X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=d2f400d3f94ed49f3dba42e133ac6fc130611b84;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=4469975cb745b13e302697a4f2c3b16245ef1e16;hpb=8ceb196758338574e45b021e0aa4f9a78a8c8bad;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 4469975..d2f400d 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,32 +1,31 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 file is part of Jalview.
*
- * 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.
+ * 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.
*
- * 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 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;
-import com.boxysystems.jgoogleanalytics.FocusPoint;
-import com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker;
-
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* list entries are separated by '|' symbols unless otherwise stated (|) clauses
@@ -43,80 +42,107 @@ import com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker;
*
*
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
- * 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
+ * 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
+ * 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
+ * www.jalview.org
* PIR_MODELLER boolean indicating if PIR files are written with MODELLER
- * descriptions
+ * 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
+ * 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
+ * service
* QUESTIONNAIRE last questionnaire:responder id string from questionnaire
- * service
- * USAGESTATS (true) 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
+ * 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)
+ * 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
+ * $SEQUENCE_ID$
+ * 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)
- * 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
+ * (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 $Revision$
*/
@@ -154,15 +180,24 @@ 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
+ // the log
+
ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
"System.err");
ap.setName("JalviewLogger");
org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
- // log output
+ // 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");
@@ -199,11 +234,31 @@ 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");
@@ -218,9 +273,7 @@ public class Cache
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));
}
@@ -230,8 +283,8 @@ 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);
@@ -259,6 +312,7 @@ public class Cache
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
if (jnlpVersion == null
+ && getDefault("VERSION_CHECK", true)
&& (System.getProperty("java.awt.headless") == null || System
.getProperty("java.awt.headless").equals("false")))
{
@@ -281,7 +335,7 @@ 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;
@@ -340,7 +394,7 @@ public class Cache
* found
*
* @param key
- * Name of property
+ * Name of property
*
* @return Property value
*/
@@ -384,20 +438,24 @@ public class Cache
* Stores property in the file "HOME_DIR/.jalview_properties"
*
* @param key
- * Name of object
+ * Name of object
* @param obj
- * String value of property
+ * 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();
+ 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
@@ -406,16 +464,33 @@ public class Cache
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);
+ }
}
}
@@ -488,6 +563,10 @@ public class Cache
// Tell the user that debug is enabled
lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
}
+ } catch (Error e)
+ {
+ groovyJarsArePresent = 0;
+ jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
@@ -499,6 +578,7 @@ public class Cache
/**
* generate Das1Sources from the local das source list
+ *
* @return Vector of Das1Sources
*/
public static Vector getLocalDasSources()
@@ -518,10 +598,14 @@ public class Cache
{
source.setUrl(source.getUrl().substring(9));
// this source also serves sequences as well as features
- source.setCapabilities(new String[] { "sequence", "features"});
- } else {
+ source.setCapabilities(new String[]
+ { "sequence", "features" });
+ }
+ else
+ {
// default is that all user added sources serve features
- source.setCapabilities(new String[] { "features"});
+ source.setCapabilities(new String[]
+ { "features" });
}
source.setNickname(token.substring(0, bar));
@@ -531,41 +615,190 @@ public class Cache
}
return localSources;
}
+
/**
- * GA tracker object - null if tracking not enabled.
+ * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
+ * enabled.
*/
- protected static JGoogleAnalyticsTracker tracker=null;
+ 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)
- {
- String vrs="No Version Accessible";
- try {
- //Google analytics tracking code for Library Finder
- tracker = new JGoogleAnalyticsTracker("Jalview Desktop",
- (vrs=jalview.bin.Cache.getProperty("VERSION")+"_"+jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")),
- "UA-9060947-1");
- tracker.trackAsynchronously(new FocusPoint("Application Started."));
- } catch (RuntimeException e)
+ if (tracker == null)
{
- if (log!=null) {
- log.debug("Caught runtime exception in googletracker init:",e);
- }
- // quietly return.
- }
- catch (Exception e)
- {
- // unexpected error
- if (log!=null)
+ if (jgoogleanalyticstracker == null)
+ {
+ // try to get the tracker class
+ try
{
- log.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "+vrs,e);
- } else {
- log.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "+vrs,e);
+ 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;
}
}