X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=5dbf5bc83ac034a2c2ed97ce7ff1cd287d0816e5;hb=bbfdb203ce3a889600caa52478478b75ab03809f;hp=f67377beefa8b43ff13f51aa19e0b3b6d595fcbd;hpb=9fe2470b6400c06457392d608763cbf65b535f4c;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index f67377b..5dbf5bc 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 2.6)
- * 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;
*
*
logs.Jalview.Level - Cache.log stringified level.
*
- * DISCOVERY_START - Boolean - controls if discovery services are queried on
- * startup
- * DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
* SCREEN_WIDTH
* SCREEN_HEIGHT
* SCREEN_Y=285
@@ -106,7 +105,7 @@ import org.biojava.dasobert.dasregistry.Das1Source;
* SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)
* VERSION_CHECK (true) check for the latest release version from
- * www.jalview.org
+ * www.jalview.org (or the alias given by the www.jalview.org property)
* SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
* ID tooltip
* SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
@@ -125,6 +124,8 @@ import org.biojava.dasobert.dasregistry.Das1Source;
* histogram.
* SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
* logo.
+ * NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo normalised to row height rather than histogram height.
* FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
*
@@ -132,13 +133,19 @@ import org.biojava.dasobert.dasregistry.Das1Source;
* warning dialog box is displayed.
* ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation when shading by annotation
* ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation when shading by annotation
- *
- *
+ * www.jalview.org (http://www.jalview.org) a property enabling all HTTP requests to be redirected to a mirror of http://www.jalview.org
*
*
*
*
- *
+ * Deprecated settings:
+ *
+ * * - DISCOVERY_START - Boolean - controls if discovery services are queried on
+ * startup (JWS1 services only)
+ * - DISCOVERY_URLS - comma separated list of Discovery Service endpoints. (JWS1 services only)
+ * - SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2 services in the desktop GUI
+ * - ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing panel in web service preferences
+ *
* @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;
+ }
}