X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=805d098c4cdb9f7767aab7f066eebd6ccfd9bf0c;hb=4e1cb9b8b058d9b633af223b1cdb7b220d5d2ccd;hp=bfd6d70eb6611f36b896e8833210241e54b3058a;hpb=87185978c81d7d07f683f0c1a1bac5f080e88192;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bfd6d70..805d098 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,24 +1,36 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
* as published by the Free Software Foundation; either version 2
* 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.
- *
+ *
* 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
*/
package jalview.bin;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.OutputStreamWriter;
+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.*;
@@ -36,7 +48,19 @@ 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
*
@@ -73,18 +97,38 @@ public class Jalview
+ "-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."
- + "\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");
@@ -118,6 +162,7 @@ public class Jalview
// "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
// "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
+
);
} catch (Exception ex)
{
@@ -127,6 +172,13 @@ public class Jalview
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");
@@ -158,8 +210,13 @@ 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
+ Vector 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
+ // extract groovy argument and execute if necessary
+ groovyscript = aparser.getValue("groovy");
file = aparser.getValue("open");
if (file == null && desktop == null)
@@ -167,7 +224,62 @@ public class Jalview
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);
@@ -190,7 +302,6 @@ public class Jalview
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
-
if (af == null)
{
System.out.println("error");
@@ -237,6 +348,15 @@ public class Jalview
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)
{
@@ -257,21 +377,39 @@ public class Jalview
}
}
getFeatures = checkDasArguments(aparser);
- if (af != null && getFeatures!=null)
+ if (af != null && getFeatures != null)
{
- startFeatureFetching(getFeatures);
+ startFeatureFetching(getFeatures);
// need to block until fetching is complete.
while (af.operationInProgress())
{
// wait around until fetching is finished.
- try {
+ try
+ {
Thread.sleep(10);
} catch (Exception e)
{
-
+
}
}
}
+ 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())
+ {
+ 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);
+ }
+ groovyscript = null;
+ }
String imageName = "unnamed.png";
while (aparser.getSize() > 1)
{
@@ -320,7 +458,7 @@ 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",
@@ -345,67 +483,205 @@ public class Jalview
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
getFeatures = checkDasArguments(aparser);
+ // extract groovy arguments before anything else.
}
// Once all loading is done. Retrieve features.
- if (getFeatures!=null)
+ if (getFeatures != null)
{
- if (startUpAlframe!=null)
+ if (startUpAlframe != null)
{
startFeatureFetching(getFeatures);
}
}
+ if (groovyscript != null)
+ {
+ if (jalview.bin.Cache.groovyJarsPresent())
+ {
+ 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);
+ }
+ }
+
+ // Once all other stuff is done, execute any groovy scripts (in order)
}
+
+ /**
+ * 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.
+ */
+ private static void executeGroovyScript(String groovyscript,
+ 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;
+ if (groovyscript.trim().equals("STDIN"))
+ {
+ // read from stdin into a tempfile and execute it
+ try
+ {
+ sfile = File.createTempFile("jalview", "groovy");
+ PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(sfile)));
+ BufferedReader br = new BufferedReader(
+ new java.io.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 "
+ + ((sfile == null) ? "(tempfile wasn't created)" : sfile
+ .toString()));
+ ex.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;
+ }
+ boolean success = false;
+ 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: 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);
+ */
+ 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 });
+ success = true;
+ } catch (Exception e)
+ {
+ System.err.println("Exception Whilst trying to execute file " + sfile
+ + " as a groovy script.");
+ e.printStackTrace(System.err);
+
+ }
+ if (success && groovyscript.equals("STDIN"))
+ {
+ // delete temp file that we made - but only if it was successfully
+ // executed
+ sfile.delete();
+ }
+ }
+
/**
* 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)
{
- Vector source=null;
+ Vector source = null;
String data;
String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
- while ((data = aparser.getValue("dasserver"))!=null)
+ while ((data = aparser.getValue("dasserver")) != null)
{
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)
{
nickname = url;
}
- if (locsources==null)
+ if (locsources == null)
+ {
+ locsources = "";
+ }
+ else
{
- locsources="";
- } else {
- locsources+="\t";
+ locsources += "\t";
}
- locsources=locsources+nickname+"|"+url;
+ 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.addElement(nickname);
}
} // 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")) != null)
{
- System.out.println("adding source '"+data+"'");
- if (source==null)
+ System.out.println("adding source '" + data + "'");
+ if (source == null)
{
source = new Vector();
}
@@ -413,24 +689,27 @@ public class Jalview
}
return source;
}
+
/**
* start a feature fetcher for every alignment frame
+ *
* @param dasSources
*/
private static void startFeatureFetching(final Vector dasSources)
{
AlignFrame afs[] = Desktop.getAlignframes();
- if (afs==null || afs.length==0)
+ if (afs == null || afs.length == 0)
{
return;
}
- for (int i = 0; i