/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* 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.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.HtmlSvgOutput;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.lang.reflect.Constructor;
+import java.net.MalformedURLException;
+import java.net.URI;
import java.net.URL;
import java.net.URLDecoder;
import java.security.AllPermission;
import java.security.PermissionCollection;
import java.security.Permissions;
import java.security.Policy;
-import java.util.*;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Vector;
-import javax.swing.*;
-
-import jalview.gui.*;
-import jalview.util.Platform;
+import javax.swing.UIManager;
+import javax.swing.UnsupportedLookAndFeelException;
/**
* 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;
if (aparser.contains("help") || aparser.contains("h"))
{
- System.out
- .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"
- + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
- + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
- + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
- + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
- + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
- + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
- + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
- + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
- + "-png FILE\tCreate PNG image FILE from alignment.\n"
- + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
- + "-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"
- + "-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");
+ showUsage();
System.exit(0);
}
- Cache.loadProperties(aparser.getValue("props")); // must do this before
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
+ {
+ System.setProperty("java.awt.headless", "true");
+ headless = true;
+ }
+ String usrPropsFile = aparser.getValue("props");
+ Cache.loadProperties(usrPropsFile); // must do this before
+ if (usrPropsFile != null)
+ {
+ System.out.println("CMD [-props " + usrPropsFile
+ + "] executed successfully!");
+ }
+
// anything else!
+
+ final String jabawsUrl = aparser.getValue("jabaws");
+ if (jabawsUrl != null)
+ {
+ try
+ {
+ Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println("CMD [-jabaws " + jabawsUrl
+ + "] executed successfully!");
+ } catch (MalformedURLException e)
+ {
+ System.err.println("Invalid jabaws parameter: " + jabawsUrl
+ + " ignored");
+ }
+ }
+
String defs = aparser.getValue("setprop");
while (defs != null)
{
}
defs = aparser.getValue("setprop");
}
- if (aparser.contains("nodisplay"))
- {
- System.setProperty("java.awt.headless", "true");
- }
if (System.getProperty("java.awt.headless") != null
&& System.getProperty("java.awt.headless").equals("true"))
{
headless = true;
}
-
+ System.setProperty("http.agent",
+ "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
try
{
Cache.initLogger();
} catch (Exception ex)
{
}
+ if (new Platform().isAMac())
+ {
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+ "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ try
+ {
+ UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
+ .getLookAndFeel());
+ } catch (UnsupportedLookAndFeelException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
if (!headless)
{
{
startUsageStats(desktop);
}
+ else
+ {
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+
if (!aparser.contains("noquestionnaire"))
{
String url = aparser.getValue("questionnaire");
// questionnaire
Cache.log.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
+ System.out.println("CMD questionnaire[-" + url
+ + "] executed successfully!");
}
else
{
}
}
}
+ else
+ {
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
+ }
+ desktop.checkForNews();
+ }
+
+ if (!isHeadlessMode())
+ {
+ BioJsHTMLOutput.updateBioJS();
}
String file = null, protocol = null, format = null, data = null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+ jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
Vector getFeatures = null; // vector of das source nicknames to fetch
// features from
// loading is done.
{
try
{
- String viprotocol = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport);
+ String viprotocol = jalview.io.AppletFormatAdapter
+ .checkProtocol(vamsasImport);
if (viprotocol == jalview.io.FormatAdapter.FILE)
{
inSession = desktop.vamsasImport(new File(vamsasImport));
}
}
}
+ long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
{
- System.out.println("Opening file: " + file);
+ if (!headless)
+ {
+ desktop.setProgressBar(MessageManager
+ .getString("status.processing_commandline_args"),
+ progress = System.currentTimeMillis());
+ }
+ System.out.println("CMD [-open " + file + "] executed successfully!");
if (!file.startsWith("http://"))
{
if (af == null)
{
System.out.println("error");
- return;
}
-
- data = aparser.getValue("colour", true);
- if (data != null)
+ else
{
- data.replaceAll("%20", " ");
- jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
- .getColour(af.getViewport().getAlignment(), data);
-
- if (cs == null)
+ data = aparser.getValue("colour", true);
+ if (data != null)
{
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- "white");
- ucs.parseAppletParameter(data);
- cs = ucs;
- }
+ data.replaceAll("%20", " ");
- System.out.println("colour is " + data);
- af.changeColour(cs);
- }
-
- // Must maintain ability to use the groups flag
- data = aparser.getValue("groups", true);
- if (data != null)
- {
- af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
- }
- data = aparser.getValue("features", true);
- if (data != null)
- {
- af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
- }
+ jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
+ .getColour(af.getViewport().getAlignment(), data);
- data = aparser.getValue("annotations", true);
- if (data != null)
- {
- af.loadJalviewDataFile(data, null, null, null);
- System.out.println("Added " + data);
- }
- // 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;
- try
- {
- fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
- if (fin != null)
+ if (cs == null)
{
- af.getViewport().setCurrentTree(
- af.ShowNewickTree(fin, data).getTree());
- System.out.println("Added tree " + data);
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ "white");
+ ucs.parseAppletParameter(data);
+ cs = ucs;
}
- } catch (IOException ex)
- {
- System.err.println("Couldn't add tree " + data);
- 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)
- {
- FeatureFetcher ff = startFeatureFetching(getFeatures);
- if (ff != null)
- while (!ff.allFinished() || af.operationInProgress())
+ else
{
- // wait around until fetching is finished.
- try
- {
- Thread.sleep(100);
- } catch (Exception e)
- {
-
- }
+ System.out.println("CMD [-color " + data
+ + "] executed successfully!");
}
- getFeatures = null; // have retrieved features - forget them now.
- }
- if (groovyscript != null)
- {
- // Execute the groovy script after we've done all the rendering stuff
- // and before any images or figures are generated.
- if (jalview.bin.Cache.groovyJarsPresent())
+ af.changeColour(cs);
+ }
+
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue("groups", true);
+ if (data != null)
{
- System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, desktop);
+ af.parseFeaturesFile(data,
+ jalview.io.AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println("CMD groups[-" + data
+ + "] executed successfully!");
}
- else
+ data = aparser.getValue("features", true);
+ if (data != null)
{
- System.err
- .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
- + groovyscript);
+ af.parseFeaturesFile(data,
+ jalview.io.AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-features " + data
+ + "] executed successfully!");
}
- groovyscript = null;
- }
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
- {
- format = aparser.nextValue();
- file = aparser.nextValue();
- if (format.equalsIgnoreCase("png"))
+ data = aparser.getValue("annotations", true);
+ if (data != null)
+ {
+ af.loadJalviewDataFile(data, null, null, null);
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-annotations " + data
+ + "] executed successfully!");
+ }
+ // set or clear the sortbytree flag.
+ if (aparser.contains("sortbytree"))
+ {
+ af.getViewport().setSortByTree(true);
+ if (af.getViewport().getSortByTree())
+ {
+ System.out.println("CMD [-sortbytree] executed successfully!");
+ }
+ }
+ if (aparser.contains("no-annotation"))
{
- af.createPNG(new java.io.File(file));
- imageName = (new java.io.File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ System.out.println("CMD no-annotation executed successfully!");
+ }
}
- else if (format.equalsIgnoreCase("imgMap"))
+ if (aparser.contains("nosortbytree"))
{
- af.createImageMap(new java.io.File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
+ af.getViewport().setSortByTree(false);
+ if (!af.getViewport().getSortByTree())
+ {
+ System.out
+ .println("CMD [-nosortbytree] executed successfully!");
+ }
}
- else if (format.equalsIgnoreCase("eps"))
+ data = aparser.getValue("tree", true);
+ if (data != null)
{
- System.out.println("Creating EPS file: " + file);
- af.createEPS(new java.io.File(file));
- continue;
+ jalview.io.NewickFile fin = null;
+ try
+ {
+ System.out.println("CMD [-tree " + data
+ + "] executed successfully!");
+ fin = new jalview.io.NewickFile(data,
+ jalview.io.AppletFormatAdapter.checkProtocol(data));
+ if (fin != null)
+ {
+ af.getViewport().setCurrentTree(
+ af.ShowNewickTree(fin, data).getTree());
+ }
+ } catch (IOException ex)
+ {
+ System.err.println("Couldn't add tree " + data);
+ ex.printStackTrace(System.err);
+ }
}
+ // TODO - load PDB structure(s) to alignment JAL-629
+ // (associate with identical sequence in alignment, or a specified
+ // sequence)
- if (af.saveAlignment(file, format))
+ getFeatures = checkDasArguments(aparser);
+ if (af != null && getFeatures != null)
{
- System.out.println("Written alignment in " + format
- + " format to " + file);
+ 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.
}
- else
+ if (groovyscript != null)
{
- System.out.println("Error writing file " + file + " in " + format
- + " format!!");
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ if (jalview.bin.Cache.groovyJarsPresent())
+ {
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, new Object[] { desktop, af });
+
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
+ }
+ else
+ {
+ System.err
+ .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ + groovyscript);
+ }
+ groovyscript = null;
}
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
+ {
+ format = aparser.nextValue();
+ file = aparser.nextValue();
- }
+ if (format.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new java.io.File(file));
+ imageName = (new java.io.File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("svg"))
+ {
+ File imageFile = new java.io.File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ System.out.println("Creating SVG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("html"))
+ {
+ File imageFile = new java.io.File(file);
+ imageName = imageFile.getName();
+ new HtmlSvgOutput(new java.io.File(file), af.alignPanel);
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new java.io.File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("eps"))
+ {
+ File outputFile = new java.io.File(file);
+ System.out.println("Creating EPS file: "
+ + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
+ continue;
+ }
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
+ if (af.saveAlignment(file, format))
+ {
+ System.out.println("Written alignment in " + format
+ + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + format + " format!!");
+ }
+
+ }
+
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
+ }
}
}
AlignFrame startUpAlframe = null;
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
+
if (!headless && file == null && vamsasImport == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
- file = jalview.bin.Cache.getDefault("STARTUP_FILE",
- "http://www.jalview.org/examples/exampleFile_2_3.jar");
+ file = jalview.bin.Cache.getDefault(
+ "STARTUP_FILE",
+ jalview.bin.Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org")
+ + "/examples/exampleFile_2_7.jar");
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ {
+ // hardwire upgrade of the startup file
+ file.replace("_2_3.jar", "_2_7.jar");
+ // and remove the stale setting
+ jalview.bin.Cache.removeProperty("STARTUP_FILE");
+ }
protocol = "File";
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, desktop);
+ executeGroovyScript(groovyscript, new Object[] { desktop,
+ startUpAlframe });
}
else
{
// and finally, turn off batch mode indicator - if the desktop still exists
if (desktop != null)
{
+ if (progress != -1)
+ {
+ desktop.setProgressBar(null, progress);
+ }
desktop.setInBatchMode(false);
}
}
+ private static void showUsage()
+ {
+ System.out
+ .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"
+ + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
+ + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
+ + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
+ + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
+ + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+ + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+ + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+ + "-json FILE\tCreate alignment file FILE in JSON format.\n"
+ + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ + "-png FILE\tCreate PNG image FILE from alignment.\n"
+ + "-svg FILE\tCreate SVG image FILE from alignment.\n"
+ + "-html FILE\tCreate HTML file from alignment.\n"
+ + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+ + "-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"
+ + "-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)"
+ + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
+ + "-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");
+ }
+
private static void startUsageStats(final Desktop desktop)
{
/**
public void run()
{
Cache.log
- .info("Initialising googletracker for usage stats.");
+ .debug("Initialising googletracker for usage stats.");
Cache.initGoogleTracker();
Cache.log.debug("Tracking enabled.");
}
{
public void run()
{
- Cache.log.info("Not enabling Google Tracking.");
+ Cache.log.debug("Not enabling Google Tracking.");
}
}, null, true);
- SwingUtilities.invokeLater(prompter);
+ desktop.addDialogThread(prompter);
}
/**
* 'Jalview' object.
*/
private static void executeGroovyScript(String groovyscript,
- Object jalviewContext)
+ Object[] jalviewContext)
{
if (jalviewContext == null)
{
System.err
.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
}
- File sfile = null;
+ /**
+ * for scripts contained in files
+ */
+ File tfile = null;
+ /**
+ * script's URI
+ */
+ URL sfile = null;
if (groovyscript.trim().equals("STDIN"))
{
// read from stdin into a tempfile and execute it
try
{
- sfile = File.createTempFile("jalview", "groovy");
+ tfile = File.createTempFile("jalview", "groovy");
PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(sfile)));
+ new FileOutputStream(tfile)));
BufferedReader br = new BufferedReader(
new java.io.InputStreamReader(System.in));
String line = null;
} catch (Exception ex)
{
System.err.println("Failed to read from STDIN into tempfile "
- + ((sfile == null) ? "(tempfile wasn't created)" : sfile
+ + ((tfile == null) ? "(tempfile wasn't created)" : tfile
.toString()));
ex.printStackTrace();
return;
}
+ try
+ {
+ sfile = tfile.toURI().toURL();
+ } catch (Exception x)
+ {
+ System.err
+ .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ + tfile.toURI());
+ x.printStackTrace();
+ return;
+ }
}
else
{
- sfile = new File(groovyscript);
- }
- if (!sfile.exists())
- {
- System.err.println("File '" + groovyscript + "' does not exist.");
- return;
- }
- if (!sfile.canRead())
- {
- System.err.println("File '" + groovyscript + "' cannot be read.");
- return;
- }
- if (sfile.length() < 1)
- {
- System.err.println("File '" + groovyscript + "' is empty.");
- return;
+ try
+ {
+ sfile = new URI(groovyscript).toURL();
+ } catch (Exception x)
+ {
+ tfile = new File(groovyscript);
+ if (!tfile.exists())
+ {
+ System.err.println("File '" + groovyscript + "' does not exist.");
+ return;
+ }
+ if (!tfile.canRead())
+ {
+ System.err.println("File '" + groovyscript + "' cannot be read.");
+ return;
+ }
+ if (tfile.length() < 1)
+ {
+ System.err.println("File '" + groovyscript + "' is empty.");
+ return;
+ }
+ try
+ {
+ sfile = tfile.getAbsoluteFile().toURI().toURL();
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to create a file URL for "
+ + tfile.getAbsoluteFile());
+ return;
+ }
+ }
}
boolean success = false;
try
* = new Binding(); binding.setVariable("input", "world");
* gse.run("hello.groovy", binding); </code>
*/
- ClassLoader cl = jalviewContext.getClass().getClassLoader();
- Class gbindingc = cl.loadClass("groovy.lang.Binding");
- Constructor gbcons = gbindingc.getConstructor(null);
- Object gbinding = gbcons.newInstance(null);
- java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable",
- new Class[]
- { String.class, Object.class });
- setvar.invoke(gbinding, new Object[]
- { "Jalview", jalviewContext });
- Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
- Constructor gseccons = gsec.getConstructor(new Class[]
- { URL[].class }); // String[].class });
- Object gse = gseccons.newInstance(new Object[]
- { new URL[]
- { sfile.toURL() } }); // .toString() } });
- java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
- { String.class, gbindingc });
- run.invoke(gse, new Object[]
- { sfile.getName(), gbinding });
+ Class<?>[] bspec;
+ Object[] binding;
+ int blen = ((jalviewContext[0] == null) ? 0 : 1)
+ + ((jalviewContext[1] == null) ? 0 : 1);
+ String cnames[] = new String[] { "Jalview", "currentAlFrame" };
+ bspec = new Class[blen * 2];
+ binding = new Object[blen * 2];
+ blen = 0;
+ ClassLoader cl = null;
+ Map<String, Object> vbinding = new HashMap<String, Object>();
+ for (int jc = 0; jc < jalviewContext.length; jc++)
+ {
+ if (jalviewContext[jc] != null)
+ {
+ if (cl == null)
+ {
+ cl = jalviewContext[jc].getClass().getClassLoader();
+ }
+ bspec[blen * 2] = String.class;
+ bspec[blen * 2 + 1] = Object.class;
+ binding[blen * 2] = cnames[jc];
+ binding[blen * 2 + 1] = jalviewContext[jc];
+ vbinding.put(cnames[jc], jalviewContext[jc]);
+ blen++;
+ }
+ }
+ Class<?> gbindingc = cl.loadClass("groovy.lang.Binding");
+ Constructor<?> gbcons;
+ Object gbinding;
+ try
+ {
+ gbcons = gbindingc.getConstructor(Map.class);
+ gbinding = gbcons.newInstance(vbinding);
+ } catch (NoSuchMethodException x)
+ {
+ // old style binding config - using series of string/object values to
+ // setVariable.
+ gbcons = gbindingc.getConstructor();
+ gbinding = gbcons.newInstance();
+ java.lang.reflect.Method setvar = gbindingc.getMethod(
+ "setVariable", bspec);
+ setvar.invoke(gbinding, binding);
+ }
+
+ Class<?> gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
+ Constructor<?> gseccons = gsec
+ .getConstructor(new Class[] { URL[].class }); // String[].class
+ // });
+ Object gse = gseccons
+ .newInstance(new Object[] { new URL[] { sfile } }); // .toString()
+ // } });
+ java.lang.reflect.Method run = gsec.getMethod("run", new Class[] {
+ String.class, gbindingc });
+ run.invoke(gse, new Object[] { sfile.toString(), gbinding });
success = true;
} catch (Exception e)
{
{
// delete temp file that we made - but only if it was successfully
// executed
- sfile.delete();
+ tfile.delete();
}
}
}
source.addElement(nickname);
}
+ System.out.println("CMD [-dasserver " + data
+ + "] executed successfully!");
} // loop until no more server entries are found.
if (locsources != null && locsources.indexOf('|') > -1)
{
private static FeatureFetcher startFeatureFetching(final Vector dasSources)
{
FeatureFetcher ff = new FeatureFetcher();
- AlignFrame afs[] = Desktop.getAlignframes();
+ AlignFrame afs[] = Desktop.getAlignFrames();
if (afs == null || afs.length == 0)
{
return null;
}
return ff;
}
+
+ public static boolean isHeadlessMode()
+ {
+ String isheadless = System.getProperty("java.awt.headless");
+ if (isheadless != null && isheadless.equalsIgnoreCase("true"))
+ {
+ return true;
+ }
+ return false;
+ }
}
/**
* @author Andrew Waterhouse and JBP documented.
*
*/
+
+class rnabuttonlistener implements ActionListener
+{
+ public void actionPerformed(ActionEvent arg0)
+ {
+ System.out.println("Good idea ! ");
+
+ }
+}
+
+class pbuttonlistener implements ActionListener
+{
+ public void actionPerformed(ActionEvent arg0)
+ {
+
+ }
+}
+
class ArgsParser
{
Vector vargs = null;
running++;
}
- af.setProgressBar("DAS features being retrieved...", id);
+ af.setProgressBar(MessageManager
+ .getString("status.das_features_being_retrived"), id);
af.featureSettings_actionPerformed(null);
af.featureSettings.fetchDasFeatures(dasSources, true);
af.setProgressBar(null, id);
{
return queued == 0 && running == 0;
}
-};
+
+}
git://source.jalview.org / jalview.git / blobdiff