X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCache.java;h=1214371cd65eb85d0521f021c197da3e1c1b4cd9;hb=8ba65cbf8dde2faeff8a84eae78127fb99b765a5;hp=cebb50414d00c84864a3e39439865d0010bc716e;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index cebb504..1214371 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,27 +1,35 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
- *
+ * 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
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
+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.text.SimpleDateFormat;
import java.util.*;
import org.apache.log4j.*;
-import org.biojava.dasobert.dasregistry.Das1Source;
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
@@ -39,9 +47,6 @@ 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 +110,7 @@ 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
@@ -124,11 +129,40 @@ 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 $author$
@@ -168,8 +202,14 @@ public class Cache
/** Default file is ~/.jalview_properties */
static String propertiesFile;
+ private static boolean propsAreReadOnly = false;
+
public static void initLogger()
{
+ if (log != null)
+ {
+ return;
+ }
try
{
// TODO: redirect stdout and stderr here in order to grab the output of
@@ -217,13 +257,37 @@ 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
{
- 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");
+
+ // remove any old build properties
+
+ deleteBuildProperties();
fis.close();
} catch (Exception ex)
{
@@ -232,13 +296,34 @@ public class Cache
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
@@ -247,8 +332,8 @@ public class Cache
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);
@@ -298,8 +383,9 @@ 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");
+ 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;
@@ -353,6 +439,15 @@ public class Cache
false);
}
+ private static void deleteBuildProperties()
+ {
+ applicationProperties.remove("LATEST_VERSION");
+ applicationProperties.remove("VERSION");
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
+ }
+
/**
* Gets Jalview application property of given key. Returns null if key not
* found
@@ -410,12 +505,16 @@ 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
@@ -440,14 +539,17 @@ public class Cache
*/
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);
+ }
}
}
@@ -534,46 +636,6 @@ public class Cache
}
/**
- * 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.
*/
@@ -603,8 +665,7 @@ public class Cache
"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;
@@ -648,10 +709,7 @@ public class Cache
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 "
@@ -694,4 +752,123 @@ 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;
+ }
+
+ 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;
+ }
}