X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=624ac582c723569dea6e1fc998201a1e0870088b;hb=0233fbee0ff0d7fad302aa2da743c51fd64be101;hp=faf98db719b17726410ba474a9d55f24b0190d47;hpb=2a6fdd3e8c315282db909efb520312505a0ceba1;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index faf98db..624ac58 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,17 +1,17 @@
/*
- * 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
@@ -25,6 +25,13 @@ import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.lang.reflect.Constructor;
+import java.net.URL;
+import java.net.URLDecoder;
+import java.security.AllPermission;
+import java.security.CodeSource;
+import java.security.PermissionCollection;
+import java.security.Permissions;
+import java.security.Policy;
import java.util.*;
import javax.swing.*;
@@ -42,12 +49,29 @@ 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
*
* @param args
- * open filename
+ * open filename
*/
public static void main(String[] args)
{
@@ -79,19 +103,43 @@ 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."
- + "-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
+ // 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 (aparser.contains("nodisplay"))
{
System.setProperty("java.awt.headless", "true");
@@ -134,6 +182,10 @@ public class Jalview
desktop = new Desktop();
desktop.setVisible(true);
desktop.discoverer.start();
+ if (!aparser.contains("nousagestats"))
+ {
+ startUsageStats(desktop);
+ }
if (!aparser.contains("noquestionnaire"))
{
String url = aparser.getValue("questionnaire");
@@ -165,19 +217,105 @@ 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
+ 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"), 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);
@@ -200,14 +338,13 @@ public class Jalview
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
-
if (af == null)
{
System.out.println("error");
return;
}
- data = aparser.getValue("colour");
+ data = aparser.getValue("colour",true);
if (data != null)
{
data.replaceAll("%20", " ");
@@ -228,26 +365,35 @@ public class Jalview
}
// Must maintain ability to use the groups flag
- data = aparser.getValue("groups");
+ data = aparser.getValue("groups",true);
if (data != null)
{
af.parseFeaturesFile(data, checkProtocol(data));
System.out.println("Added " + data);
}
- data = aparser.getValue("features");
+ data = aparser.getValue("features",true);
if (data != null)
{
af.parseFeaturesFile(data, checkProtocol(data));
System.out.println("Added " + data);
}
- data = aparser.getValue("annotations");
+ data = aparser.getValue("annotations",true);
if (data != null)
{
af.loadJalviewDataFile(data);
System.out.println("Added " + data);
}
- data = aparser.getValue("tree");
+ // 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;
@@ -266,32 +412,42 @@ public class Jalview
ex.printStackTrace(System.err);
}
}
+ // todo - load PDB structure to alignment
+ // (associate with identical sequence in alignment, or a specified sequence)
+
+
getFeatures = checkDasArguments(aparser);
- if (af != null && getFeatures!=null)
+ if (af != null && getFeatures != null)
{
- startFeatureFetching(getFeatures);
- // need to block until fetching is complete.
- while (af.operationInProgress())
- {
- // wait around until fetching is finished.
- try {
- Thread.sleep(10);
+ FeatureFetcher ff = startFeatureFetching(getFeatures);
+ if (ff!=null)
+ while (!ff.allFinished() || af.operationInProgress())
+ {
+ // wait around until fetching is finished.
+ try
+ {
+ Thread.sleep(100);
} catch (Exception e)
{
-
+
}
}
+ getFeatures = null; // have retrieved features - forget them now.
}
- if (groovyscript!=null)
+ if (groovyscript != null)
{
- // Execute the groovy script after we've done all the rendering stuff
+ // 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);
+ 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);
+ }
+ else
+ {
+ System.err
+ .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ + groovyscript);
}
groovyscript = null;
}
@@ -343,7 +499,7 @@ 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",
@@ -370,170 +526,240 @@ public class Jalview
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)
+ // execute a groovy script.
+ if (groovyscript != null)
{
if (jalview.bin.Cache.groovyJarsPresent())
{
- System.out.println("Executing script "+groovyscript);
+ 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);
+ }
+ 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)
}
+
+ private static void startUsageStats(final Desktop desktop)
+ {
+ /**
+ * start a User Config prompt asking if we can log usage statistics.
+ */
+ jalview.gui.PromptUserConfig prompter = new jalview.gui.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()
+ {
+ public void run()
+ {
+ Cache.log
+ .info("Initialising googletracker for usage stats.");
+ Cache.initGoogleTracker();
+ Cache.log.debug("Tracking enabled.");
+ }
+ }, new Runnable()
+ {
+ public void run()
+ {
+ Cache.log.info("Not enabling Google Tracking.");
+ }
+ }, null, true);
+ SwingUtilities.invokeLater(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 static void executeGroovyScript(String groovyscript,
+ Object jalviewContext)
{
- if (jalviewContext==null)
+ if (jalviewContext == null)
{
- System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
+ 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 {
+ 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)
+ 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");
+ 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()));
+ System.err.println("Failed to read from STDIN into tempfile "
+ + ((sfile == null) ? "(tempfile wasn't created)" : sfile
+ .toString()));
ex.printStackTrace();
return;
}
- } else {
+ }
+ else
+ {
sfile = new File(groovyscript);
}
if (!sfile.exists())
{
- System.err.println("File '"+groovyscript+"' does not exist.");
+ System.err.println("File '" + groovyscript + "' does not exist.");
return;
}
if (!sfile.canRead())
{
- System.err.println("File '"+groovyscript+"' cannot be read.");
+ System.err.println("File '" + groovyscript + "' cannot be read.");
return;
}
- if (sfile.length()<1)
+ if (sfile.length() < 1)
{
- System.err.println("File '"+groovyscript+"' is empty.");
+ 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[] { String[].class });
- Object gse = gseccons.newInstance(new Object[] { new String[] { sfile.toURL().toString() } });
- java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
- run.invoke(gse, new Object[] { sfile.toURL().toString(), gbinding });
- success = true;
+ 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.");
+ 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
+ // 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",true)) != 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",true)) != null)
{
- System.out.println("adding source '"+data+"'");
- if (source==null)
+ System.out.println("adding source '" + data + "'");
+ if (source == null)
{
source = new Vector();
}
@@ -541,31 +767,26 @@ public class Jalview
}
return source;
}
+
/**
* start a feature fetcher for every alignment frame
+ *
* @param dasSources
*/
- private static void startFeatureFetching(final Vector dasSources)
+ private static FeatureFetcher startFeatureFetching(final Vector dasSources)
{
+ FeatureFetcher ff = new FeatureFetcher();
AlignFrame afs[] = Desktop.getAlignframes();
- if (afs==null || afs.length==0)
+ if (afs == null || afs.length == 0)
{
- return;
+ return null;
}
- for (int i = 0; i