X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=68edf1bcef3ea849136fabd24dc7daac64bed5cc;hb=5e34c2ccda1cf0d409618a564804408350c932d0;hp=48837ff99f68878911d9f01f9bb7535b3317bd83;hpb=077fea81a02a33eefed6895bfa7cff993609dab8;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 48837ff..68edf1b 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -17,6 +17,7 @@
  */
 package jalview.bin;
 
+import java.awt.Color;
 import java.io.*;
 import java.util.*;
 
@@ -105,7 +106,7 @@ 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
@@ -129,8 +130,9 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * </li>
  * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
  * warning dialog box is displayed.</li>
- * 
- * <li></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>
  * 
@@ -173,6 +175,8 @@ public class Cache
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
+  private static boolean propsAreReadOnly=false;
+
   public static void initLogger()
   {
     if (log != null)
@@ -225,11 +229,31 @@ 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");
@@ -306,7 +330,7 @@ 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;
@@ -417,12 +441,16 @@ 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
@@ -447,14 +475,17 @@ public class Cache
    */
   public static void saveProperties()
   {
-    try
-    {
-      FileOutputStream out = new FileOutputStream(propertiesFile);
-      applicationProperties.store(out, "---JalviewX Properties File---");
-      out.close();
-    } catch (Exception ex)
+    if (!propsAreReadOnly)
     {
-      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);
+      }
     }
   }
 
@@ -697,4 +728,40 @@ 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));
+  }
 }