*/
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.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
-import java.lang.reflect.Constructor;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
-import java.net.URLDecoder;
import java.security.AllPermission;
import java.security.CodeSource;
import java.security.PermissionCollection;
import java.util.Vector;
import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
/**
* 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();
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
*/
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") + " "
try
{
Cache.initLogger();
- } catch (java.lang.NoClassDefFoundError error)
+ } catch (NoClassDefFoundError error)
{
error.printStackTrace();
System.out
System.exit(0);
}
- Desktop desktop = null;
+ desktop = null;
try
{
} catch (Exception ex)
{
}
- if (new Platform().isAMac())
+ if (Platform.isAMac())
{
System.setProperty("com.apple.mrj.application.apple.menu.about.name",
"Jalview");
{
UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
.getLookAndFeel());
- } catch (UnsupportedLookAndFeelException e)
+ } catch (Throwable e)
{
- // TODO Auto-generated catch block
- e.printStackTrace();
+ 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();
Cache.log.debug("Starting questionnaire with default url: "
+ defurl);
desktop.checkForQuestionnaire(defurl);
-
}
}
}
else
{
- System.err
-.println("CMD [-noquestionnaire] executed successfully!");
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
+ }
+
+ if (!aparser.contains("nonews"))
+ {
+ desktop.checkForNews();
}
- desktop.checkForNews();
- }
- if (!isHeadlessMode())
- {
BioJsHTMLOutput.updateBioJS();
}
String file = null, protocol = null, format = null, data = null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
- Vector getFeatures = null; // vector of das source nicknames to fetch
+ 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
System.out.println("No files to open!");
System.exit(1);
}
- String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser
- .getValue("vsess");
+ String vamsasImport = aparser.getValue("vdoc");
+ String vamsasSession = aparser.getValue("vsess");
if (vamsasImport != null || vamsasSession != null)
{
if (desktop == null || headless)
{
try
{
- String viprotocol = jalview.io.AppletFormatAdapter
+ String viprotocol = AppletFormatAdapter
.checkProtocol(vamsasImport);
if (viprotocol == jalview.io.FormatAdapter.FILE)
{
inSession = desktop.vamsasImport(new File(vamsasImport));
}
- else if (viprotocol == jalview.io.FormatAdapter.URL)
+ else if (viprotocol == FormatAdapter.URL)
{
inSession = desktop.vamsasImport(new URL(vamsasImport));
}
{
if (!headless)
{
- desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
+ 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 = jalview.io.AppletFormatAdapter.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);
}
else
{
-
+ 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");
+ UserColourScheme ucs = new UserColourScheme("white");
ucs.parseAppletParameter(data);
cs = ucs;
}
if (data != null)
{
af.parseFeaturesFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
System.out.println("CMD groups[-" + data
+ "] executed successfully!");
if (data != null)
{
af.parseFeaturesFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
System.out.println("CMD [-features " + data
+ "] executed successfully!");
af.getViewport().setSortByTree(true);
if (af.getViewport().getSortByTree())
{
- System.out
-.println("CMD [-sortbytree] executed successfully!");
+ System.out.println("CMD [-sortbytree] executed successfully!");
}
}
if (aparser.contains("no-annotation"))
af.getViewport().setShowAnnotation(false);
if (!af.getViewport().isShowAnnotation())
{
- System.out
-.println("CMD no-annotation executed successfully!");
+ System.out.println("CMD no-annotation executed successfully!");
}
}
if (aparser.contains("nosortbytree"))
{
System.out.println("CMD [-tree " + data
+ "] executed successfully!");
- fin = new jalview.io.NewickFile(data,
- jalview.io.AppletFormatAdapter.checkProtocol(data));
+ fin = new NewickFile(data,
+ AppletFormatAdapter.checkProtocol(data));
if (fin != null)
{
af.getViewport().setCurrentTree(
{
// 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, new Object[]
- { desktop, af });
-
- System.out.println("CMD groovy[" + groovyscript
- + "] executed successfully!");
- }
- else
- {
- System.err
- .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
- + groovyscript);
- }
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, af);
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
groovyscript = null;
}
String imageName = "unnamed.png";
if (format.equalsIgnoreCase("png"))
{
- af.createPNG(new java.io.File(file));
- imageName = (new java.io.File(file)).getName();
+ 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 java.io.File(file);
+ File imageFile = new File(file);
imageName = imageFile.getName();
af.createSVG(imageFile);
System.out.println("Creating SVG image: " + file);
}
else if (format.equalsIgnoreCase("html"))
{
- File imageFile = new java.io.File(file);
+ File imageFile = new File(file);
imageName = imageFile.getName();
- new HtmlSvgOutput(new java.io.File(file), af.alignPanel);
+ new HtmlSvgOutput(new File(file), af.alignPanel);
System.out.println("Creating HTML image: " + file);
continue;
}
else if (format.equalsIgnoreCase("imgMap"))
{
- af.createImageMap(new java.io.File(file), imageName);
+ af.createImageMap(new File(file), imageName);
System.out.println("Creating image map: " + file);
continue;
}
else if (format.equalsIgnoreCase("eps"))
{
- File outputFile = new java.io.File(file);
+ File outputFile = new File(file);
System.out.println("Creating EPS file: "
+ outputFile.getAbsolutePath());
af.createEPS(outputFile);
}
else
{
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
// Once all other stuff is done, execute any groovy scripts (in order)
if (groovyscript != null)
{
- if (jalview.bin.Cache.groovyJarsPresent())
+ if (Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[]
- { desktop, startUpAlframe });
+ executeGroovyScript(groovyscript, startUpAlframe);
}
else
{
+ "-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"
+ "-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"
// +
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
- desktop.desktop,
+ PromptUserConfig prompter = new PromptUserConfig(
+ Desktop.desktop,
"USAGESTATS",
"Jalview Usage Statistics",
"Do you want to help make Jalview better by enabling "
+ "\n\n(you can enable or disable usage tracking in the preferences)",
new Runnable()
{
+ @Override
public void run()
{
Cache.log
}
}, new Runnable()
{
+ @Override
public void run()
{
Cache.log.debug("Not enabling Google Tracking.");
* 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.");
- }
/**
* for scripts contained in files
*/
tfile = File.createTempFile("jalview", "groovy");
PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(tfile)));
- BufferedReader br = new BufferedReader(
- new java.io.InputStreamReader(System.in));
+ BufferedReader br = new BufferedReader(new InputStreamReader(
+ System.in));
String line = null;
while ((line = br.readLine()) != null)
{
}
}
}
- 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: <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>
- */
- Class<?>[] bspec;
- Object[] binding;
- int blen = ((jalviewContext[0] == null) ? 0 : 1)
- + ((jalviewContext[1] == null) ? 0 : 1);
- String cnames[] = new String[]
- { "Jalview", "currentAlFrame" };
- bspec = new Class[blen * 2];
- binding = new Object[blen * 2];
- blen = 0;
- ClassLoader cl = null;
Map<String, Object> vbinding = new HashMap<String, Object>();
- for (int jc = 0; jc < jalviewContext.length; jc++)
+ vbinding.put("Jalview", this);
+ if (af != null)
{
- if (jalviewContext[jc] != null)
- {
- if (cl == null)
- {
- cl = jalviewContext[jc].getClass().getClassLoader();
- }
- bspec[blen * 2] = String.class;
- bspec[blen * 2 + 1] = Object.class;
- binding[blen * 2] = cnames[jc];
- binding[blen * 2 + 1] = jalviewContext[jc];
- vbinding.put(cnames[jc], jalviewContext[jc]);
- blen++;
- }
+ vbinding.put("currentAlFrame", af);
}
- Class<?> gbindingc = cl.loadClass("groovy.lang.Binding");
- Constructor<?> gbcons;
- Object gbinding;
- try
+ Binding gbinding = new Binding(vbinding);
+ GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
+ gse.run(sfile.toString(), gbinding);
+ if ("STDIN".equals(groovyscript))
{
- gbcons = gbindingc.getConstructor(Map.class);
- gbinding = gbcons.newInstance(vbinding);
- } catch (NoSuchMethodException x)
- {
- // old style binding config - using series of string/object values to
- // setVariable.
- gbcons = gbindingc.getConstructor();
- gbinding = gbcons.newInstance();
- java.lang.reflect.Method setvar = gbindingc.getMethod(
- "setVariable", bspec);
- setvar.invoke(gbinding, binding);
+ // delete temp file that we made -
+ // only if it was successfully executed
+ tfile.delete();
}
-
- 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 } }); // .toString() } });
- java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
- { String.class, gbindingc });
- run.invoke(gse, new Object[]
- { sfile.toString(), gbinding });
- success = true;
} catch (Exception e)
{
System.err.println("Exception Whilst trying to execute file " + sfile
e.printStackTrace(System.err);
}
- if (success && groovyscript.equals("STDIN"))
- {
- // delete temp file that we made - but only if it was successfully
- // executed
- tfile.delete();
- }
}
/**
*
* @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", true)) != null)
{
String nickname = null;
String url = null;
- boolean seq = false, feat = true;
int pos = data.indexOf('=');
// determine capabilities
if (pos > 0)
+ nickname + "|" + url);
if (source == null)
{
- source = new Vector();
+ source = new Vector<String>();
}
source.addElement(nickname);
}
System.out.println("adding source '" + data + "'");
if (source == null)
{
- source = new Vector();
+ source = new Vector<String>();
}
source.addElement(data);
}
*
* @param dasSources
*/
- private static FeatureFetcher startFeatureFetching(final Vector dasSources)
+ private FeatureFetcher startFeatureFetching(
+ final Vector<String> dasSources)
{
FeatureFetcher ff = new FeatureFetcher();
AlignFrame afs[] = Desktop.getAlignFrames();
}
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 rnabuttonlistener implements ActionListener
-{
- public void actionPerformed(ActionEvent arg0)
- {
- System.out.println("Good idea ! ");
-
- }
-}
-class pbuttonlistener implements ActionListener
-{
- public void actionPerformed(ActionEvent arg0)
+ public AlignFrame[] getAlignFrames()
{
+ return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
+ : Desktop.getAlignFrames();
}
-}
-
-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.
+ * Quit method delegates to Desktop.quit - unless running in headless mode
+ * when it just ends the JVM
*/
- public String getValue(String arg)
- {
- return getValue(arg, false);
- }
-
- public String getValue(String arg, boolean utf8decode)
+ public void quit()
{
- int index = vargs.indexOf(arg);
- String dc = null, ret = null;
- if (index != -1)
- {
- ret = vargs.elementAt(index + 1).toString();
- vargs.removeElementAt(index);
- vargs.removeElementAt(index);
- if (utf8decode && ret != null)
- {
- try
- {
- dc = URLDecoder.decode(ret, "UTF-8");
- ret = dc;
- } catch (Exception e)
- {
- // TODO: log failure to decode
- }
- }
- }
- 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))
+ if (desktop != null)
{
- vargs.removeElement(arg);
- return true;
+ desktop.quit();
}
else
{
- return false;
+ System.exit(0);
}
}
- public String nextValue()
- {
- return vargs.remove(0).toString();
- }
-
- public int getSize()
- {
- return vargs.size();
- }
-
-}
-
-/**
- * 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 dasSources)
+ public static AlignFrame getCurrentAlignFrame()
{
- final long id = System.currentTimeMillis();
- queued++;
- final FeatureFetcher us = this;
- new Thread(new Runnable()
- {
-
- 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();
+ return Jalview.currentAlignFrame;
}
- public synchronized boolean allFinished()
+ public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
- return queued == 0 && running == 0;
+ Jalview.currentAlignFrame = currentAlignFrame;
}
-
}
git://source.jalview.org / jalview.git / blobdiff