X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=d791cb66761dc78a5cc8ba331e5ba913abcc91f2;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=141470af33d9296afddd224d70ce7d0bb503a8ed;hpb=d0b386f1c8c27a08c8b65bd23603f3d23f241670;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 141470a..d791cb6 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.bin;
 
@@ -133,23 +134,35 @@ import org.apache.log4j.*;
  * </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>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>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported alignment figure to accommodate even the longest sequence ID or annotation label.</li>
- * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true will override this).</li>
+ * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
+ * alignment figure to accommodate even the longest sequence ID or annotation
+ * label.</li>
+ * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
+ * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
+ * will override this).</li>
  * <li></li>
  * 
  * </ul>
  * Deprecated settings:
  * <ul>
- *  * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
+ * *
+ * <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</li>
- * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing panel in web service preferences</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</li>
+ * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
+ * panel in web service preferences</li>
  * </ul>
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -187,7 +200,7 @@ public class Cache
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
-  private static boolean propsAreReadOnly=false;
+  private static boolean propsAreReadOnly = false;
 
   public static void initLogger()
   {
@@ -241,7 +254,9 @@ public class Cache
     {
       propertiesFile = System.getProperty("user.home") + File.separatorChar
               + ".jalview_properties";
-    } else {
+    }
+    else
+    {
       // don't corrupt the file we've been given.
       propsAreReadOnly = true;
     }
@@ -277,12 +292,12 @@ public class Cache
 
     if (getDefault("USE_PROXY", false))
     {
-      String proxyServer=getDefault("PROXY_SERVER", ""), proxyPort=getDefault("PROXY_PORT", "8080");
-      
-      System.out.println("Using proxyServer: "
-              + proxyServer + " proxyPort: "
-              + proxyPort );
-      
+      String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
+              "PROXY_PORT", "8080");
+
+      System.out.println("Using proxyServer: " + proxyServer
+              + " proxyPort: " + proxyPort);
+
       System.setProperty("http.proxyHost", proxyServer);
       System.setProperty("http.proxyPort", proxyPort);
     }
@@ -290,9 +305,9 @@ public class Cache
     // LOAD THE AUTHORS FROM THE authors.props file
     try
     {
-      String authorDetails = "jar:".concat(Cache.class.getProtectionDomain()
-              .getCodeSource().getLocation().toString()
-              .concat("!/authors.props"));
+      String authorDetails = "jar:".concat(Cache.class
+              .getProtectionDomain().getCodeSource().getLocation()
+              .toString().concat("!/authors.props"));
 
       java.net.URL localJarFileURL = new java.net.URL(authorDetails);
 
@@ -364,8 +379,9 @@ public class Cache
           {
             System.setProperty("sun.net.client.defaultConnectTimeout",
                     "5000");
-            java.net.URL url = new java.net.URL(
-                    Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/webstart/jalview.jnlp");
+            java.net.URL url = new java.net.URL(Cache.getDefault(
+                    "www.jalview.org", "http://www.jalview.org")
+                    + "/webstart/jalview.jnlp");
             BufferedReader in = new BufferedReader(new InputStreamReader(
                     url.openStream()));
             String line = null;
@@ -725,6 +741,7 @@ public class Cache
 
   /**
    * get the user's default colour if available
+   * 
    * @param property
    * @param defcolour
    * @return
@@ -732,38 +749,44 @@ public class Cache
   public static Color getDefaultColour(String property, Color defcolour)
   {
     String colprop = getProperty(property);
-    if (colprop==null) {
+    if (colprop == null)
+    {
       return defcolour;
     }
-    Color col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName(colprop);
-    if (col==null)
+    Color col = jalview.schemes.ColourSchemeProperty
+            .getAWTColorFromName(colprop);
+    if (col == null)
     {
-      try {
+      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;
+        log.warn("Couldn't parse '" + colprop + "' as a colour for "
+                + property);
+        col = null;
       }
     }
-    return (col==null) ? defcolour: col;
+    return (col == null) ? defcolour : col;
   }
 
   /**
    * store a colour as a Jalview user default property
+   * 
    * @param property
-   * @param colour     
+   * @param colour
    */
   public static void setColourProperty(String property, Color colour)
   {
-    setProperty(property, jalview.util.Format
-          .getHexString(colour));
+    setProperty(property, jalview.util.Format.getHexString(colour));
   }
 
-  public static final DateFormat  date_format = SimpleDateFormat.getDateTimeInstance();
+  public static final DateFormat date_format = SimpleDateFormat
+          .getDateTimeInstance();
 
   /**
    * store a date in a jalview property
+   * 
    * @param string
    * @param time
    */
@@ -771,8 +794,10 @@ public class Cache
   {
     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
    * 
@@ -780,46 +805,54 @@ public class Cache
   public static Date getDateProperty(String property)
   {
     String val = getProperty(property);
-    if (val!=null)
+    if (val != null)
     {
-      try {
+      try
+      {
         return date_format.parse(val);
       } catch (Exception ex)
       {
-        System.err.println("Invalid or corrupt date in property '"+property+"' : value was '"+val+"'");
+        System.err.println("Invalid or corrupt date in property '"
+                + property + "' : value was '" + val + "'");
       }
     }
     return null;
   }
 
   /**
-   * get and parse a property as an integer. send any parsing problems to System.err
+   * get and parse a property as an integer. send any parsing problems to
+   * System.err
+   * 
    * @param property
    * @return null or Integer
    */
   public static Integer getIntegerProperty(String property)
   {
-    String val=getProperty(property);
-    if (val!=null && (val=val.trim()).length()>0)
+    String val = getProperty(property);
+    if (val != null && (val = val.trim()).length() > 0)
     {
-      try {
+      try
+      {
         return Integer.valueOf(val);
       } catch (NumberFormatException x)
       {
-        System.err.println("Invalid integer in property '"+property+"' (value was '"+val+"')");
+        System.err.println("Invalid integer in property '" + property
+                + "' (value was '" + val + "')");
       }
     }
     return null;
   }
 
-  private static DasSourceRegistryI sourceRegistry=null;
+  private static DasSourceRegistryI sourceRegistry = null;
+
   /**
    * initialise and ..
+   * 
    * @return instance of the das source registry
    */
   public static DasSourceRegistryI getDasSourceRegistry()
   {
-    if (sourceRegistry==null)
+    if (sourceRegistry == null)
     {
       sourceRegistry = new DasSourceRegistry();
     }