X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=9edd712df33ea193226a0f5778ef6c8be14e245a;hb=9d7c487b4a2774d380d0807527e365e9002a1fd5;hp=a7c002c85a315726cc993ae61dab38a1057a23d8;hpb=1e085f14ae2f19adfac0153c437ee891f0ad07bc;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index a7c002c..9edd712 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,8 +20,12 @@
  */
 package jalview.bin;
 
+import jalview.datamodel.PDBEntry;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.Color;
 import java.io.BufferedReader;
@@ -35,6 +39,7 @@ import java.text.SimpleDateFormat;
 import java.util.Collections;
 import java.util.Date;
 import java.util.Enumeration;
+import java.util.Locale;
 import java.util.Properties;
 import java.util.TreeSet;
 
@@ -118,6 +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>
@@ -175,6 +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:
@@ -217,6 +228,42 @@ 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
+          + ".sifts_downloads" + File.separatorChar;
+
+  private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
+
+  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
+          .toString();
+
+  private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+          .toString();
+
+  /*
+   * a date formatter using a fixed (rather than the user's) locale; 
+   * this ensures that date properties can be written and re-read successfully
+   * even if the user changes their locale setting
+   */
+  private static final DateFormat date_format = SimpleDateFormat
+          .getDateTimeInstance(SimpleDateFormat.MEDIUM,
+                  SimpleDateFormat.MEDIUM, Locale.UK);
+
+  /**
    * Initialises the Jalview Application Log
    */
   public static Logger log;
@@ -394,9 +441,35 @@ public class Cache
       codeInstallation = " (" + codeInstallation + ")";
     }
     new BuildDetails(codeVersion, null, codeInstallation);
+
+    SiftsSettings
+            .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+
+    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
+            "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+
+    SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault(
+            "sifts_fail_safe_pid_threshold",
+            DEFAULT_FAIL_SAFE_PID_THRESHOLD));
+
+    SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault(
+            "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);
 
+    StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
+            .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+    StructureImportSettings
+            .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+    // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
     if (jnlpVersion == null
@@ -407,6 +480,7 @@ public class Cache
 
       class VersionChecker extends Thread
       {
+        @Override
         public void run()
         {
           String orgtimeout = System
@@ -842,30 +916,31 @@ public class Cache
     setProperty(property, jalview.util.Format.getHexString(colour));
   }
 
-  public static final DateFormat date_format = SimpleDateFormat
-          .getDateTimeInstance();
-
   /**
-   * store a date in a jalview property
+   * Stores a formatted date in a jalview property, using a fixed locale.
    * 
-   * @param string
-   * @param time
+   * @param propertyName
+   * @param date
+   * @return the formatted date string
    */
-  public static void setDateProperty(String property, Date time)
+  public static String setDateProperty(String propertyName, Date date)
   {
-    setProperty(property, date_format.format(time));
+    String formatted = date_format.format(date);
+    setProperty(propertyName, formatted);
+    return formatted;
   }
 
   /**
-   * read a date stored in a jalview property
+   * Reads a date stored in a Jalview property, parses it (using a fixed locale
+   * format) and returns as a Date, or null if parsing fails
    * 
-   * @param property
-   * @return valid date as stored by setDateProperty, or null
+   * @param propertyName
+   * @return
    * 
    */
-  public static Date getDateProperty(String property)
+  public static Date getDateProperty(String propertyName)
   {
-    String val = getProperty(property);
+    String val = getProperty(propertyName);
     if (val != null)
     {
       try
@@ -874,7 +949,7 @@ public class Cache
       } catch (Exception ex)
       {
         System.err.println("Invalid or corrupt date in property '"
-                + property + "' : value was '" + val + "'");
+                + propertyName + "' : value was '" + val + "'");
       }
     }
     return null;