X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=624ac582c723569dea6e1fc998201a1e0870088b;hb=0233fbee0ff0d7fad302aa2da743c51fd64be101;hp=8205374d31fe25222bd55113ced7a9595662dc66;hpb=0bb18e76033e7b8f4f76b23747793302ed4d9881;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8205374..624ac58 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,6 +1,6 @@
/*
- * 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 (Development Version 2.4.1)
+ * Copyright (C) 2009 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
@@ -26,6 +26,12 @@ import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.lang.reflect.Constructor;
import java.net.URL;
+import java.net.URLDecoder;
+import java.security.AllPermission;
+import java.security.CodeSource;
+import java.security.PermissionCollection;
+import java.security.Permissions;
+import java.security.Policy;
import java.util.*;
import javax.swing.*;
@@ -43,12 +49,29 @@ import jalview.io.AppletFormatAdapter;
*/
public class Jalview
{
+ static
+ {
+ // grab all the rights we can the JVM
+ Policy.setPolicy(new Policy()
+ {
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ public void refresh()
+ {
+ }
+ });
+ }
/**
* main class for Jalview application
*
* @param args
- * open filename
+ * open filename
*/
public static void main(String[] args)
{
@@ -83,18 +106,40 @@ public class Jalview
+ "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ "-noquestionnaire\tTurn off questionnaire check.\n"
- + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments.\n"
- +"\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
- +"\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+ + "-nousagestats\tTurn off google analytics tracking for this session.\n"
+ + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
+ // +
+ // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
+ + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
+ + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
+ + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+ // +
+ // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
+ // + "-vses vamsas-session\tJoin session with given URN\n"
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
System.exit(0);
}
-
Cache.loadProperties(aparser.getValue("props")); // must do this before
// anything else!
-
+ String defs = aparser.getValue("setprop");
+ while (defs != null)
+ {
+ int p = defs.indexOf('=');
+ if (p == -1)
+ {
+ System.err.println("Ignoring invalid setprop argument : " + defs);
+ }
+ else
+ {
+ System.out.println("Executing setprop argument: " + defs);
+ // DISABLED FOR SECURITY REASONS
+ // TODO: add a property to allow properties to be overriden by cli args
+ // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+ }
+ defs = aparser.getValue("setprop");
+ }
if (aparser.contains("nodisplay"))
{
System.setProperty("java.awt.headless", "true");
@@ -137,6 +182,10 @@ public class Jalview
desktop = new Desktop();
desktop.setVisible(true);
desktop.discoverer.start();
+ if (!aparser.contains("nousagestats"))
+ {
+ startUsageStats(desktop);
+ }
if (!aparser.contains("noquestionnaire"))
{
String url = aparser.getValue("questionnaire");
@@ -169,20 +218,104 @@ public class Jalview
String file = null, protocol = null, format = null, data = null;
jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
Vector getFeatures = null; // vector of das source nicknames to fetch
- // features from
+ // features from
// loading is done.
String groovyscript = null; // script to execute after all loading is
- // completed one way or another
+ // completed one way or another
// extract groovy argument and execute if necessary
- groovyscript = aparser.getValue("groovy");
- file = aparser.getValue("open");
+ groovyscript = aparser.getValue("groovy",true);
+ file = aparser.getValue("open",true);
if (file == null && desktop == null)
{
System.out.println("No files to open!");
System.exit(1);
}
+ String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser
+ .getValue("vsess");
+ if (vamsasImport != null || vamsasSession != null)
+ {
+ if (desktop == null || headless)
+ {
+ System.out
+ .println("Headless vamsas sessions not yet supported. Sorry.");
+ System.exit(1);
+ }
+ // if we have a file, start a new session and import it.
+ boolean inSession = false;
+ if (vamsasImport != null)
+ {
+ try
+ {
+ String viprotocol = Jalview.checkProtocol(vamsasImport);
+ if (viprotocol == jalview.io.FormatAdapter.FILE)
+ {
+ inSession = desktop.vamsasImport(new File(vamsasImport));
+ }
+ else if (viprotocol == jalview.io.FormatAdapter.URL)
+ {
+ inSession = desktop.vamsasImport(new URL(vamsasImport));
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Exeption when importing " + vamsasImport
+ + " as a vamsas document.");
+ e.printStackTrace();
+ }
+ if (!inSession)
+ {
+ System.err.println("Failed to import " + vamsasImport
+ + " as a vamsas document.");
+ }
+ else
+ {
+ System.out.println("Imported Successfully into new session "
+ + desktop.getVamsasApplication().getCurrentSession());
+ }
+ }
+ if (vamsasSession != null)
+ {
+ if (vamsasImport != null)
+ {
+ // close the newly imported session and import the Jalview specific
+ // remnants into the new session later on.
+ desktop.vamsasStop_actionPerformed(null);
+ }
+ // now join the new session
+ try
+ {
+ if (desktop.joinVamsasSession(vamsasSession))
+ {
+ System.out.println("Successfully joined vamsas session "
+ + vamsasSession);
+ }
+ else
+ {
+ System.err.println("WARNING: Failed to join vamsas session "
+ + vamsasSession);
+ }
+ } catch (Exception e)
+ {
+ System.err.println("ERROR: Failed to join vamsas session "
+ + vamsasSession);
+ e.printStackTrace();
+ }
+ if (vamsasImport != null)
+ {
+ // the Jalview specific remnants can now be imported into the new
+ // session at the user's leisure.
+ Cache.log
+ .info("Skipping Push for import of data into existing vamsas session."); // TODO:
+ // enable
+ // this
+ // when
+ // debugged
+ // desktop.getVamsasApplication().push_update();
+ }
+ }
+ }
+ // Finally, deal with the remaining input data.
if (file != null)
{
System.out.println("Opening file: " + file);
@@ -205,14 +338,13 @@ public class Jalview
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
-
if (af == null)
{
System.out.println("error");
return;
}
- data = aparser.getValue("colour");
+ data = aparser.getValue("colour",true);
if (data != null)
{
data.replaceAll("%20", " ");
@@ -233,26 +365,35 @@ public class Jalview
}
// Must maintain ability to use the groups flag
- data = aparser.getValue("groups");
+ data = aparser.getValue("groups",true);
if (data != null)
{
af.parseFeaturesFile(data, checkProtocol(data));
System.out.println("Added " + data);
}
- data = aparser.getValue("features");
+ data = aparser.getValue("features",true);
if (data != null)
{
af.parseFeaturesFile(data, checkProtocol(data));
System.out.println("Added " + data);
}
- data = aparser.getValue("annotations");
+ data = aparser.getValue("annotations",true);
if (data != null)
{
af.loadJalviewDataFile(data);
System.out.println("Added " + data);
}
- data = aparser.getValue("tree");
+ // set or clear the sortbytree flag.
+ if (aparser.contains("sortbytree"))
+ {
+ af.getViewport().setSortByTree(true);
+ }
+ if (aparser.contains("nosortbytree"))
+ {
+ af.getViewport().setSortByTree(false);
+ }
+ data = aparser.getValue("tree",true);
if (data != null)
{
jalview.io.NewickFile fin = null;
@@ -271,22 +412,27 @@ public class Jalview
ex.printStackTrace(System.err);
}
}
+ // todo - load PDB structure to alignment
+ // (associate with identical sequence in alignment, or a specified sequence)
+
+
getFeatures = checkDasArguments(aparser);
if (af != null && getFeatures != null)
{
- startFeatureFetching(getFeatures);
- // need to block until fetching is complete.
- while (af.operationInProgress())
- {
- // wait around until fetching is finished.
+ FeatureFetcher ff = startFeatureFetching(getFeatures);
+ if (ff!=null)
+ while (!ff.allFinished() || af.operationInProgress())
+ {
+ // wait around until fetching is finished.
try
{
- Thread.sleep(10);
+ Thread.sleep(100);
} catch (Exception e)
{
}
}
+ getFeatures = null; // have retrieved features - forget them now.
}
if (groovyscript != null)
{
@@ -353,7 +499,7 @@ public class Jalview
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
- if (!headless && file == null
+ if (!headless && file == null && vamsasImport == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
file = jalview.bin.Cache.getDefault("STARTUP_FILE",
@@ -380,7 +526,10 @@ public class Jalview
getFeatures = checkDasArguments(aparser);
// extract groovy arguments before anything else.
}
- // Once all loading is done. Retrieve features.
+ // If the user has specified features to be retrieved,
+ // or a groovy script to be executed, do them if they
+ // haven't been done already
+ // fetch features for the default alignment
if (getFeatures != null)
{
if (startUpAlframe != null)
@@ -388,6 +537,7 @@ public class Jalview
startFeatureFetching(getFeatures);
}
}
+ // execute a groovy script.
if (groovyscript != null)
{
if (jalview.bin.Cache.groovyJarsPresent())
@@ -406,14 +556,45 @@ public class Jalview
// Once all other stuff is done, execute any groovy scripts (in order)
}
+ private static void startUsageStats(final Desktop desktop)
+ {
+ /**
+ * start a User Config prompt asking if we can log usage statistics.
+ */
+ jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
+ desktop.desktop,
+ "USAGESTATS",
+ "Jalview Usage Statistics",
+ "Do you want to help make Jalview better by enabling "
+ +"the collection of usage statistics with Google Analytics ?"
+ +"\n\n(you can enable or disable usage tracking in the preferences)",
+ new Runnable()
+ {
+ public void run()
+ {
+ Cache.log
+ .info("Initialising googletracker for usage stats.");
+ Cache.initGoogleTracker();
+ Cache.log.debug("Tracking enabled.");
+ }
+ }, new Runnable()
+ {
+ public void run()
+ {
+ Cache.log.info("Not enabling Google Tracking.");
+ }
+ }, null, true);
+ SwingUtilities.invokeLater(prompter);
+ }
+
/**
* Locate the given string as a file and pass it to the groovy interpreter.
*
* @param groovyscript
- * the script to execute
+ * the script to execute
* @param jalviewContext
- * the Jalview Desktop object passed in to the groovy binding
- * as the 'Jalview' object.
+ * the Jalview Desktop object passed in to the groovy binding as the
+ * 'Jalview' object.
*/
private static void executeGroovyScript(String groovyscript,
Object jalviewContext)
@@ -481,8 +662,8 @@ public class Jalview
* groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
*
* String[] roots = new String[] { "/my/groovy/script/path" };
- * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding =
- * new Binding(); binding.setVariable("input", "world");
+ * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding
+ * = new Binding(); binding.setVariable("input", "world");
* gse.run("hello.groovy", binding);
*/
ClassLoader cl = jalviewContext.getClass().getClassLoader();
@@ -530,11 +711,11 @@ public class Jalview
Vector source = null;
String data;
String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
- while ((data = aparser.getValue("dasserver")) != null)
+ while ((data = aparser.getValue("dasserver",true)) != null)
{
String nickname = null;
String url = null;
- boolean seq=false,feat=true;
+ boolean seq = false, feat = true;
int pos = data.indexOf('=');
// determine capabilities
if (pos > 0)
@@ -542,7 +723,9 @@ public class Jalview
nickname = data.substring(0, pos);
}
url = data.substring(pos + 1);
- if (url != null && (url.startsWith("http:") || url.startsWith("sequence:http:")))
+ if (url != null
+ && (url.startsWith("http:") || url
+ .startsWith("sequence:http:")))
{
if (nickname == null)
{
@@ -573,7 +756,7 @@ public class Jalview
+ locsources);
Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
}
- while ((data = aparser.getValue("fetchfrom")) != null)
+ while ((data = aparser.getValue("fetchfrom",true)) != null)
{
System.out.println("adding source '" + data + "'");
if (source == null)
@@ -590,28 +773,20 @@ public class Jalview
*
* @param dasSources
*/
- private static void startFeatureFetching(final Vector dasSources)
+ private static FeatureFetcher startFeatureFetching(final Vector dasSources)
{
+ FeatureFetcher ff = new FeatureFetcher();
AlignFrame afs[] = Desktop.getAlignframes();
if (afs == null || afs.length == 0)
{
- return;
+ return null;
}
for (int i = 0; i < afs.length; i++)
{
- final AlignFrame af = afs[i];
- SwingUtilities.invokeLater(new Runnable()
- {
-
- public void run()
- {
- af.featureSettings_actionPerformed(null);
- af.featureSettings.fetchDasFeatures(dasSources);
- }
- });
+ ff.addFetcher(afs[i], dasSources);
}
+ return ff;
}
-
private static String checkProtocol(String file)
{
String protocol = jalview.io.FormatAdapter.FILE;
@@ -659,13 +834,27 @@ class ArgsParser
*/
public String getValue(String arg)
{
+ return getValue(arg, false);
+ }
+ public String getValue(String arg, boolean utf8decode)
+ {
int index = vargs.indexOf(arg);
- String ret = null;
+ String dc=null,ret = null;
if (index != -1)
{
ret = vargs.elementAt(index + 1).toString();
vargs.removeElementAt(index);
vargs.removeElementAt(index);
+ if (utf8decode && ret!=null)
+ {
+ try {
+ dc = URLDecoder.decode(ret,"UTF-8");
+ ret = dc;
+ } catch (Exception e)
+ {
+ // TODO: log failure to decode
+ }
+ }
}
return ret;
}
@@ -700,3 +889,48 @@ class ArgsParser
}
}
+/**
+ * keep track of feature fetching tasks.
+ * @author JimP
+ *
+ */
+class FeatureFetcher {
+ /*
+ * TODO: generalise to track all jalview events to orchestrate batch processing events.
+ */
+
+ private int queued=0;
+ private int running=0;
+ public FeatureFetcher()
+ {
+
+ }
+ public void addFetcher(final AlignFrame af, final Vector dasSources)
+ {
+ final long id = System.currentTimeMillis();
+ queued++;
+ final FeatureFetcher us=this;
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ synchronized (us) {
+ queued--;
+ running++;
+ }
+
+ af.setProgressBar("DAS features being retrieved...", id);
+ af.featureSettings_actionPerformed(null);
+ af.featureSettings.fetchDasFeatures(dasSources, true);
+ af.setProgressBar(null, id);
+ synchronized (us) {
+ running --;
+ }
+ }
+ }).start();
+ }
+ public synchronized boolean allFinished() {
+ return queued==0 && running==0;
+ }
+};