/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* histogram.</li>
* <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
* logo.</li>
+ * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
+ * respond to selections made in other alignments containing the same sequences.
+ * </li>
+ * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
+ * warning dialog box is displayed.</li>
*
* <li></li>
*
/** Default file is ~/.jalview_properties */
static String propertiesFile;
+ private static boolean propsAreReadOnly=false;
+
public static void initLogger()
{
- if (log!=null)
+ if (log != null)
{
return;
}
{
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ ".jalview_properties";
+ } else {
+ // don't corrupt the file we've been given.
+ propsAreReadOnly = true;
}
try
{
- FileInputStream fis = new FileInputStream(propertiesFile);
+ InputStream fis;
+ try
+ {
+ fis = new java.net.URL(propertiesFile).openStream();
+ 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);
applicationProperties.remove("LATEST_VERSION");
applicationProperties.remove("VERSION");
System.out.println("Using proxyServer: "
+ getDefault("PROXY_SERVER", null) + " proxyPort: "
+ getDefault("PROXY_PORT", null));
- System
- .setProperty("http.proxyHost", getDefault("PROXY_SERVER",
- null));
+ System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
}
try
{
String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString().concat(
- "!/.build_properties"));
+ .getCodeSource().getLocation().toString()
+ .concat("!/.build_properties"));
java.net.URL localJarFileURL = new java.net.URL(buildDetails);
*/
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
*/
public static void saveProperties()
{
- try
- {
- FileOutputStream out = new FileOutputStream(propertiesFile);
- applicationProperties.store(out, "---JalviewX Properties File---");
- out.close();
- } catch (Exception ex)
+ if (!propsAreReadOnly)
{
- 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);
+ }
}
}
"com.boxysystems.jgoogleanalytics.FocusPoint");
} catch (Exception e)
{
- log
- .debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
tracker = null;
jgoogleanalyticstracker = null;
trackerfocus = null;
if (log != null)
{
if (re != null)
- log
- .debug(
- "Caught runtime exception in googletracker init:",
- re);
+ log.debug("Caught runtime exception in googletracker init:", re);
if (ex != null)
log.warn(
"Failed to initialise GoogleTracker for Jalview Desktop with version "