efficiency, and ensure mouseover messages originating from a source are not broadcast...

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

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index fab075e..5692c49 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.
  * 
@@ -124,6 +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>
@@ -133,6 +135,8 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * <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></li>
  * 
  * </ul>
@@ -141,7 +145,8 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  *  * <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>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 $Revision$
@@ -277,6 +282,26 @@ 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
@@ -801,4 +826,24 @@ public class Cache
     }
     return null;
   }
+
+  /**
+   * 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)
+    {
+      try {
+        return Integer.valueOf(val);
+      } catch (NumberFormatException x)
+      {
+        System.err.println("Invalid integer in property '"+property+"' (value was '"+val+"')");
+      }
+    }
+    return null;
+  }
 }