/*
- * 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 2.5)
+ * Copyright (C) 2010 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 <http://www.gnu.org/licenses/>.
*/
package jalview.bin;
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 javax.swing.*;
import jalview.gui.*;
-import jalview.io.AppletFormatAdapter;
+import jalview.util.Platform;
/**
* Main class for Jalview Application <br>
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+ if (new Platform().isAMac())
+ {
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ }
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ "-nodisplay\tRun Jalview without User Interface.\n"
+ "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+ + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
+ "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
+ "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
+ "-features FILE\tUse the given file to mark features on the alignment.\n"
try
{
- UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()
- // UIManager.getCrossPlatformLookAndFeelClassName()
- // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
- // "javax.swing.plaf.metal.MetalLookAndFeel"
- // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
- // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
-
- );
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
} catch (Exception ex)
{
}
+
if (!headless)
{
desktop = new Desktop();
+ desktop.setInBatchMode(true); // indicate we are starting up
desktop.setVisible(true);
- desktop.discoverer.start();
+ desktop.startServiceDiscovery();
if (!aparser.contains("nousagestats"))
{
startUsageStats(desktop);
String groovyscript = null; // script to execute after all loading is
// 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)
{
// session at the user's leisure.
Cache.log
.info("Skipping Push for import of data into existing vamsas session."); // TODO:
- // enable
- // this
- // when
- // debugged
+ // enable
+ // this
+ // when
+ // debugged
// desktop.getVamsasApplication().push_update();
}
}
return;
}
- data = aparser.getValue("colour");
+ data = aparser.getValue("colour", true);
if (data != null)
{
data.replaceAll("%20", " ");
}
// 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);
{
af.getViewport().setSortByTree(false);
}
- data = aparser.getValue("tree");
+ data = aparser.getValue("tree", true);
if (data != null)
{
jalview.io.NewickFile fin = null;
ex.printStackTrace(System.err);
}
}
+ // TODO - load PDB structure(s) to alignment JAL-629
+ // (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.
- try
- {
- Thread.sleep(10);
- } catch (Exception e)
+ FeatureFetcher ff = startFeatureFetching(getFeatures);
+ if (ff != null)
+ while (!ff.allFinished() || af.operationInProgress())
{
+ // wait around until fetching is finished.
+ try
+ {
+ Thread.sleep(100);
+ } catch (Exception e)
+ {
+ }
}
- }
+ getFeatures = null; // have retrieved features - forget them now.
}
if (groovyscript != null)
{
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)
startFeatureFetching(getFeatures);
}
}
+ // Once all other stuff is done, execute any groovy scripts (in order)
if (groovyscript != null)
{
if (jalview.bin.Cache.groovyJarsPresent())
+ groovyscript);
}
}
-
- // Once all other stuff is done, execute any groovy scripts (in order)
+ // and finally, turn off batch mode indicator - if the desktop still exists
+ if (desktop!=null)
+ {
+ desktop.setInBatchMode(false);
+ }
}
private static void startUsageStats(final 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)",
+ + "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()
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;
+ 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)
*
* @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)
*/
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;
}
}
}
+
+/**
+ * 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;
+ }
+};
git://source.jalview.org / jalview.git / blobdiff