Merge branch 'apifix/JAL-1926_JAL-2106' into develop

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

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 10aba00..6f16a6e 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,8 +20,11 @@
  */
 package jalview.bin;
 
+import jalview.datamodel.PDBEntry;
+import jalview.structure.StructureImportSettings;
 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;
@@ -216,17 +219,37 @@ public class Cache
 
   public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
 
+  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";
+  
+  /**
+   * Allowed values are PDB or mmCIF
+   */
+  private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF
+          .toString();
+
+  private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+          .toString();
+
   /**
    * Initialises the Jalview Application Log
    */
   public static Logger log;
 
   /** Jalview Properties */
-  public static Properties applicationProperties = new Properties() {
+  public static Properties applicationProperties = new Properties()
+  {
     // override results in properties output in alphabetical order
     @Override
-    public synchronized Enumeration<Object> keys() {
-        return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+    public synchronized Enumeration<Object> keys()
+    {
+      return Collections.enumeration(new TreeSet<Object>(super.keySet()));
     }
   };
 
@@ -315,9 +338,9 @@ public class Cache
         fis = new FileInputStream(propertiesFile);
       }
       applicationProperties.load(fis);
-      
+
       // remove any old build properties
-      
+
       deleteBuildProperties();
       fis.close();
     } catch (Exception ex)
@@ -391,10 +414,33 @@ 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));
 
     System.out
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
+    StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
+            .getDefault(
+            "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
+    StructureImportSettings
+            .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+                    "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
+    StructureImportSettings.setProcessHETATMs(jalview.bin.Cache.getDefault(
+            "PROCESS_HETATM", false));
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
     if (jnlpVersion == null
@@ -405,6 +451,7 @@ public class Cache
 
       class VersionChecker extends Thread
       {
+        @Override
         public void run()
         {
           String orgtimeout = System
@@ -415,7 +462,7 @@ public class Cache
             System.out.println("# INFO: Setting default net timeout to "
                     + orgtimeout + " seconds.");
           }
-          String jnlpVersion = null;
+          String remoteVersion = null;
           try
           {
             System.setProperty("sun.net.client.defaultConnectTimeout",
@@ -435,20 +482,20 @@ public class Cache
 
               line = line.substring(line.indexOf("value=") + 7);
               line = line.substring(0, line.lastIndexOf("\""));
-              jnlpVersion = line;
+              remoteVersion = line;
               break;
             }
           } catch (Exception ex)
           {
             System.out
-                    .println("Non-fatal exceptions when checking version at www.jalview.org :");
+                    .println("Non-fatal exception when checking version at www.jalview.org :");
             System.out.println(ex);
-            jnlpVersion = getProperty("VERSION");
+            remoteVersion = getProperty("VERSION");
           }
           System.setProperty("sun.net.client.defaultConnectTimeout",
                   orgtimeout);
 
-          setProperty("LATEST_VERSION", jnlpVersion);
+          setProperty("LATEST_VERSION", remoteVersion);
         }
       }
 
@@ -718,21 +765,22 @@ public class Cache
       try
       {
         // Google analytics tracking code for Library Finder
-        tracker = jgoogleanalyticstracker.getConstructor(new Class[]
-        { String.class, String.class, String.class }).newInstance(
-                new Object[]
-                {
-                    "Jalview Desktop",
-                    (vrs = jalview.bin.Cache.getProperty("VERSION")
-                            + "_"
-                            + jalview.bin.Cache.getDefault("BUILD_DATE",
-                                    "unknown")), "UA-9060947-1" });
+        tracker = jgoogleanalyticstracker.getConstructor(
+                new Class[] { String.class, String.class, String.class })
+                .newInstance(
+                        new Object[] {
+                            "Jalview Desktop",
+                            (vrs = jalview.bin.Cache.getProperty("VERSION")
+                                    + "_"
+                                    + jalview.bin.Cache.getDefault(
+                                            "BUILD_DATE", "unknown")),
+                            "UA-9060947-1" });
         jgoogleanalyticstracker.getMethod("trackAsynchronously",
-                new Class[]
-                { trackerfocus }).invoke(tracker, new Object[]
-        { trackerfocus.getConstructor(new Class[]
-        { String.class }).newInstance(new Object[]
-        { "Application Started." }) });
+                new Class[] { trackerfocus }).invoke(
+                tracker,
+                new Object[] { trackerfocus.getConstructor(
+                        new Class[] { String.class }).newInstance(
+                        new Object[] { "Application Started." }) });
       } catch (RuntimeException e)
       {
         re = e;