X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=5692c496de7ac6712c2df13cd427609f8864be40;hb=d98019da2b9c4babbd0d981579a90adf11e9911a;hp=f80d729e095c3c8919373791d933508411535d01;hpb=179f28db07e2e45e98ad141e42299547fe0e77c0;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index f80d729..5692c49 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.
*
@@ -17,7 +17,10 @@
*/
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.*;
@@ -39,9 +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
@@ -105,7 +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
@@ -124,18 +124,30 @@ 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.
*
* SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
* 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
*
- *
- *
+ * FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported alignment figure to accommodate even the longest sequence ID or annotation label.
+ * 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).
*
*
*
- *
+ * 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 $Revision$
*/
@@ -173,6 +185,8 @@ public class Cache
/** Default file is ~/.jalview_properties */
static String propertiesFile;
+ private static boolean propsAreReadOnly=false;
+
public static void initLogger()
{
if (log != null)
@@ -225,16 +239,29 @@ 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
{
InputStream fis;
- try {
+ try
+ {
fis = new java.net.URL(propertiesFile).openStream();
- System.out.println("Loading jalview properties from : "+propertiesFile);
- } catch (Exception ex) {fis=null;}
- if (fis==null) {
+ 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);
@@ -255,6 +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
@@ -313,7 +360,7 @@ 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;
@@ -424,12 +471,16 @@ 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
@@ -454,14 +505,17 @@ public class Cache
*/
public static void saveProperties()
{
- try
+ if (!propsAreReadOnly)
{
- FileOutputStream out = new FileOutputStream(propertiesFile);
- applicationProperties.store(out, "---JalviewX Properties File---");
- out.close();
- } catch (Exception ex)
- {
- 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);
+ }
}
}
@@ -704,4 +758,92 @@ 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));
+ }
+
+ 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;
+ }
+
+ /**
+ * 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;
+ }
}