X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=d2f400d3f94ed49f3dba42e133ac6fc130611b84;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=5688ae1eb06727bd13811434fa182c475068677a;hpb=c6822c7a7219f23523c94c68cc361f6a861c4185;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 5688ae1..d2f400d 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 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,7 +17,10 @@
  */
 package jalview.bin;
 
+import java.awt.Color;
 import java.io.*;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
 import java.util.*;
 
 import org.apache.log4j.*;
@@ -39,9 +42,6 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * </li>
  * <li>logs.Jalview.Level - Cache.log stringified level. <br>
  * </li>
- * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
- * startup</li>
- * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.</li>
  * <li>SCREEN_WIDTH</li>
  * <li>SCREEN_HEIGHT</li>
  * <li>SCREEN_Y=285</li>
@@ -105,7 +105,7 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * <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
- * www.jalview.org</li>
+ * www.jalview.org (or the alias given by the www.jalview.org property)</li>
  * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
  * ID tooltip</li>
  * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
@@ -124,13 +124,25 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * histogram.</li>
  * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
  * logo.</li>
- * 
- * <li></li>
+ * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
+ * respond to selections made in other alignments containing the same sequences.
+ * </li>
+ * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
+ * warning dialog box is displayed.</li>
+ * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation 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></li>
  * 
  * </ul>
- * 
+ * Deprecated settings:
+ * <ul>
+ *  * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
+ * startup (JWS1 services only)</li>
+ * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints. (JWS1 services only)</li>
+ * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2 services in the desktop GUI
+ * </ul>
  * @author $author$
  * @version $Revision$
  */
@@ -168,9 +180,11 @@ public class Cache
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
+  private static boolean propsAreReadOnly=false;
+
   public static void initLogger()
   {
-    if (log!=null)
+    if (log != null)
     {
       return;
     }
@@ -220,11 +234,31 @@ public class Cache
     {
       propertiesFile = System.getProperty("user.home") + File.separatorChar
               + ".jalview_properties";
+    } else {
+      // don't corrupt the file we've been given.
+      propsAreReadOnly = true;
     }
 
     try
     {
-      FileInputStream fis = new FileInputStream(propertiesFile);
+      InputStream fis;
+      try
+      {
+        fis = new java.net.URL(propertiesFile).openStream();
+        System.out.println("Loading jalview properties from : "
+                + propertiesFile);
+        System.out
+                .println("Disabling Jalview writing to user's local properties file.");
+        propsAreReadOnly = true;
+
+      } catch (Exception ex)
+      {
+        fis = null;
+      }
+      if (fis == null)
+      {
+        fis = new FileInputStream(propertiesFile);
+      }
       applicationProperties.load(fis);
       applicationProperties.remove("LATEST_VERSION");
       applicationProperties.remove("VERSION");
@@ -239,9 +273,7 @@ public class Cache
       System.out.println("Using proxyServer: "
               + getDefault("PROXY_SERVER", null) + " proxyPort: "
               + getDefault("PROXY_PORT", null));
-      System
-              .setProperty("http.proxyHost", getDefault("PROXY_SERVER",
-                      null));
+      System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
       System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
     }
 
@@ -251,8 +283,8 @@ public class Cache
     try
     {
       String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
-              .getCodeSource().getLocation().toString().concat(
-                      "!/.build_properties"));
+              .getCodeSource().getLocation().toString()
+              .concat("!/.build_properties"));
 
       java.net.URL localJarFileURL = new java.net.URL(buildDetails);
 
@@ -303,7 +335,7 @@ public class Cache
             System.setProperty("sun.net.client.defaultConnectTimeout",
                     "5000");
             java.net.URL url = new java.net.URL(
-                    "http://www.jalview.org/webstart/jalview.jnlp");
+                    Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/webstart/jalview.jnlp");
             BufferedReader in = new BufferedReader(new InputStreamReader(
                     url.openStream()));
             String line = null;
@@ -414,12 +446,16 @@ public class Cache
    */
   public static String setProperty(String key, String obj)
   {
+
     try
     {
-      FileOutputStream out = new FileOutputStream(propertiesFile);
       applicationProperties.setProperty(key, obj);
-      applicationProperties.store(out, "---JalviewX Properties File---");
-      out.close();
+      if (!propsAreReadOnly)
+      {
+        FileOutputStream out = new FileOutputStream(propertiesFile);
+        applicationProperties.store(out, "---JalviewX Properties File---");
+        out.close();
+      }
     } catch (Exception ex)
     {
       System.out.println("Error setting property: " + key + " " + obj
@@ -444,14 +480,17 @@ public class Cache
    */
   public static void saveProperties()
   {
-    try
+    if (!propsAreReadOnly)
     {
-      FileOutputStream out = new FileOutputStream(propertiesFile);
-      applicationProperties.store(out, "---JalviewX Properties File---");
-      out.close();
-    } catch (Exception ex)
-    {
-      System.out.println("Error saving properties: " + ex);
+      try
+      {
+        FileOutputStream out = new FileOutputStream(propertiesFile);
+        applicationProperties.store(out, "---JalviewX Properties File---");
+        out.close();
+      } catch (Exception ex)
+      {
+        System.out.println("Error saving properties: " + ex);
+      }
     }
   }
 
@@ -607,8 +646,7 @@ public class Cache
                   "com.boxysystems.jgoogleanalytics.FocusPoint");
         } catch (Exception e)
         {
-          log
-                  .debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+          log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
           tracker = null;
           jgoogleanalyticstracker = null;
           trackerfocus = null;
@@ -652,10 +690,7 @@ public class Cache
         if (log != null)
         {
           if (re != null)
-            log
-                    .debug(
-                            "Caught runtime exception in googletracker init:",
-                            re);
+            log.debug("Caught runtime exception in googletracker init:", re);
           if (ex != null)
             log.warn(
                     "Failed to initialise GoogleTracker for Jalview Desktop with version "
@@ -698,4 +733,72 @@ public class Cache
     }
   }
 
+  /**
+   * get the user's default colour if available
+   * @param property
+   * @param defcolour
+   * @return
+   */
+  public static Color getDefaultColour(String property, Color defcolour)
+  {
+    String colprop = getProperty(property);
+    if (colprop==null) {
+      return defcolour;
+    }
+    Color col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName(colprop);
+    if (col==null)
+    {
+      try {
+        col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
+      } catch (Exception ex)
+      {
+        log.warn("Couldn't parse '"+colprop+"' as a colour for "+property);
+        col=null;
+      }
+    }
+    return (col==null) ? defcolour: col;
+  }
+
+  /**
+   * store a colour as a Jalview user default property
+   * @param property
+   * @param colour     
+   */
+  public static void setColourProperty(String property, Color colour)
+  {
+    setProperty(property, jalview.util.Format
+          .getHexString(colour));
+  }
+
+  public static final DateFormat  date_format = SimpleDateFormat.getDateTimeInstance();
+
+  /**
+   * store a date in a jalview property
+   * @param string
+   * @param time
+   */
+  public static void setDateProperty(String property, Date time)
+  {
+    setProperty(property, date_format.format(time));
+  }
+  /**
+   * read a date stored in a jalview property
+   * @param property
+   * @return valid date as stored by setDateProperty, or null
+   * 
+   */
+  public static Date getDateProperty(String property)
+  {
+    String val = getProperty(property);
+    if (val!=null)
+    {
+      try {
+        return date_format.parse(val);
+      } catch (Exception ex)
+      {
+        System.err.println("Invalid or corrupt date in property '"+property+"' : value was '"+val+"'");
+      }
+    }
+    return null;
+  }
 }