X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=8418d6888e68cc006137767ea0390e3af07d030d;hb=80238b0ded8d29f9f50399c51bc550bc1df9c426;hp=62eb7de0bb5a94b14c5b456047d438a00fe9121f;hpb=cef7be0f9008ff15318e3479a5de35e127071ef3;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 62eb7de..8418d68 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -28,8 +28,6 @@ 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;
 import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.Color;
@@ -116,7 +114,6 @@ import org.apache.log4j.SimpleLayout;
  * service</li>
  * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
  * collecting usage statistics</li>
- * <li>DAS_LOCAL_SOURCE list of local das sources</li>
  * <li>SHOW_OVERVIEW boolean for overview window display</li>
  * <li>ANTI_ALIAS boolean for smooth fonts</li>
  * <li>RIGHT_ALIGN_IDS boolean</li>
@@ -136,9 +133,7 @@ import org.apache.log4j.SimpleLayout;
  * 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>
  * <li>DEFAULT_BROWSER for unix</li>
- * <li>DAS_ACTIVE_SOURCE list of active sources</li>
  * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
  * (false)</li>
  * <li>VERSION_CHECK (true) check for the latest release version from
@@ -228,12 +223,6 @@ public class Cache
    */
   public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
 
-  public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
-
-  public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
-
-  public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
-
   /**
    * Sifts settings
    */
@@ -260,8 +249,6 @@ public class Cache
   private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
           .toString();
 
-  private static String HMMER_PATH;
-
   /*
    * a date formatter using a fixed (rather than the user's) locale; 
    * this ensures that date properties can be written and re-read successfully
@@ -336,7 +323,10 @@ public class Cache
     }
   }
 
-  /** Called when Jalview is started */
+  /**
+   * Loads properties from the given properties file. Any existing properties
+   * are first cleared.
+   */
   public static void loadProperties(String propsFile)
   {
     propertiesFile = propsFile;
@@ -371,6 +361,7 @@ public class Cache
       {
         fis = new FileInputStream(propertiesFile);
       }
+      applicationProperties.clear();
       applicationProperties.load(fis);
 
       // remove any old build properties
@@ -414,41 +405,7 @@ public class Cache
       applicationProperties.remove("YEAR");
     }
 
-    // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
-    // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
-    // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
-    try
-    {
-      String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
-              .getCodeSource().getLocation().toString()
-              .concat("!/.build_properties"));
-
-      java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
-      InputStream in = localJarFileURL.openStream();
-      applicationProperties.load(in);
-      in.close();
-    } catch (Exception ex)
-    {
-      System.out.println("Error reading build details: " + ex);
-      applicationProperties.remove("VERSION");
-    }
-
-    String jnlpVersion = System.getProperty("jalview.version");
-    String codeVersion = getProperty("VERSION");
-    String codeInstallation = getProperty("INSTALLATION");
-    if (codeVersion == null)
-    {
-      // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
-      codeVersion = "Test";
-      jnlpVersion = "Test";
-      codeInstallation = "";
-    }
-    else
-    {
-      codeInstallation = " (" + codeInstallation + ")";
-    }
-    new BuildDetails(codeVersion, null, codeInstallation);
+    loadBuildProperties(false);
 
     SiftsSettings
             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
@@ -468,9 +425,6 @@ public class Cache
             "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
@@ -478,8 +432,13 @@ public class Cache
     // StructureImportSettings
     // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
     // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
-    // jnlpVersion will be null if we're using InstallAnywhere
+
+    String jnlpVersion = System.getProperty("jalview.version");
+
+    // jnlpVersion will be null if a latest version check for the channel needs to
+    // be done
     // Dont do this check if running in headless mode
+
     if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
             && (System.getProperty("java.awt.headless") == null || System
                     .getProperty("java.awt.headless").equals("false")))
@@ -550,8 +509,6 @@ public class Cache
       }
     }
 
-    setProperty("VERSION", codeVersion);
-
     // LOAD USERDEFINED COLOURS
     jalview.bin.Cache
             .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
@@ -559,6 +516,50 @@ public class Cache
             false);
   }
 
+  public static void loadBuildProperties(boolean reportVersion)
+  {
+    String codeInstallation = getProperty("INSTALLATION");
+    boolean printV = codeInstallation == null;
+
+    // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+    try
+    {
+      String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
+              .getCodeSource().getLocation().toString()
+              .concat("!/.build_properties"));
+
+      java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+
+      InputStream in = localJarFileURL.openStream();
+      applicationProperties.load(in);
+      in.close();
+    } catch (Exception ex)
+    {
+      System.out.println("Error reading build details: " + ex);
+      applicationProperties.remove("VERSION");
+    }
+    String codeVersion = getProperty("VERSION");
+    codeInstallation = getProperty("INSTALLATION");
+
+    if (codeVersion == null)
+    {
+      // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+      codeVersion = "Test";
+      codeInstallation = "";
+    }
+    else
+    {
+      codeInstallation = " (" + codeInstallation + ")";
+    }
+    setProperty("VERSION", codeVersion);
+    new BuildDetails(codeVersion, null, codeInstallation);
+    if (printV && reportVersion)
+    {
+      System.out
+            .println("Jalview Version: " + codeVersion + codeInstallation);
+    }
+  }
+
   private static void deleteBuildProperties()
   {
     applicationProperties.remove("LATEST_VERSION");
@@ -600,6 +601,24 @@ public class Cache
     return def;
   }
 
+  public static int getDefault(String property, int def)
+  {
+    String string = getProperty(property);
+    if (string != null)
+    {
+      try
+      {
+        def = Integer.parseInt(string);
+      } catch (NumberFormatException e)
+      {
+        System.out.println("Error parsing int property '" + property
+                + "' with value '" + string + "'");
+      }
+    }
+
+    return def;
+  }
+
   /**
    * These methods are used when checking if the saved preference is different
    * to the default setting
@@ -623,15 +642,15 @@ public class Cache
    * @param obj
    *          String value of property
    * 
-   * @return String value of property
+   * @return previous value of property (or null)
    */
-  public static String setProperty(String key, String obj)
+  public static Object setProperty(String key, String obj)
   {
-
+    Object oldValue = null;
     try
     {
-      applicationProperties.setProperty(key, obj);
-      if (!propsAreReadOnly)
+      oldValue = applicationProperties.setProperty(key, obj);
+      if (propertiesFile != null && !propsAreReadOnly)
       {
         FileOutputStream out = new FileOutputStream(propertiesFile);
         applicationProperties.store(out, "---JalviewX Properties File---");
@@ -642,7 +661,7 @@ public class Cache
       System.out.println(
               "Error setting property: " + key + " " + obj + "\n" + ex);
     }
-    return obj;
+    return oldValue;
   }
 
   /**
@@ -980,22 +999,6 @@ public class Cache
     return null;
   }
 
-  private static DasSourceRegistryI sourceRegistry = null;
-
-  /**
-   * initialise and ..
-   * 
-   * @return instance of the das source registry
-   */
-  public static DasSourceRegistryI getDasSourceRegistry()
-  {
-    if (sourceRegistry == null)
-    {
-      sourceRegistry = new DasSourceRegistry();
-    }
-    return sourceRegistry;
-  }
-
   /**
    * Set the specified value, or remove it if null or empty. Does not save the
    * properties file.
@@ -1070,4 +1073,43 @@ public class Cache
       }
     }
   }
+
+  /**
+   * 
+   * @return Jalview version, build details and JVM platform version for console
+   */
+  public static String getVersionDetailsForConsole()
+  {
+    return "Jalview Version: "
+            + jalview.bin.Cache.getDefault("VERSION", "TEST")
+            + "\n" + "Jalview Installation: "
+            + jalview.bin.Cache.getDefault("INSTALLATION",
+                    "unknown")
+            + "\n" + "Build Date: "
+            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+            + "\n" + "Java version: "
+            + System.getProperty("java.version") + "\n"
+            + System.getProperty("os.arch") + " "
+            + System.getProperty("os.name") + " "
+            + System.getProperty("os.version")
+            + (jalview.bin.Cache.getDefault("VERSION", "TEST")
+                    .equals("DEVELOPMENT")
+								? "\nGetdown appdir: " + System.getProperty("getdownappdir") + "\nJava path: "
+                                    + System.getProperty(
+                                            "java.home")
+                                    + File.separator + "bin"
+                                    + File.separator + "java"
+								: "");
+  }
+
+  /**
+   * 
+   * @return build details as reported in splashscreen
+   */
+  public static String getBuildDetailsForSplash()
+  {
+    // consider returning more human friendly info
+    // eg 'built from Source' or update channel
+    return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+  }
 }