X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=d2f400d3f94ed49f3dba42e133ac6fc130611b84;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=8d003efc685847f30d8b4c4bb0bb548fa1614bb8;hpb=fd29e047719a470cf304c5a41abfff5c1eac3ee8;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 8d003ef..d2f400d 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,96 +1,148 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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
+ * 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 .
*/
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.*;
+import org.biojava.dasobert.dasregistry.Das1Source;
/**
- * Stores and retrieves Jalview Application Properties
- * Lists and fields within list entries are separated by '|' symbols unless otherwise stated
- * (|) clauses are alternative values for a tag.
- *
Current properties include:
- *
- *
logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
+ * Stores and retrieves Jalview Application Properties Lists and fields within
+ * list entries are separated by '|' symbols unless otherwise stated (|) clauses
+ * are alternative values for a tag.
*
- * - logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
- *
- * - logs.Jalview.Level - Cache.log stringified level.
+ * Current properties include:
+ *
- 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
- *
- SCREEN_X=371
- *
- SHOW_FULLSCREEN boolean
- *
- FONT_NAME java font name for alignment text display
- *
- FONT_SIZE size of displayed alignment text
- *
- FONT_STYLE style of font displayed (sequence labels are always italic)
- *
- GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
- *
- LAST_DIRECTORY last directory for browsing alignment
- *
- USER_DEFINED_COLOURS list of user defined colour scheme files
- *
- SHOW_FULL_ID show id with '/start-end' numbers appended
- *
- SHOW_IDENTITY show percentage identity annotation
- *
- SHOW_QUALITY show alignment quality annotation
- *
- SHOW_ANNOTATIONS show alignment annotation rows
- *
- SHOW_CONSERVATION show alignment conservation annotation
- *
- CENTRE_COLUMN_LABELS centre the labels at each column in a displayed annotation row
- *
- DEFAULT_COLOUR default colour scheme to apply for a new alignment
- *
- DEFAULT_FILE_FORMAT file format used to save
- *
- STARTUP_FILE file loaded on startup (may be a fully qualified url)
- *
- SHOW_STARTUP_FILE flag to control loading of startup file
- *
- VERSION the version of the jalview build
- *
- BUILD_DATE date of this build
- *
- LATEST_VERSION the latest jalview version advertised on the www.jalview.org
- *
- PIR_MODELLER boolean indicating if PIR files are written with MODELLER descriptions
- *
- (FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv suffix to file
- *
- RECENT_URL list of recently retrieved URLs
- *
- RECENT_FILE list of recently opened files
- *
- USE_PROXY flag for whether a http proxy is to be used
- *
- PROXY_SERVER the proxy
- *
- PROXY_PORT
- *
- NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire service
- *
- QUESTIONNAIRE last questionnaire:responder id string from questionnaire service
- *
- DAS_LOCAL_SOURCE list of local das sources
- *
- SHOW_OVERVIEW boolean for overview window display
- *
- ANTI_ALIAS boolean for smooth fonts
- *
- RIGHT_ALIGN_IDS boolean
- *
- AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
- *
- PAD_GAPS boolean
- *
- ID_ITALICS boolean
- *
- SHOW_JV_SUFFIX
- *
- WRAP_ALIGNMENT
- *
- EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering style check
- *
- SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
- *
- SEQUENCE_LINKS list of name|URL pairs for opening a url with $SEQUENCE_ID$
- *
- DAS_REGISTRY_URL the registry to query
- *
- DEFAULT_BROWSER for unix
- *
- DAS_ACTIVE_SOURCE list of active sources
- *
- SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop (false)
- *
-
+ * logs.Axis.Level - one of the stringified Levels for log4j controlling the
+ * logging level for axis (used for web services)
+ *
+ * - logs.Castor.Level - one of the stringified Levels for log4j controlling
+ * the logging level for castor (used for serialization)
+ *
+ * - logs.Jalview.Level - Cache.log stringified level.
+ *
+ * - SCREEN_WIDTH
+ * - SCREEN_HEIGHT
+ * - SCREEN_Y=285
+ * - SCREEN_X=371
+ * - SHOW_FULLSCREEN boolean
+ * - FONT_NAME java font name for alignment text display
+ * - FONT_SIZE size of displayed alignment text
+ * - FONT_STYLE style of font displayed (sequence labels are always italic)
+ * - GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
+ * - LAST_DIRECTORY last directory for browsing alignment
+ * - USER_DEFINED_COLOURS list of user defined colour scheme files
+ * - SHOW_FULL_ID show id with '/start-end' numbers appended
+ * - SHOW_IDENTITY show percentage identity annotation
+ * - SHOW_QUALITY show alignment quality annotation
+ * - SHOW_ANNOTATIONS show alignment annotation rows
+ * - SHOW_CONSERVATION show alignment conservation annotation
+ * - CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
+ * annotation row
+ * - DEFAULT_COLOUR default colour scheme to apply for a new alignment
+ * - DEFAULT_FILE_FORMAT file format used to save
+ * - STARTUP_FILE file loaded on startup (may be a fully qualified url)
+ * - SHOW_STARTUP_FILE flag to control loading of startup file
+ * - VERSION the version of the jalview build
+ * - BUILD_DATE date of this build
+ * - LATEST_VERSION the latest jalview version advertised on the
+ * www.jalview.org
+ * - PIR_MODELLER boolean indicating if PIR files are written with MODELLER
+ * descriptions
+ * - (FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
+ * suffix to file
+ * - RECENT_URL list of recently retrieved URLs
+ * - RECENT_FILE list of recently opened files
+ * - USE_PROXY flag for whether a http proxy is to be used
+ * - PROXY_SERVER the proxy
+ * - PROXY_PORT
+ * - NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
+ * service
+ * - QUESTIONNAIRE last questionnaire:responder id string from questionnaire
+ * service
+ * - USAGESTATS (false - user prompted) Enable google analytics tracker for
+ * collecting usage statistics
+ * - DAS_LOCAL_SOURCE list of local das sources
+ * - SHOW_OVERVIEW boolean for overview window display
+ * - ANTI_ALIAS boolean for smooth fonts
+ * - RIGHT_ALIGN_IDS boolean
+ * - AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
+ * - PAD_GAPS boolean
+ * - ID_ITALICS boolean
+ * - SHOW_JV_SUFFIX
+ * - WRAP_ALIGNMENT
+ * - EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
+ * style check
+ * - SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
+ * - SEQUENCE_LINKS list of name|URL pairs for opening a url with
+ * $SEQUENCE_ID$
+ * - GROUP_LINKS list of name|URL[|<separator>] tuples - see
+ * jalview.utils.GroupURLLink for more info
+ * - DAS_REGISTRY_URL the registry to query
+ * - DEFAULT_BROWSER for unix
+ * - DAS_ACTIVE_SOURCE list of active sources
+ * - 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 (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
+ * ID tooltip
+ * - SHOW_UNCONSERVED (false) only render unconserved residues - conserved
+ * displayed as '.'
+ * - SORT_BY_TREE (false) sort the current alignment view according to the
+ * order of a newly displayed tree
+ * - DBFETCH_USEPICR (false) use PICR to recover valid DB references from
+ * sequence ID strings before attempting retrieval from any datasource
+ * - SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
+ * alignment.
+ * - SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
+ * in the alignment.
+ * - SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
+ * histogram.
+ * - SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo.
+ * - 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
+ *
+ *
*
*
-
+ * 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
+ *
* @author $author$
* @version $Revision$
*/
@@ -100,16 +152,23 @@ public class Cache
* property giving log4j level for CASTOR loggers
*/
public static final String CASTORLOGLEVEL = "logs.Castor.level";
+
/**
* property giving log4j level for AXIS loggers
*/
public static final String AXISLOGLEVEL = "logs.Axis.level";
+
/**
* property giving log4j level for Jalview Log
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+
public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
+ public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
+
+ public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
+
/**
* Initialises the Jalview Application Log
*/
@@ -118,41 +177,49 @@ public class Cache
/** Jalview Properties */
public static Properties applicationProperties = new Properties();
- /** Default file is ~/.jalview_properties */
+ /** 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
+ // the log
+
ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
- "System.err");
+ "System.err");
ap.setName("JalviewLogger");
- org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for log output
+ org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
+ // log output
Logger laxis = Logger.getLogger("org.apache.axis");
Logger lcastor = Logger.getLogger("org.exolab.castor");
jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
- Level.INFO.toString())));
+ Level.INFO.toString())));
lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- Level.INFO.toString())));
+ Level.INFO.toString())));
lcastor = Logger.getLogger("org.exolab.castor.xml");
lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
Level.INFO.toString())));
- //lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
- //lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- // Level.INFO.toString())));
+ // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
+ // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ // Level.INFO.toString())));
jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
- "logs.Jalview.level",
- Level.INFO.toString())));
- //laxis.addAppender(ap);
- //lcastor.addAppender(ap);
- //jalview.bin.Cache.log.addAppender(ap);
+ "logs.Jalview.level", Level.INFO.toString())));
+ // laxis.addAppender(ap);
+ // lcastor.addAppender(ap);
+ // jalview.bin.Cache.log.addAppender(ap);
// Tell the user that debug is enabled
jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.err.println("Problems initializing the log4j system\n");
ex.printStackTrace(System.err);
@@ -165,27 +232,47 @@ public class Cache
propertiesFile = propsFile;
if (propsFile == null)
{
- propertiesFile = System.getProperty("user.home") + File.separatorChar +
- ".jalview_properties";
+ 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");
fis.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.out.println("Error reading properties file: " + ex);
}
if (getDefault("USE_PROXY", false))
{
- System.out.println("Using proxyServer: " + getDefault("PROXY_SERVER", null) +
- " proxyPort: " + getDefault("PROXY_PORT", null));
+ 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));
}
@@ -195,20 +282,16 @@ public class Cache
// VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
try
{
- String buildDetails = "jar:"
- .concat(
- Cache.class.getProtectionDomain().getCodeSource().getLocation().
- toString()
- .concat("!/.build_properties")
- );
+ String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString()
+ .concat("!/.build_properties"));
java.net.URL localJarFileURL = new java.net.URL(buildDetails);
InputStream in = localJarFileURL.openStream();
applicationProperties.load(in);
in.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.out.println("Error reading build details: " + ex);
applicationProperties.remove("VERSION");
@@ -228,25 +311,35 @@ public class Cache
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
- if (jnlpVersion == null && (
- System.getProperty("java.awt.headless") == null
- || System.getProperty("java.awt.headless").equals("false")))
+ if (jnlpVersion == null
+ && getDefault("VERSION_CHECK", true)
+ && (System.getProperty("java.awt.headless") == null || System
+ .getProperty("java.awt.headless").equals("false")))
{
- class VersionChecker
- extends Thread
+ class VersionChecker extends Thread
{
public void run()
{
+ String orgtimeout = System
+ .getProperty("sun.net.client.defaultConnectTimeout");
+ if (orgtimeout == null)
+ {
+ orgtimeout = "30";
+ System.out.println("# INFO: Setting default net timeout to "
+ + orgtimeout + " seconds.");
+ }
String jnlpVersion = null;
try
{
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ "5000");
java.net.URL url = new java.net.URL(
- "http://www.jalview.org/webstart/jalview.jnlp");
- BufferedReader in = new BufferedReader(new InputStreamReader(url.
- openStream()));
+ Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/webstart/jalview.jnlp");
+ BufferedReader in = new BufferedReader(new InputStreamReader(
+ url.openStream()));
String line = null;
- while ( (line = in.readLine()) != null)
+ while ((line = in.readLine()) != null)
{
if (line.indexOf("jalview.version") == -1)
{
@@ -258,12 +351,15 @@ public class Cache
jnlpVersion = line;
break;
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
+ System.out
+ .println("Non-fatal exceptions when checking version at www.jalview.org :");
System.out.println(ex);
jnlpVersion = getProperty("VERSION");
}
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ orgtimeout);
setProperty("LATEST_VERSION", jnlpVersion);
}
@@ -286,18 +382,20 @@ public class Cache
setProperty("VERSION", codeVersion);
- //LOAD USERDEFINED COLOURS
- jalview.gui.UserDefinedColours.initUserColourSchemes(getProperty(
- "USER_DEFINED_COLOURS"));
- jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+ // LOAD USERDEFINED COLOURS
+ jalview.gui.UserDefinedColours
+ .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+ jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
+ false);
}
/**
- * Gets Jalview application property of given key. Returns null
- * if key not found
- *
- * @param key Name of property
- *
+ * Gets Jalview application property of given key. Returns null if key not
+ * found
+ *
+ * @param key
+ * Name of property
+ *
* @return Property value
*/
public static String getProperty(String key)
@@ -305,8 +403,9 @@ public class Cache
return applicationProperties.getProperty(key);
}
- /** These methods are used when checking if the saved preference
- * is different to the default setting
+ /**
+ * These methods are used when checking if the saved preference is different
+ * to the default setting
*/
public static boolean getDefault(String property, boolean def)
@@ -320,8 +419,9 @@ public class Cache
return def;
}
- /** These methods are used when checking if the saved preference
- * is different to the default setting
+ /**
+ * These methods are used when checking if the saved preference is different
+ * to the default setting
*/
public static String getDefault(String property, String def)
{
@@ -336,40 +436,61 @@ public class Cache
/**
* Stores property in the file "HOME_DIR/.jalview_properties"
- *
- * @param key Name of object
- * @param obj String value of property
- *
+ *
+ * @param key
+ * Name of object
+ * @param obj
+ * String value of property
+ *
* @return String value of property
*/
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();
- }
- catch (Exception ex)
+ 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 + "\n" +
- ex);
+ System.out.println("Error setting property: " + key + " " + obj
+ + "\n" + ex);
}
return obj;
}
+ /**
+ * remove the specified property from the jalview properties file
+ *
+ * @param string
+ */
+ public static void removeProperty(String string)
+ {
+ applicationProperties.remove(string);
+ saveProperties();
+ }
+
+ /**
+ * save the properties to the jalview properties path
+ */
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);
+ }
}
}
@@ -377,8 +498,10 @@ public class Cache
* internal vamsas class discovery state
*/
private static int vamsasJarsArePresent = -1;
+
/**
* Searches for vamsas client classes on class path.
+ *
* @return true if vamsas client is present on classpath
*/
public static boolean vamsasJarsPresent()
@@ -388,21 +511,20 @@ public class Cache
try
{
if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
- "uk.ac.vamsas.client.VorbaId") != null)
+ "uk.ac.vamsas.client.VorbaId") != null)
{
- jalview.bin.Cache.log.debug(
- "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ jalview.bin.Cache.log
+ .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
Logger lvclient = Logger.getLogger("uk.ac.vamsas");
- lvclient.setLevel(Level.toLevel(Cache.getDefault("logs.Vamsas.Level",
- Level.INFO.toString())));
+ lvclient.setLevel(Level.toLevel(Cache.getDefault(
+ "logs.Vamsas.Level", Level.INFO.toString())));
lvclient.addAppender(log.getAppender("JalviewLogger"));
// Tell the user that debug is enabled
lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
vamsasJarsArePresent = 0;
jalview.bin.Cache.log.debug("Vamsas Classes are not present");
@@ -410,12 +532,15 @@ public class Cache
}
return (vamsasJarsArePresent > 0);
}
+
/**
* internal vamsas class discovery state
*/
private static int groovyJarsArePresent = -1;
+
/**
* Searches for vamsas client classes on class path.
+ *
* @return true if vamsas client is present on classpath
*/
public static boolean groovyJarsPresent()
@@ -425,21 +550,24 @@ public class Cache
try
{
if (Cache.class.getClassLoader().loadClass(
- "groovy.lang.GroovyObject") != null)
+ "groovy.lang.GroovyObject") != null)
{
- jalview.bin.Cache.log.debug(
- "Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ jalview.bin.Cache.log
+ .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
Logger lgclient = Logger.getLogger("groovy");
- lgclient.setLevel(Level.toLevel(Cache.getDefault("logs.Groovy.Level",
- Level.INFO.toString())));
+ lgclient.setLevel(Level.toLevel(Cache.getDefault(
+ "logs.Groovy.Level", Level.INFO.toString())));
lgclient.addAppender(log.getAppender("JalviewLogger"));
// Tell the user that debug is enabled
lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
}
- }
- catch (Exception e)
+ } catch (Error e)
+ {
+ groovyJarsArePresent = 0;
+ jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+ } catch (Exception e)
{
groovyJarsArePresent = 0;
jalview.bin.Cache.log.debug("Groovy Classes are not present");
@@ -448,4 +576,229 @@ public class Cache
return (groovyJarsArePresent > 0);
}
+ /**
+ * 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.
+ */
+ protected static Object tracker = null;
+
+ protected static Class trackerfocus = null;
+
+ protected static Class jgoogleanalyticstracker = null;
+
+ /**
+ * Initialise the google tracker if it is not done already.
+ */
+ public static void initGoogleTracker()
+ {
+ if (tracker == null)
+ {
+ if (jgoogleanalyticstracker == null)
+ {
+ // try to get the tracker class
+ try
+ {
+ jgoogleanalyticstracker = Cache.class
+ .getClassLoader()
+ .loadClass(
+ "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+ trackerfocus = Cache.class.getClassLoader().loadClass(
+ "com.boxysystems.jgoogleanalytics.FocusPoint");
+ } catch (Exception e)
+ {
+ log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ tracker = null;
+ jgoogleanalyticstracker = null;
+ trackerfocus = null;
+ return;
+ }
+ }
+ // now initialise tracker
+ Exception re = null, ex = null;
+ Error err = null;
+ String vrs = "No Version Accessible";
+ try
+ {
+ // Google analytics tracking code for Library Finder
+ tracker = jgoogleanalyticstracker.getConstructor(new Class[]
+ { String.class, String.class, String.class }).newInstance(
+ new Object[]
+ {
+ "Jalview Desktop",
+ (vrs = jalview.bin.Cache.getProperty("VERSION")
+ + "_"
+ + jalview.bin.Cache.getDefault("BUILD_DATE",
+ "unknown")), "UA-9060947-1" });
+ jgoogleanalyticstracker.getMethod("trackAsynchronously",
+ new Class[]
+ { trackerfocus }).invoke(tracker, new Object[]
+ { trackerfocus.getConstructor(new Class[]
+ { String.class }).newInstance(new Object[]
+ { "Application Started." }) });
+ } catch (RuntimeException e)
+ {
+ re = e;
+ } catch (Exception e)
+ {
+ ex = e;
+ } catch (Error e)
+ {
+ err = e;
+ }
+ if (re != null || ex != null || err != null)
+ {
+ if (log != null)
+ {
+ if (re != null)
+ log.debug("Caught runtime exception in googletracker init:", re);
+ if (ex != null)
+ log.warn(
+ "Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs, ex);
+ if (err != null)
+ log.error(
+ "Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs, err);
+ }
+ else
+ {
+ if (re != null)
+ {
+ System.err
+ .println("Debug: Caught runtime exception in googletracker init:"
+ + vrs);
+ re.printStackTrace();
+ }
+ if (ex != null)
+ {
+ System.err
+ .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs);
+ ex.printStackTrace();
+ }
+
+ if (err != null)
+ {
+ System.err
+ .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs);
+ err.printStackTrace();
+ }
+ }
+ }
+ else
+ {
+ log.debug("Successfully initialised tracker.");
+ }
+ }
+ }
+
+ /**
+ * 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;
+ }
}