JAL-3253 preliminary static fixes for JavaScript part 3 of 3

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

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index b2f6e95..d7542b8 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -221,36 +221,8 @@ public class Cache
    */
   public static Cache getInstance()
   {
-
-    // BH 2019.05.08 need to isolate static fields in JavaScript
-
-    Cache i = instance;
-    @SuppressWarnings("unused")
-    ThreadGroup g = null;
-    if (Platform.isJS())
-    {
-      g = Thread.currentThread().getThreadGroup();
-      /**
-       * @j2sNative i = g._jalviewCacheInstance;
-       * 
-       */
-    }
-    if (i == null)
-    {
-      i = new Cache();
-      if (Platform.isJS())
-      {
-        /**
-         * @j2sNative g._jalviewCacheInstance = i;
-         * 
-         */
-      }
-      else
-      {
-        instance = i;
-      }
-    }
-    return i;
+    Jalview j = Jalview.getInstance();
+    return (j.cache == null ? j.cache = new Cache() : j.cache);
   }
 
   /**
@@ -358,14 +330,14 @@ public class Cache
       jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
 
       laxis.setLevel(Level.toLevel(
-              Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
-      lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
-              Level.INFO.toString())));
+              getDefault("logs.Axis.Level", Level.INFO.toString())));
+      lcastor.setLevel(Level.toLevel(
+              getDefault("logs.Castor.Level", Level.INFO.toString())));
       lcastor = Logger.getLogger("org.exolab.castor.xml");
-      lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
-              Level.INFO.toString())));
+      lcastor.setLevel(Level.toLevel(
+              getDefault("logs.Castor.Level", Level.INFO.toString())));
       // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
-      // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+      // lcastor.setLevel(Level.toLevel(getDefault("logs.Castor.Level",
       // Level.INFO.toString())));
       jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
               .getDefault("logs.Jalview.level", Level.INFO.toString())));
@@ -528,18 +500,17 @@ public class Cache
     }
     new BuildDetails(codeVersion, null, codeInstallation);
 
-    SiftsSettings
-            .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+    SiftsSettings.setMapWithSifts(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",
+            getDefault("sifts_fail_safe_pid_threshold",
                     DEFAULT_FAIL_SAFE_PID_THRESHOLD));
 
     SiftsSettings.setCacheThresholdInDays(
-            jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+            getDefault("sifts_cache_threshold_in_days",
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
     IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
@@ -554,7 +525,7 @@ public class Cache
     StructureImportSettings
             .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
     // StructureImportSettings
-    // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+    // .setDefaultPDBFileParser(jalview.bin.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
@@ -630,13 +601,9 @@ public class Cache
     setProperty("VERSION", codeVersion);
 
     // LOAD USERDEFINED COLOURS
-    jalview.bin.Cache
-            .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
-    jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
-            false);
+    initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
   }
 
-
   private void deleteBuildProperties()
   {
     applicationProperties.remove("LATEST_VERSION");
@@ -947,8 +914,7 @@ public class Cache
                 .newInstance(new Object[]
                 { "Jalview Desktop",
                     (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
-                            + jalview.bin.Cache.getDefault("BUILD_DATE",
-                                    "unknown")),
+                            + getDefault("BUILD_DATE", "unknown")),
                     "UA-9060947-1" });
         jgoogleanalyticstracker
                 .getMethod("trackAsynchronously", new Class[]