/*
- * 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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
*/
package jalview.bin;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+
import java.awt.Color;
import java.io.*;
+import java.text.DateFormat;
import java.util.*;
import org.apache.log4j.*;
-import org.biojava.dasobert.dasregistry.Das1Source;
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* 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>
* <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
* 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>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>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>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>
* Deprecated settings:
* <ul>
- * * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
+ * *
+ * <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>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 $Revision$
*/
/** Default file is ~/.jalview_properties */
static String propertiesFile;
- private static boolean propsAreReadOnly=false;
+ private static boolean propsAreReadOnly = false;
public static void initLogger()
{
{
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ ".jalview_properties";
- } else {
+ }
+ else
+ {
// don't corrupt the file we've been given.
propsAreReadOnly = true;
}
if (getDefault("USE_PROXY", false))
{
- 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.proxyPort", getDefault("PROXY_PORT", null));
+ String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
+ "PROXY_PORT", "8080");
+
+ System.out.println("Using proxyServer: " + proxyServer
+ + " proxyPort: " + proxyPort);
+
+ System.setProperty("http.proxyHost", proxyServer);
+ System.setProperty("http.proxyPort", proxyPort);
+ }
+
+ // 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
{
System.setProperty("sun.net.client.defaultConnectTimeout",
"5000");
- java.net.URL url = new java.net.URL(
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/webstart/jalview.jnlp");
+ java.net.URL url = new java.net.URL(Cache.getDefault(
+ "www.jalview.org", "http://www.jalview.org")
+ + "/webstart/jalview.jnlp");
BufferedReader in = new BufferedReader(new InputStreamReader(
url.openStream()));
String line = null;
}
/**
- * generate Das1Sources from the local das source list
- *
- * @return Vector of Das1Sources
- */
- public static Vector getLocalDasSources()
- {
- Vector localSources = new Vector();
- String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
- if (local != null)
- {
- StringTokenizer st = new StringTokenizer(local, "\t");
- while (st.hasMoreTokens())
- {
- String token = st.nextToken();
- int bar = token.indexOf("|");
- Das1Source source = new Das1Source();
- source.setUrl(token.substring(bar + 1));
- if (source.getUrl().startsWith("sequence:"))
- {
- source.setUrl(source.getUrl().substring(9));
- // this source also serves sequences as well as features
- source.setCapabilities(new String[]
- { "sequence", "features" });
- }
- else
- {
- // default is that all user added sources serve features
- source.setCapabilities(new String[]
- { "features" });
- }
-
- source.setNickname(token.substring(0, bar));
-
- localSources.addElement(source);
- }
- }
- return localSources;
- }
-
- /**
* GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
* enabled.
*/
/**
* 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) {
+ if (colprop == null)
+ {
return defcolour;
}
- Color col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName(colprop);
- if (col==null)
+ Color col = jalview.schemes.ColourSchemeProperty
+ .getAWTColorFromName(colprop);
+ if (col == null)
{
- try {
+ 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;
+ log.warn("Couldn't parse '" + colprop + "' as a colour for "
+ + property);
+ col = null;
}
}
- return (col==null) ? defcolour: col;
+ return (col == null) ? defcolour : col;
}
/**
* store a colour as a Jalview user default property
+ *
* @param property
- * @param colour
+ * @param colour
*/
public static void setColourProperty(String property, Color colour)
{
- setProperty(property, jalview.util.Format
- .getHexString(colour));
+ setProperty(property, jalview.util.Format.getHexString(colour));
+ }
+
+ public static final DateFormat date_format = DateFormat.getDateInstance(DateFormat.LONG,MessageManager.getLocale());
+
+ /**
+ * 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;
+ }
+
+ private static DasSourceRegistryI sourceRegistry = null;
+
+ /**
+ * initialise and ..
+ *
+ * @return instance of the das source registry
+ */
+ public static DasSourceRegistryI getDasSourceRegistry()
+ {
+ if (sourceRegistry == null)
+ {
+ sourceRegistry = new DasSourceRegistry();
+ }
+ return sourceRegistry;
}
}