   public static void loadProperties(String propsFile)
   {
@@ -523,7 +523,7 @@ public class Cache
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
     IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
-            "http://www.jalview.org/services/identifiers"));
+            "https://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
@@ -710,11 +710,10 @@ public class Cache
   }
 
   /**
-   * Gets Jalview application property of given key. Returns null if key not
-   * found
+   * Gets Jalview application property of given key. Returns null if key not found
    * 
    * @param key
-   *          Name of property
+   *              Name of property
    * 
    * @return Property value
    */
@@ -730,8 +729,8 @@ public class Cache
   }
 
   /**
-   * These methods are used when checking if the saved preference is different
-   * to the default setting
+   * These methods are used when checking if the saved preference is different to
+   * the default setting
    */
 
   public static boolean getDefault(String property, boolean def)
@@ -764,8 +763,8 @@ public class Cache
   }
 
   /**
-   * Answers the value of the given property, or the supplied default value if
-   * the property is not set
+   * Answers the value of the given property, or the supplied default value if the
+   * property is not set
    */
   public static String getDefault(String property, String def)
   {
@@ -777,9 +776,9 @@ public class Cache
    * Stores property in the file "HOME_DIR/.jalview_properties"
    * 
    * @param key
-   *          Name of object
+   *              Name of object
    * @param obj
-   *          String value of property
+   *              String value of property
    * 
    * @return previous value of property (or null)
    */
@@ -1167,7 +1166,7 @@ public class Cache
    * Loads in user colour schemes from files.
    * 
    * @param files
-   *          a '|'-delimited list of file paths
+   *                a '|'-delimited list of file paths
    */
   public static void initUserColourSchemes(String files)
   {
@@ -1476,8 +1475,8 @@ public class Cache
                   // open Preferences -> Connections
                   String message = MessageManager
                           .getString("label.proxy_password_required");
-                  Preferences.openPreferences(Preferences.CONNECTIONS_TAB,
-                          message);
+                  Preferences.openPreferences(
+                          Preferences.TabRef.CONNECTIONS_TAB, message);
                   Preferences.getInstance()
                           .proxyAuthPasswordCheckHighlight(true, true);
                 }