normalised logo rendering (JAL-958)

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

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index f67377b..5dbf5bc 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -19,6 +19,8 @@ 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.*;
@@ -40,9 +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>
@@ -106,7 +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
@@ -125,6 +124,8 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * histogram.</li>
  * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
  * logo.</li>
+ * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo normalised to row height rather than histogram height.</li>
  * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
  * respond to selections made in other alignments containing the same sequences.
  * </li>
@@ -132,13 +133,19 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * 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></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</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 $Revision$
  */
@@ -273,6 +280,26 @@ public class Cache
       System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
     }
 
+    // LOAD THE AUTHORS FROM THE authors.props file
+    try
+    {
+      String authorDetails = "jar:".concat(Cache.class.getProtectionDomain()
+              .getCodeSource().getLocation().toString()
+              .concat("!/authors.props"));
+
+      java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+
+      InputStream in = localJarFileURL.openStream();
+      applicationProperties.load(in);
+      in.close();
+    } catch (Exception ex)
+    {
+      System.out.println("Error reading author details: " + ex);
+      applicationProperties.remove("AUTHORS");
+      applicationProperties.remove("AUTHORFNAMES");
+      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
@@ -331,7 +358,7 @@ 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;
@@ -765,4 +792,36 @@ public class Cache
     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;
+  }
 }