/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
- * 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 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
+import jalview.ext.so.SequenceOntology;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
+
+import java.io.BufferedReader;
import java.io.File;
+import java.io.FileOutputStream;
import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.*;
-
-import javax.swing.*;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URL;
+import java.security.AllPermission;
+import java.security.CodeSource;
+import java.security.PermissionCollection;
+import java.security.Permissions;
+import java.security.Policy;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Vector;
-import jalview.gui.*;
-import jalview.io.AppletFormatAdapter;
+import javax.swing.UIManager;
/**
* Main class for Jalview Application <br>
*/
public class Jalview
{
+ /*
+ * singleton instance of this class
+ */
+ private static Jalview instance;
+
+ private Desktop desktop;
+
+ public static AlignFrame currentAlignFrame;
+
+ static
+ {
+ // grab all the rights we can the JVM
+ Policy.setPolicy(new Policy()
+ {
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ @Override
+ public void refresh()
+ {
+ }
+ });
+ }
+
+ /**
+ * 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<String> dasSources)
+ {
+ final long id = System.currentTimeMillis();
+ queued++;
+ final FeatureFetcher us = this;
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ synchronized (us)
+ {
+ queued--;
+ running++;
+ }
+
+ af.setProgressBar(MessageManager
+ .getString("status.das_features_being_retrived"), 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;
+ }
+
+ }
+
+ public static Jalview getInstance()
+ {
+ return instance;
+ }
/**
* main class for Jalview application
*
* @param args
- * open <em>filename</em>
+ * open <em>filename</em>
*/
public static void main(String[] args)
{
+ instance = new Jalview();
+ instance.doMain(args);
+ }
+
+ /**
+ * @param args
+ */
+ void doMain(String[] args)
+ {
+ System.setSecurityManager(null);
System.out.println("Java version: "
+ System.getProperty("java.version"));
System.out.println(System.getProperty("os.arch") + " "
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"
- + "-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."
- + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires."
- + "-noquestionnaire\tTurn off questionnaire check."
- + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments."
- + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them."
- + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed."
- + "\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);
}
+ 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!");
+ }
- Cache.loadProperties(aparser.getValue("props")); // must do this before
// anything else!
- if (aparser.contains("nodisplay"))
+ final String jabawsUrl = aparser.getValue("jabaws");
+ if (jabawsUrl != null)
{
- System.setProperty("java.awt.headless", "true");
+ 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)
+ {
+ 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 (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 (java.lang.NoClassDefFoundError error)
+ } catch (NoClassDefFoundError error)
{
error.printStackTrace();
System.out
System.exit(0);
}
- Desktop desktop = null;
+ desktop = null;
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 (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 (Throwable e)
+ {
+ System.err.println("Failed to set QuaQua look and feel: "
+ + e.toString());
+ }
+ }
+
+ /*
+ * configure 'full' SO model if preferences say to,
+ * else use the default (SO Lite)
+ */
+ if (Cache.getDefault("USE_FULL_SO", false))
+ {
+ SequenceOntologyFactory.setInstance(new SequenceOntology());
+ }
+
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);
+ }
+ 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
{
Cache.log.debug("Starting questionnaire with default url: "
+ defurl);
desktop.checkForQuestionnaire(defurl);
-
}
}
}
+ else
+ {
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
+ }
+
+ if (!aparser.contains("nonews"))
+ {
+ desktop.checkForNews();
+ }
+
+ BioJsHTMLOutput.updateBioJS();
}
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
+ FileLoader fileLoader = new FileLoader(!headless);
+ Vector<String> getFeatures = null; // vector of das source nicknames to
+ // fetch
+ // features from
// loading is done.
- String groovyscript = null; // script to execute after all loading is completed one way or another
+ 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)
{
System.out.println("No files to open!");
System.exit(1);
}
+ String vamsasImport = aparser.getValue("vdoc");
+ String 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 = AppletFormatAdapter
+ .checkProtocol(vamsasImport);
+ if (viprotocol == jalview.io.FormatAdapter.FILE)
+ {
+ inSession = desktop.vamsasImport(new File(vamsasImport));
+ }
+ else if (viprotocol == 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();
+ }
+ }
+ }
+ 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 (!(new java.io.File(file)).exists())
+ if (!(new File(file)).exists())
{
System.out.println("Can't find " + file);
if (headless)
}
}
- protocol = checkProtocol(file);
+ protocol = AppletFormatAdapter.checkProtocol(file);
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
-
if (af == null)
{
System.out.println("error");
- return;
}
-
- data = aparser.getValue("colour");
- if (data != null)
+ else
{
- data.replaceAll("%20", " ");
+ setCurrentAlignFrame(af);
+ data = aparser.getValue("colour", true);
+ if (data != null)
+ {
+ data.replaceAll("%20", " ");
- jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
- .getColour(af.getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty.getColour(af
+ .getViewport().getAlignment(), data);
- if (cs == null)
- {
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- "white");
- ucs.parseAppletParameter(data);
- cs = ucs;
+ if (cs == null)
+ {
+ UserColourScheme ucs = new UserColourScheme("white");
+ ucs.parseAppletParameter(data);
+ cs = ucs;
+ }
+ else
+ {
+ System.out.println("CMD [-color " + data
+ + "] executed successfully!");
+ }
+ af.changeColour(cs);
}
- System.out.println("colour is " + data);
- af.changeColour(cs);
- }
-
- // Must maintain ability to use the groups flag
- data = aparser.getValue("groups");
- if (data != null)
- {
- af.parseFeaturesFile(data, checkProtocol(data));
- System.out.println("Added " + data);
- }
- data = aparser.getValue("features");
- if (data != null)
- {
- af.parseFeaturesFile(data, checkProtocol(data));
- System.out.println("Added " + data);
- }
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue("groups", true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println("CMD groups[-" + data
+ + "] executed successfully!");
+ }
+ data = aparser.getValue("features", true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-features " + data
+ + "] executed successfully!");
+ }
- data = aparser.getValue("annotations");
- if (data != null)
- {
- af.loadJalviewDataFile(data);
- System.out.println("Added " + data);
- }
- data = aparser.getValue("tree");
- if (data != null)
- {
- jalview.io.NewickFile fin = null;
- try
+ 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"))
{
- fin = new jalview.io.NewickFile(data, checkProtocol(data));
- if (fin != null)
+ af.getViewport().setSortByTree(true);
+ if (af.getViewport().getSortByTree())
{
- af.getViewport().setCurrentTree(
- af.ShowNewickTree(fin, data).getTree());
- System.out.println("Added tree " + data);
+ System.out.println("CMD [-sortbytree] executed successfully!");
}
- } catch (IOException ex)
+ }
+ if (aparser.contains("no-annotation"))
{
- System.err.println("Couldn't add tree " + data);
- ex.printStackTrace(System.err);
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ System.out.println("CMD no-annotation executed successfully!");
+ }
}
- }
- getFeatures = checkDasArguments(aparser);
- if (af != null && getFeatures!=null)
- {
- startFeatureFetching(getFeatures);
- // need to block until fetching is complete.
- while (af.operationInProgress())
+ if (aparser.contains("nosortbytree"))
{
- // wait around until fetching is finished.
- try {
- Thread.sleep(10);
- } catch (Exception e)
+ af.getViewport().setSortByTree(false);
+ if (!af.getViewport().getSortByTree())
{
-
+ System.out
+ .println("CMD [-nosortbytree] executed successfully!");
}
}
- }
- 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())
+ data = aparser.getValue("tree", true);
+ if (data != null)
{
- System.out.println("Executing script "+groovyscript);
- executeGroovyScript(groovyscript, desktop);
- } else {
- System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+ jalview.io.NewickFile fin = null;
+ try
+ {
+ System.out.println("CMD [-tree " + data
+ + "] executed successfully!");
+ fin = new NewickFile(data,
+ 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);
+ }
}
- groovyscript = null;
- }
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
- {
- format = aparser.nextValue();
- file = aparser.nextValue();
+ // TODO - load PDB structure(s) to alignment JAL-629
+ // (associate with identical sequence in alignment, or a specified
+ // sequence)
- if (format.equalsIgnoreCase("png"))
+ getFeatures = checkDasArguments(aparser);
+ if (af != null && getFeatures != null)
{
- af.createPNG(new java.io.File(file));
- imageName = (new java.io.File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
+ 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 (format.equalsIgnoreCase("imgMap"))
+ if (groovyscript != null)
{
- af.createImageMap(new java.io.File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, af);
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
+ groovyscript = null;
}
- else if (format.equalsIgnoreCase("eps"))
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
{
- System.out.println("Creating EPS file: " + file);
- af.createEPS(new java.io.File(file));
- continue;
- }
+ format = aparser.nextValue();
+ file = aparser.nextValue();
+
+ if (format.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("svg"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ System.out.println("Creating SVG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("html"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ new HtmlSvgOutput(new File(file), af.alignPanel);
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("eps"))
+ {
+ File outputFile = new File(file);
+ System.out.println("Creating EPS file: "
+ + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
+ continue;
+ }
+
+ 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!!");
+ }
- if (af.saveAlignment(file, format))
- {
- System.out.println("Written alignment in " + format
- + " format to " + file);
}
- else
+
+ while (aparser.getSize() > 0)
{
- System.out.println("Error writing file " + file + " in " + format
- + " format!!");
+ System.out.println("Unknown arg: " + aparser.nextValue());
}
-
- }
-
- 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
+
+ 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";
}
else
{
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
getFeatures = checkDasArguments(aparser);
// extract groovy arguments before anything else.
}
- // Once all loading is done. Retrieve features.
- if (getFeatures!=null)
+ // 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)
+ if (startUpAlframe != null)
{
startFeatureFetching(getFeatures);
}
}
- if (groovyscript!=null)
+ // Once all other stuff is done, execute any groovy scripts (in order)
+ if (groovyscript != null)
+ {
+ if (Cache.groovyJarsPresent())
+ {
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, startUpAlframe);
+ }
+ else
+ {
+ System.err
+ .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ + groovyscript);
+ }
+ }
+ // and finally, turn off batch mode indicator - if the desktop still exists
+ if (desktop != null)
{
- if (jalview.bin.Cache.groovyJarsPresent())
+ if (progress != -1)
{
- System.out.println("Executing script "+groovyscript);
- executeGroovyScript(groovyscript, desktop);
- } else {
- System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+ desktop.setProgressBar(null, progress);
}
+ desktop.setInBatchMode(false);
}
+ }
- // Once all other stuff is done, execute any groovy scripts (in order)
+ 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"
+ + "-nonews\tTurn off check for Jalview news.\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)
+ {
+ /**
+ * start a User Config prompt asking if we can log usage statistics.
+ */
+ PromptUserConfig prompter = new 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()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log
+ .debug("Initialising googletracker for usage stats.");
+ Cache.initGoogleTracker();
+ Cache.log.debug("Tracking enabled.");
+ }
+ }, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Not enabling Google Tracking.");
+ }
+ }, null, true);
+ desktop.addDialogThread(prompter);
+ }
+
/**
* Locate the given string as a file and pass it to the groovy interpreter.
- * @param groovyscript the script to execute
- * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object.
+ *
+ * @param groovyscript
+ * the script to execute
+ * @param jalviewContext
+ * the Jalview Desktop object passed in to the groovy binding as the
+ * 'Jalview' object.
*/
- private static void executeGroovyScript(String groovyscript, Object jalviewContext)
+ private void executeGroovyScript(String groovyscript, AlignFrame af)
{
- if (jalviewContext==null)
- {
- System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
- }
- File sfile = new File(groovyscript);
- if (!sfile.exists())
+ /**
+ * for scripts contained in files
+ */
+ File tfile = null;
+ /**
+ * script's URI
+ */
+ URL sfile = null;
+ if (groovyscript.trim().equals("STDIN"))
{
- System.err.println("File '"+groovyscript+"' does not exist.");
- return;
+ // read from stdin into a tempfile and execute it
+ try
+ {
+ tfile = File.createTempFile("jalview", "groovy");
+ PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(tfile)));
+ BufferedReader br = new BufferedReader(new InputStreamReader(
+ System.in));
+ String line = null;
+ while ((line = br.readLine()) != null)
+ {
+ outfile.write(line + "\n");
+ }
+ br.close();
+ outfile.flush();
+ outfile.close();
+
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to read from STDIN into tempfile "
+ + ((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;
+ }
}
- if (!sfile.canRead())
+ else
{
- System.err.println("File '"+groovyscript+"' cannot be read.");
- 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;
+ }
+ }
}
- if (sfile.length()<1)
+ try
{
- System.err.println("File '"+groovyscript+"' is empty.");
- return;
- }
- try {
- /* The following code performs the GroovyScriptEngine invocation using reflection,
- * and is equivalent to this fragment from the embedding groovy documentation on
- * the groovy site:
- * <code>
- import 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");
- 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[] { String[].class });
- Object gse = gseccons.newInstance(new Object[] { new String[] { groovyscript } });
- java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
- run.invoke(gse, new Object[] { sfile.getName(), gbinding });
+ Map<String, Object> vbinding = new HashMap<String, Object>();
+ vbinding.put("Jalview", this);
+ if (af != null)
+ {
+ vbinding.put("currentAlFrame", af);
+ }
+ Binding gbinding = new Binding(vbinding);
+ GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
+ gse.run(sfile.toString(), gbinding);
+ if ("STDIN".equals(groovyscript))
+ {
+ // delete temp file that we made -
+ // only if it was successfully executed
+ tfile.delete();
+ }
} catch (Exception e)
{
- System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script.");
+ System.err.println("Exception Whilst trying to execute file " + sfile
+ + " as a groovy script.");
e.printStackTrace(System.err);
+
}
}
+
/**
* Check commandline for any das server definitions or any fetchfrom switches
+ *
* @return vector of DAS source nicknames to retrieve from
*/
- private static Vector checkDasArguments(ArgsParser aparser)
+ private static Vector<String> checkDasArguments(ArgsParser aparser)
{
- Vector source=null;
+ Vector<String> 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;
int pos = data.indexOf('=');
+ // determine capabilities
if (pos > 0)
{
nickname = data.substring(0, pos);
}
url = data.substring(pos + 1);
- if (url != null && url.startsWith("http:"))
+ if (url != null
+ && (url.startsWith("http:") || url
+ .startsWith("sequence:http:")))
{
if (nickname == null)
{
nickname = url;
}
- if (locsources==null)
+ if (locsources == null)
{
- locsources="";
- } else {
- locsources+="\t";
+ locsources = "";
}
- locsources=locsources+nickname+"|"+url;
+ else
+ {
+ locsources += "\t";
+ }
+ locsources = locsources + nickname + "|" + url;
System.err
.println("NOTE! dasserver parameter not yet really supported (got args of "
+ nickname + "|" + url);
- if (source==null)
+ if (source == null)
{
- source = new Vector();
+ source = new Vector<String>();
}
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)
+ if (locsources != null && locsources.indexOf('|') > -1)
{
- Cache.log.debug("Setting local source list in properties file to:\n"+locsources);
+ Cache.log.debug("Setting local source list in properties file to:\n"
+ + 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)
+ System.out.println("adding source '" + data + "'");
+ if (source == null)
{
- source = new Vector();
+ source = new Vector<String>();
}
source.addElement(data);
}
return source;
}
+
/**
* start a feature fetcher for every alignment frame
+ *
* @param dasSources
*/
- private static void startFeatureFetching(final Vector dasSources)
+ private FeatureFetcher startFeatureFetching(
+ final Vector<String> dasSources)
{
- AlignFrame afs[] = Desktop.getAlignframes();
- if (afs==null || afs.length==0)
+ 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++)
+ 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 static boolean isHeadlessMode()
{
- String protocol = jalview.io.FormatAdapter.FILE;
-
- if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ String isheadless = System.getProperty("java.awt.headless");
+ if (isheadless != null && isheadless.equalsIgnoreCase("true"))
{
- protocol = jalview.io.FormatAdapter.URL;
+ return true;
}
- return protocol;
+ return false;
}
-}
-
-/**
- * Notes: this argParser does not distinguish between parameter switches,
- * parameter values and argument text. If an argument happens to be identical
- * to a parameter, it will be taken as such (even though it didn't have a '-' prefixing it).
- *
- * @author Andrew Waterhouse and JBP documented.
- *
- */
-class ArgsParser
-{
- Vector vargs = null;
- public ArgsParser(String[] args)
- {
- vargs = new Vector();
- for (int i = 0; i < args.length; i++)
- {
- String arg = args[i].trim();
- if (arg.charAt(0) == '-')
- {
- arg = arg.substring(1);
- }
- vargs.addElement(arg);
- }
- }
- /**
- * check for and remove first occurence of arg+parameter in arglist.
- * @param arg
- * @return return the argument following the given arg if arg was in list.
- */
- public String getValue(String arg)
+ public AlignFrame[] getAlignFrames()
{
- int index = vargs.indexOf(arg);
- String ret = null;
- if (index != -1)
- {
- ret = vargs.elementAt(index + 1).toString();
- vargs.removeElementAt(index);
- vargs.removeElementAt(index);
- }
- return ret;
+ return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
+ : Desktop.getAlignFrames();
+
}
+
/**
- * check for and remove first occurence of arg in arglist.
- * @param arg
- * @return true if arg was present in argslist.
+ * Quit method delegates to Desktop.quit - unless running in headless mode
+ * when it just ends the JVM
*/
- public boolean contains(String arg)
+ public void quit()
{
- if (vargs.contains(arg))
+ if (desktop != null)
{
- vargs.removeElement(arg);
- return true;
+ desktop.quit();
}
else
{
- return false;
+ System.exit(0);
}
}
- public String nextValue()
+ public static AlignFrame getCurrentAlignFrame()
{
- return vargs.remove(0).toString();
+ return Jalview.currentAlignFrame;
}
- public int getSize()
+ public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
- return vargs.size();
+ Jalview.currentAlignFrame = currentAlignFrame;
}
-
}
git://source.jalview.org / jalview.git / blobdiff