/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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, J Engelhardt, LM Lui, 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 <http://www.gnu.org/licenses/>.
*/
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.*;
* </li>
* <li>logs.Jalview.Level - Cache.log stringified level. <br>
* </li>
- * <li>DISCOVERY_START - Boolean - controls if discovery services are queried
- * on startup </li>
- * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
- * </li>
- * <li>SCREEN_WIDTH </li>
- * <li>SCREEN_HEIGHT </li>
- * <li>SCREEN_Y=285 </li>
- * <li>SCREEN_X=371 </li>
- * <li>SHOW_FULLSCREEN boolean </li>
- * <li>FONT_NAME java font name for alignment text display </li>
- * <li>FONT_SIZE size of displayed alignment text </li>
- * <li>FONT_STYLE style of font displayed (sequence labels are always italic)
- * </li>
- * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ') </li>
- * <li>LAST_DIRECTORY last directory for browsing alignment </li>
- * <li>USER_DEFINED_COLOURS list of user defined colour scheme files </li>
- * <li>SHOW_FULL_ID show id with '/start-end' numbers appended </li>
- * <li>SHOW_IDENTITY show percentage identity annotation </li>
- * <li>SHOW_QUALITY show alignment quality annotation </li>
- * <li>SHOW_ANNOTATIONS show alignment annotation rows </li>
- * <li>SHOW_CONSERVATION show alignment conservation annotation </li>
+ * <li>SCREEN_WIDTH</li>
+ * <li>SCREEN_HEIGHT</li>
+ * <li>SCREEN_Y=285</li>
+ * <li>SCREEN_X=371</li>
+ * <li>SHOW_FULLSCREEN boolean</li>
+ * <li>FONT_NAME java font name for alignment text display</li>
+ * <li>FONT_SIZE size of displayed alignment text</li>
+ * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
+ * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
+ * <li>LAST_DIRECTORY last directory for browsing alignment</li>
+ * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
+ * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
+ * <li>SHOW_IDENTITY show percentage identity annotation</li>
+ * <li>SHOW_QUALITY show alignment quality annotation</li>
+ * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
+ * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
* <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
- * annotation row </li>
- * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment </li>
- * <li>DEFAULT_FILE_FORMAT file format used to save </li>
- * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url) </li>
- * <li>SHOW_STARTUP_FILE flag to control loading of startup file </li>
- * <li>VERSION the version of the jalview build </li>
- * <li>BUILD_DATE date of this build </li>
+ * annotation row</li>
+ * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
+ * <li>DEFAULT_FILE_FORMAT file format used to save</li>
+ * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
+ * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
+ * <li>VERSION the version of the jalview build</li>
+ * <li>BUILD_DATE date of this build</li>
* <li>LATEST_VERSION the latest jalview version advertised on the
- * www.jalview.org </li>
+ * www.jalview.org</li>
* <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
- * descriptions </li>
+ * descriptions</li>
* <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
- * suffix to file </li>
- * <li>RECENT_URL list of recently retrieved URLs </li>
- * <li>RECENT_FILE list of recently opened files </li>
- * <li>USE_PROXY flag for whether a http proxy is to be used </li>
- * <li>PROXY_SERVER the proxy </li>
- * <li>PROXY_PORT </li>
+ * suffix to file</li>
+ * <li>RECENT_URL list of recently retrieved URLs</li>
+ * <li>RECENT_FILE list of recently opened files</li>
+ * <li>USE_PROXY flag for whether a http proxy is to be used</li>
+ * <li>PROXY_SERVER the proxy</li>
+ * <li>PROXY_PORT</li>
* <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
- * service </li>
+ * service</li>
* <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
- * service </li>
- * <li>DAS_LOCAL_SOURCE list of local das sources </li>
- * <li>SHOW_OVERVIEW boolean for overview window display </li>
- * <li>ANTI_ALIAS boolean for smooth fonts </li>
- * <li>RIGHT_ALIGN_IDS boolean </li>
- * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
- * </li>
- * <li>PAD_GAPS boolean </li>
- * <li>ID_ITALICS boolean </li>
- * <li>SHOW_JV_SUFFIX </li>
- * <li>WRAP_ALIGNMENT </li>
+ * service</li>
+ * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
+ * collecting usage statistics</li>
+ * <li>DAS_LOCAL_SOURCE list of local das sources</li>
+ * <li>SHOW_OVERVIEW boolean for overview window display</li>
+ * <li>ANTI_ALIAS boolean for smooth fonts</li>
+ * <li>RIGHT_ALIGN_IDS boolean</li>
+ * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
+ * <li>PAD_GAPS boolean</li>
+ * <li>ID_ITALICS boolean</li>
+ * <li>SHOW_JV_SUFFIX</li>
+ * <li>WRAP_ALIGNMENT</li>
* <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
- * style check </li>
- * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity) </li>
+ * style check</li>
+ * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
* <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
- * $SEQUENCE_ID$ </li>
- * <li>DAS_REGISTRY_URL the registry to query </li>
- * <li>DEFAULT_BROWSER for unix </li>
- * <li>DAS_ACTIVE_SOURCE list of active sources </li>
+ * $SEQUENCE_ID$</li>
+ * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
+ * jalview.utils.GroupURLLink for more info</li>
+ * <li>DAS_REGISTRY_URL the registry to query</li>
+ * <li>DEFAULT_BROWSER for unix</li>
+ * <li>DAS_ACTIVE_SOURCE list of active sources</li>
* <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
- * (false) </li>
- * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence ID tooltip</li>
- * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence ID tooltip</li>
- * <li> </li>
+ * (false)</li>
+ * <li>VERSION_CHECK (true) check for the latest release version from
+ * www.jalview.org (or the alias given by the www.jalview.org property)</li>
+ * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
+ * ID tooltip</li>
+ * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
+ * ID tooltip</li>
+ * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
+ * displayed as '.'</li>
+ * <li>SORT_BY_TREE (false) sort the current alignment view according to the
+ * order of a newly displayed tree</li>
+ * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
+ * sequence ID strings before attempting retrieval from any datasource</li>
+ * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
+ * alignment.</li>
+ * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
+ * in the alignment.</li>
+ * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
+ * 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>
*
- * </ul>
+ * <li></li>
*
+ * </ul>
+ * Deprecated settings:
+ * <ul>
+ * * <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>
+ * <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;
+
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");
{
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));
}
+ // 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
// MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
// VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
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);
// 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")))
{
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;
* found
*
* @param key
- * Name of property
+ * Name of property
*
* @return Property value
*/
* 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
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);
+ }
}
}
// 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;
/**
* generate Das1Sources from the local das source list
+ *
* @return Vector of Das1Sources
*/
public static Vector getLocalDasSources()
{
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));
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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff