/*
- * 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
import java.io.PrintWriter;
import java.lang.reflect.Constructor;
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.*;
import javax.swing.*;
*/
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
*
+ "-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 (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");
+ + "-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");
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
+ // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+ }
+ defs = aparser.getValue("setprop");
+ }
if (aparser.contains("nodisplay"))
{
System.setProperty("java.awt.headless", "true");
// "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
// "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
+
);
} catch (Exception ex)
{
desktop = new Desktop();
desktop.setVisible(true);
desktop.discoverer.start();
+ if (!aparser.contains("nousagestats") && Cache.getDefault("USAGESTATS", true)) {
+ Cache.log.info("Initialising googletracker for usage stats.");
+ Cache.initGoogleTracker();
+ Cache.log.debug("Tracking enabled.");
+ } else {
+ Cache.log.info("Not enabling Google Tracking.");
+ }
if (!aparser.contains("noquestionnaire"))
{
String url = aparser.getValue("questionnaire");
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);
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
-
if (af == null)
{
System.out.println("error");
af.loadJalviewDataFile(data);
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");
if (data != 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",
{
String nickname = null;
String url = null;
+ boolean seq=false,feat=true;
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)
{
git://source.jalview.org / jalview.git / blobdiff