X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=8205374d31fe25222bd55113ced7a9595662dc66;hb=74666bccffce69d865cfc5479f81f394e2d14d5e;hp=f23bcc966780a48234fcd0ca59cf84414209e136;hpb=028bc343135a72515c6b109eb0deb8d6034ca520;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index f23bcc9..8205374 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,97 +1,702 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
-
-package jalview.bin;
-
-import jalview.gui.*;
-import javax.swing.*;
-import java.awt.event.*;
-import java.applet.Applet;
-
-public class Jalview extends JApplet
-{
- public static JApplet applet;
- Desktop frame;
- public void init()
- {
- applet = this;
-
- frame = new Desktop();
- frame.setResizable(true);
- frame.setVisible(true);
- frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
- frame.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent e)
- {
- applet.stop();
- applet.destroy();
- }
- });
-
- String file = getParameter("alignment");
-
- if(file!=null)
- {
- jalview.bin.Cache.LAST_DIRECTORY = file;
- String protocol = "File";
- if (file.indexOf("http:") > -1)
- protocol = "URL";
-
- String format = jalview.io.IdentifyFile.Identify(file, protocol);
-
- frame.LoadFile(file, protocol, format);
- }
- }
-
- public void destroy()
- {
- if(applet!=null)
- applet.stop();
- else
- System.exit(0);
- frame.setVisible(false);
- }
-
- public static void main(String[] args) {
- try{
- UIManager.setLookAndFeel(
- // "javax.swing.plaf.metal.MetalLookAndFeel"
- // "javax.swing.plaf.multi.MultiLookAndFeel"
- UIManager.getCrossPlatformLookAndFeelClassName()
- // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
- // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
- // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
- );
- }
- catch (Exception ex)
- {}
-
- // JFrame.setDefaultLookAndFeelDecorated(true);
- Desktop frame = new Desktop();
- frame.setResizable(true);
- frame.setVisible(true);
-
-
- if(args!=null && args.length>0)
- {
- String file = args[0];
- jalview.bin.Cache.LAST_DIRECTORY = file;
- String protocol = "File";
- if(file.indexOf("http:")>-1)
- protocol = "URL";
-
- String format = jalview.io.IdentifyFile.Identify(file, protocol);
-
- frame.LoadFile(file, protocol, format);
- }
-
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.util.*;
+
+import javax.swing.*;
+
+import jalview.gui.*;
+import jalview.io.AppletFormatAdapter;
+
+/**
+ * Main class for Jalview Application
+ *
+ * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview
+{
+
+ /**
+ * main class for Jalview application
+ *
+ * @param args
+ * open filename
+ */
+ public static void main(String[] args)
+ {
+ System.out.println("Java version: "
+ + System.getProperty("java.version"));
+ System.out.println(System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
+
+ 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"
+ + "-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"
+ + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments.\n"
+ +"\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
+ +"\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"
+ + "-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!
+
+ 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;
+ }
+
+ try
+ {
+ Cache.initLogger();
+ } catch (java.lang.NoClassDefFoundError error)
+ {
+ error.printStackTrace();
+ System.out
+ .println("\nEssential logging libraries not found."
+ + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+ System.exit(0);
+ }
+
+ Desktop 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"
+
+ );
+ } catch (Exception ex)
+ {
+ }
+ if (!headless)
+ {
+ desktop = new Desktop();
+ desktop.setVisible(true);
+ desktop.discoverer.start();
+ if (!aparser.contains("noquestionnaire"))
+ {
+ String url = aparser.getValue("questionnaire");
+ if (url != null)
+ {
+ // Start the desktop questionnaire prompter with the specified
+ // questionnaire
+ Cache.log.debug("Starting questionnaire url at " + url);
+ desktop.checkForQuestionnaire(url);
+ }
+ else
+ {
+ if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ {
+ // Start the desktop questionnaire prompter with the specified
+ // questionnaire
+ // String defurl =
+ // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
+ // //
+ String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+ Cache.log.debug("Starting questionnaire with default url: "
+ + defurl);
+ desktop.checkForQuestionnaire(defurl);
+
+ }
+ }
+ }
+ }
+
+ 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
+ // 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)
+ {
+ System.out.println("No files to open!");
+ System.exit(1);
+ }
+
+ if (file != null)
+ {
+ System.out.println("Opening file: " + file);
+
+ if (!file.startsWith("http://"))
+ {
+ if (!(new java.io.File(file)).exists())
+ {
+ System.out.println("Can't find " + file);
+ if (headless)
+ {
+ System.exit(1);
+ }
+ }
+ }
+
+ protocol = checkProtocol(file);
+
+ format = new jalview.io.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)
+ {
+ data.replaceAll("%20", " ");
+
+ jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
+ .getColour(af.getViewport().getAlignment(), data);
+
+ if (cs == null)
+ {
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ "white");
+ ucs.parseAppletParameter(data);
+ cs = ucs;
+ }
+
+ 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);
+ }
+
+ 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
+ {
+ fin = new jalview.io.NewickFile(data, checkProtocol(data));
+ if (fin != null)
+ {
+ af.getViewport().setCurrentTree(
+ af.ShowNewickTree(fin, data).getTree());
+ System.out.println("Added tree " + data);
+ }
+ } catch (IOException ex)
+ {
+ System.err.println("Couldn't add tree " + data);
+ ex.printStackTrace(System.err);
+ }
+ }
+ getFeatures = checkDasArguments(aparser);
+ 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);
+ } 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)
+ {
+ 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("imgMap"))
+ {
+ af.createImageMap(new java.io.File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("eps"))
+ {
+ System.out.println("Creating EPS file: " + file);
+ af.createEPS(new java.io.File(file));
+ 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!!");
+ }
+
+ }
+
+ 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
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ {
+ file = jalview.bin.Cache.getDefault("STARTUP_FILE",
+ "http://www.jalview.org/examples/exampleFile_2_3.jar");
+
+ protocol = "File";
+
+ if (file.indexOf("http:") > -1)
+ {
+ protocol = "URL";
+ }
+
+ if (file.endsWith(".jar"))
+ {
+ format = "Jalview";
+ }
+ else
+ {
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ }
+
+ 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 (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;
+ String data;
+ String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
+ 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:") || url.startsWith("sequence:http:")))
+ {
+ if (nickname == null)
+ {
+ nickname = url;
+ }
+ if (locsources == null)
+ {
+ locsources = "";
+ }
+ 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)
+ {
+ source = new Vector();
+ }
+ source.addElement(nickname);
+ }
+ } // loop until no more server entries are found.
+ if (locsources != null && locsources.indexOf('|') > -1)
+ {
+ 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)
+ {
+ System.out.println("adding source '" + data + "'");
+ if (source == null)
+ {
+ source = new Vector();
+ }
+ source.addElement(data);
+ }
+ 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)
+ {
+ return;
+ }
+ 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);
+ }
+ });
+ }
+ }
+
+ private static String checkProtocol(String file)
+ {
+ String protocol = jalview.io.FormatAdapter.FILE;
+
+ if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ {
+ protocol = jalview.io.FormatAdapter.URL;
+ }
+ return protocol;
+ }
+}
+
+/**
+ * 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)
+ {
+ 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;
+ }
+
+ /**
+ * check for and remove first occurence of arg in arglist.
+ *
+ * @param arg
+ * @return true if arg was present in argslist.
+ */
+ public boolean contains(String arg)
+ {
+ if (vargs.contains(arg))
+ {
+ vargs.removeElement(arg);
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ public String nextValue()
+ {
+ return vargs.remove(0).toString();
+ }
+
+ public int getSize()
+ {
+ return vargs.size();
+ }
+
+}