X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=60fae3739f8a24c94dcc019b6293134d44134e03;hb=74666bccffce69d865cfc5479f81f394e2d14d5e;hp=195ad2987e08cad8809fa47f44198a00c84884d1;hpb=88bc025708f1b7881bababb92d14351760e0f9da;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 195ad29..60fae37 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,17 +1,17 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -22,64 +22,166 @@ import java.io.*;
import java.util.*;
import org.apache.log4j.*;
+import org.biojava.dasobert.dasregistry.Das1Source;
/**
- * Stores and retrieves Jalview Application Properties
- *
Current properties include:
- *
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.
- *
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
- * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR
- * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,
- * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE
-
+ * 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)
+ *
+ * - 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.
+ *
+ * - 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)
+ * - 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 '.'
+ * -
+ *
+ *
+ *
* @author $author$
* @version $Revision$
*/
public class Cache
{
/**
- * Initialises the Apache Axis logger
+ * 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
*/
public static Logger log;
/** Jalview Properties */
public static Properties applicationProperties = new Properties();
- /** Default file is ~/.jalview_properties */
+ /** Default file is ~/.jalview_properties */
static String propertiesFile;
public static void initLogger()
{
try
{
+ ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+ "System.err");
+ ap.setName("JalviewLogger");
+ 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())));
jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
- "logs.Jalview.level",
- Level.INFO.toString())));
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
- "System.err");
- ap.setName("JalviewLogger");
-
- 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);
}
}
@@ -89,8 +191,8 @@ 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";
}
try
@@ -100,17 +202,19 @@ public class Cache
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.setProperty("http.proxyHost", getDefault("PROXY_SERVER", 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));
}
@@ -119,20 +223,16 @@ 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");
@@ -152,25 +252,34 @@ 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
+ && (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()));
+ "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)
{
@@ -182,12 +291,15 @@ 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);
}
@@ -210,18 +322,20 @@ 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)
@@ -229,8 +343,9 @@ 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)
@@ -244,8 +359,9 @@ 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)
{
@@ -260,10 +376,12 @@ 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)
@@ -274,11 +392,10 @@ public class Cache
applicationProperties.setProperty(key, obj);
applicationProperties.store(out, "---JalviewX Properties File---");
out.close();
- }
- catch (Exception ex)
+ } 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;
}
@@ -290,8 +407,7 @@ public class Cache
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.out.println("Error saving properties: " + ex);
}
@@ -301,8 +417,10 @@ 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()
@@ -312,21 +430,20 @@ 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");
@@ -334,12 +451,15 @@ 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()
@@ -349,21 +469,20 @@ 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 (Exception e)
{
groovyJarsArePresent = 0;
jalview.bin.Cache.log.debug("Groovy Classes are not present");
@@ -372,4 +491,39 @@ 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;
+ }
+
}