*/
package jalview.bin;
-import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignFrameI;
-import jalview.api.AlignViewportI;
-import jalview.api.JalviewApp;
-import jalview.api.StructureSelectionManagerProvider;
-import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
-import jalview.gui.Preferences;
import jalview.gui.PromptUserConfig;
-import jalview.gui.StructureViewer;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.gff.SequenceOntologyFactory;
-import jalview.javascript.JSFunctionExec;
-import jalview.javascript.MouseOverStructureListener;
-import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.structure.SelectionSource;
-import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
-import java.applet.AppletContext;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
-import java.util.Hashtable;
import java.util.Map;
import java.util.Vector;
+import java.util.logging.ConsoleHandler;
+import java.util.logging.Level;
+import java.util.logging.Logger;
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
+import com.threerings.getdown.util.LaunchUtil;
+
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
-import netscape.javascript.JSObject;
/**
* Main class for Jalview Application <br>
* @author $author$
* @version $Revision$
*/
-public class Jalview implements ApplicationSingletonI, JalviewJSApi
+public class Jalview
{
-
- public static Jalview getInstance()
- {
- return (Jalview) ApplicationSingletonProvider
- .getInstance(Jalview.class);
- }
-
- private Jalview()
- {
- }
-
static
{
Platform.getURLCommandArguments();
}
- private boolean headless;
+ // singleton instance of this class
- public static boolean isHeadlessMode()
- {
- return getInstance().headless;
- }
+ private static Jalview instance;
private Desktop desktop;
- private AlignFrame currentAlignFrame;
-
- public boolean isJavaAppletTag;
-
- public String appletResourcePath;
-
- JalviewAppLoader appLoader;
-
- protected JSFunctionExec jsFunctionExec;
-
- private boolean noCalculation, noMenuBar, noStatus;
-
- private boolean noAnnotation;
-
- public boolean getStartCalculations()
- {
- return !noCalculation;
- }
-
- public boolean getAllowMenuBar()
- {
- return !noMenuBar;
- }
-
- public boolean getShowStatus()
- {
- return !noStatus;
- }
-
- public boolean getShowAnnotation()
- {
- return !noAnnotation;
- }
-
- public static AlignFrame getCurrentAlignFrame()
- {
- return getInstance().currentAlignFrame;
- }
-
- public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
- {
- getInstance().currentAlignFrame = currentAlignFrame;
- }
+ public static AlignFrame currentAlignFrame;
static
{
*/
{
// grab all the rights we can for the JVM
- Policy.setPolicy(new Policy()
- {
- @Override
- public PermissionCollection getPermissions(CodeSource codesource)
- {
- Permissions perms = new Permissions();
- perms.add(new AllPermission());
- return (perms);
- }
-
- @Override
- public void refresh()
- {
- }
- });
+ Policy.setPolicy(new Policy()
+ {
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ @Override
+ public void refresh()
+ {
+ }
+ });
}
}
}
+ public static Jalview getInstance()
+ {
+ return instance;
+ }
+
/**
* main class for Jalview application
*
*/
public static void main(String[] args)
{
- // Platform.startJavaLogging();
- getInstance().doMain(args);
- }
+// setLogging(); // BH - for event debugging in JavaScript
+ instance = new Jalview();
+ instance.doMain(args);
+}
+ private static void logClass(String name)
+ {
+ // BH - for event debugging in JavaScript
+ ConsoleHandler consoleHandler = new ConsoleHandler();
+ consoleHandler.setLevel(Level.ALL);
+ Logger logger = Logger.getLogger(name);
+ logger.setLevel(Level.ALL);
+ logger.addHandler(consoleHandler);
+ }
@SuppressWarnings("unused")
+ private static void setLogging()
+ {
+
+ /**
+ * @j2sIgnore
+ *
+ */
+ {
+ System.out.println("not in js");
+ }
+
+ // BH - for event debugging in JavaScript (Java mode only)
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ Logger.getLogger("").setLevel(Level.ALL);
+ logClass("java.awt.EventDispatchThread");
+ logClass("java.awt.EventQueue");
+ logClass("java.awt.Component");
+ logClass("java.awt.focus.Component");
+ logClass("java.awt.focus.DefaultKeyboardFocusManager");
+ }
+
+ }
+
+
+
+
/**
* @param args
*/
void doMain(String[] args)
{
- boolean isJS = Platform.isJS();
- if (isJS)
- {
- Platform.setAppClass(this);
- }
- else
+ if (!Platform.isJS())
{
System.setSecurityManager(null);
}
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+ String appdirString = System.getProperty("getdownappdir");
+ if (appdirString != null && appdirString.length() > 0)
+ {
+ final File appdir = new File(appdirString);
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+ }.start();
+
+ }
ArgsParser aparser = new ArgsParser(args);
+ boolean headless = false;
- String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
- Cache.loadProperties(usrPropsFile);
- if (isJS)
+ String usrPropsFile = aparser.getValue("props");
+ Cache.loadProperties(usrPropsFile); // must do this before
+ if (usrPropsFile != null)
{
- isJavaAppletTag = aparser.isApplet();
- if (isJavaAppletTag)
- {
- Preferences.setAppletDefaults();
- Cache.loadProperties(usrPropsFile); // again, because we
- // might be changing defaults here?
- }
System.out.println(
- "<Applet> found: " + aparser.getValue("Info.j2sAppletID"));
- appletResourcePath = aparser.getValue("Info.resourcePath");
+ "CMD [-props " + usrPropsFile + "] executed successfully!");
}
- else
+
+ if (!Platform.isJS())
/**
* Java only
*
* @j2sIgnore
*/
{
- if (usrPropsFile != null)
- {
- System.out.println(
- "CMD [-props " + usrPropsFile + "] executed successfully!");
- }
-
if (aparser.contains("help") || aparser.contains("h"))
{
showUsage();
System.exit(0);
}
- if (aparser.contains(ArgsParser.NODISPLAY)
- || aparser.contains(ArgsParser.NOGUI)
- || aparser.contains(ArgsParser.HEADLESS)
- || "true".equals(System.getProperty("java.awt.headless")))
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
{
+ System.setProperty("java.awt.headless", "true");
headless = true;
}
-
// anything else!
- final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
+ final String jabawsUrl = aparser.getValue("jabaws");
if (jabawsUrl != null)
{
try
{
- Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl);
+ Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
System.out.println(
"CMD [-jabaws " + jabawsUrl + "] executed successfully!");
} catch (MalformedURLException e)
}
}
- // check for property setting
- String defs = aparser.getValue(ArgsParser.SETPROP);
+ String defs = aparser.getValue("setprop");
while (defs != null)
{
int p = defs.indexOf('=');
else
{
System.out.println("Executing setprop argument: " + defs);
- if (isJS)
+ if (Platform.isJS())
{
- Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
+ Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
}
}
- defs = aparser.getValue(ArgsParser.SETPROP);
+ defs = aparser.getValue("setprop");
+ }
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ headless = true;
}
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
"Failed to set QuaQua look and feel: " + e.toString());
}
}
- if (lookAndFeel == null
- || !(lookAndFeel.getClass().isAssignableFrom(
- UIManager.getLookAndFeel().getClass()))
+ if (lookAndFeel == null || !(lookAndFeel.getClass()
+ .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
|| !UIManager.getLookAndFeel().getClass().toString()
.toLowerCase().contains("quaqua"))
{
* configure 'full' SO model if preferences say to,
* else use the default (SO Lite)
*/
- if (Cache.getDefault(Preferences.USE_FULL_SO, false))
+ if (Cache.getDefault("USE_FULL_SO", false))
{
- SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
+ SequenceOntologyFactory.setInstance(new SequenceOntology());
}
if (!headless)
{
- desktop = Desktop.getInstance();
+ desktop = new Desktop()
+// {
+// // BH testing
+// @Override
+// protected void processEvent(AWTEvent e) {
+// System.out.println("Jalview.java " + e);
+// super.processEvent(e);
+// }
+// }
+ ;
desktop.setInBatchMode(true); // indicate we are starting up
+
+ try
+ {
+ if (! Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ JalviewTaskbar.setTaskbar(this);
+ }
+ } catch (Exception e)
+ {
+ System.out.println("Cannot set Taskbar");
+ // e.printStackTrace();
+ } catch (Throwable t)
+ {
+ System.out.println("Cannot set Taskbar");
+ // t.printStackTrace();
+ }
+
desktop.setVisible(true);
- if (!isJS)
+ if (!Platform.isJS())
/**
* Java only
*
*/
{
desktop.startServiceDiscovery();
- if (!aparser.contains(ArgsParser.NOUSAGESTATS))
+ if (!aparser.contains("nousagestats"))
{
startUsageStats(desktop);
}
System.err.println("CMD [-nousagestats] executed successfully!");
}
- if (!aparser.contains(ArgsParser.NOQUESTIONNAIRE))
+ if (!aparser.contains("noquestionnaire"))
{
- String url = aparser.getValue(ArgsParser.QUESTIONNAIRE);
+ String url = aparser.getValue("questionnaire");
if (url != null)
{
// Start the desktop questionnaire prompter with the specified
}
else
{
- if (Cache.getProperty(Preferences.NOQUESTIONNAIRES) == null)
+ if (Cache.getProperty("NOQUESTIONNAIRES") == null)
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
.println("CMD [-noquestionnaire] executed successfully!");
}
- if (!aparser.contains(ArgsParser.NONEWS))
+ if (!aparser.contains("nonews"))
{
desktop.checkForNews();
}
}
}
- parseArguments(aparser, true);
- }
-
- /**
- * Allow an outside entity to initiate the second half of argument parsing
- * (only).
- *
- * @param args
- * @return null is good
- */
- @Override
- public Object parseArguments(String[] args)
- {
-
- try
- {
- ArgsParser aparser = new ArgsParser(args);
- return parseArguments(aparser, false);
- } catch (Throwable t)
- {
- return t;
- }
- }
-
- /**
- *
- * @param aparser
- * @param isStartup
- * @return
- */
- private Object parseArguments(ArgsParser aparser, boolean isStartup)
- {
- boolean isJS = Platform.isJS();
+ String file = null, data = null;
+ FileFormatI format = null;
+ DataSourceType protocol = null;
+ FileLoader fileLoader = new FileLoader(!headless);
- Desktop desktop = (headless ? null : Desktop.getInstance());
- // script to execute after all loading is
+ String groovyscript = null; // script to execute after all loading is
// completed one way or another
// extract groovy argument and execute if necessary
- String groovyscript = (isJS ? null
- : aparser.getValue(ArgsParser.GROOVY, true));
- String file = aparser.getValue(ArgsParser.OPEN, true);
- // BH this here to allow split frame; not working as of 5/17/2019
- String file2 = aparser.getValue(ArgsParser.OPEN2, true);
- String fileFormat = (isJavaAppletTag
- ? aparser.getAppletValue("format", null)
- : null);
- FileFormatI format = null;
- DataSourceType protocol = null;
+ 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);
}
- boolean haveImport = checkStartVamas(aparser);
- // Finally, deal with the remaining input data.
- long progress = -1;
- if (file == null && isJavaAppletTag)
+ String vamsasImport = aparser.getValue("vdoc");
+ String vamsasSession = aparser.getValue("vsess");
+ if (vamsasImport != null || vamsasSession != null)
{
- // Maybe the sequences are added as parameters
- StringBuffer data = new StringBuffer("PASTE");
- int i = 1;
- while ((file = aparser.getAppletValue("sequence" + i, null)) != null)
+ if (desktop == null || headless)
{
- data.append(file.toString() + "\n");
- i++;
+ 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
+ {
+ DataSourceType viprotocol = AppletFormatAdapter
+ .checkProtocol(vamsasImport);
+ if (viprotocol == DataSourceType.FILE)
+ {
+ inSession = desktop.vamsasImport(new File(vamsasImport));
+ }
+ else if (viprotocol == DataSourceType.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 (data.length() > 5)
+ if (vamsasSession != null)
{
- file = data.toString();
+ 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();
+ }
}
}
-
- String data;
-
+ long progress = -1;
+ // Finally, deal with the remaining input data.
if (file != null)
{
-
if (!headless)
{
desktop.setProgressBar(
.getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
+ System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!isJS)
- /**
- * ignore in JavaScript -- can't just check file existence - could load
- * it?
- *
- * @j2sIgnore
- */
+ if (!Platform.isJS())
+ /**
+ * ignore in JavaScript -- can't just file existence - could load it?
+ *
+ * @j2sIgnore
+ */
{
if (!file.startsWith("http://") && !file.startsWith("https://"))
// BH 2019 added https check for Java
}
}
- protocol = AppletFormatAdapter.checkProtocol(file);
+ protocol = AppletFormatAdapter.checkProtocol(file);
try
{
- format = (isJavaAppletTag && fileFormat != null
- ? FileFormats.getInstance().forName(fileFormat)
- : null);
- if (format == null)
- {
- format = new IdentifyFile().identify(file, protocol);
- }
+ format = new IdentifyFile().identify(file, protocol);
} catch (FileFormatException e1)
{
// TODO ?
}
- if (aparser.contains(ArgsParser.NOMENUBAR))
- {
- noMenuBar = true;
- System.out.println("CMD [nomenu] executed successfully!");
- }
-
- if (aparser.contains(ArgsParser.NOSTATUS))
- {
- noStatus = true;
- System.out.println("CMD [nostatus] executed successfully!");
- }
-
- if (aparser.contains(ArgsParser.NOANNOTATION)
- || aparser.contains(ArgsParser.NOANNOTATION2))
- {
- noAnnotation = true;
- System.out.println("CMD no-annotation executed successfully!");
- }
- if (aparser.contains(ArgsParser.NOCALCULATION))
- {
- noCalculation = true;
- System.out.println("CMD [nocalculation] executed successfully!");
- }
-
- AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file,
- protocol, format);
+ AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ format);
if (af == null)
{
System.out.println("error");
}
else
{
- System.out
- .println("CMD [-open " + file + "] executed successfully!");
- if (file2 != null)
- {
- protocol = AppletFormatAdapter.checkProtocol(file2);
- try
- {
- format = new IdentifyFile().identify(file2, protocol);
- } catch (FileFormatException e1)
- {
- // TODO ?
- }
- AlignFrame af2 = new FileLoader(!headless)
- .loadFileWaitTillLoaded(file2, protocol, format);
- if (af2 == null)
- {
- System.out.println("error");
- }
- else
- {
- AlignViewport.openLinkedAlignmentAs(af,
- af.getViewport().getAlignment(),
- af2.getViewport().getAlignment(), "",
- AlignViewport.SPLIT_FRAME);
- System.out.println(
- "CMD [-open2 " + file2 + "] executed successfully!");
- }
- }
-
setCurrentAlignFrame(af);
-
- // TODO: file2 How to implement file2 for the applet spit screen?
-
- data = aparser.getValue(ArgsParser.COLOUR, true);
+ data = aparser.getValue("colour", true);
if (data != null)
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
- af.getViewport(), af.getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty
+ .getColourScheme(af.getViewport(),
+ af.getViewport().getAlignment(), data);
if (cs != null)
{
}
// Must maintain ability to use the groups flag
- data = aparser.getValue(ArgsParser.GROUPS, true);
+ data = aparser.getValue("groups", true);
if (data != null)
{
af.parseFeaturesFile(data,
System.out.println(
"CMD groups[-" + data + "] executed successfully!");
}
- data = aparser.getValue(ArgsParser.FEATURES, true);
+ data = aparser.getValue("features", true);
if (data != null)
{
af.parseFeaturesFile(data,
"CMD [-features " + data + "] executed successfully!");
}
- data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
+ data = aparser.getValue("annotations", true);
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
System.out.println(
"CMD [-annotations " + data + "] executed successfully!");
}
-
- if (aparser.contains(ArgsParser.SHOWOVERVIEW))
- {
- af.overviewMenuItem_actionPerformed(null);
- System.out.println("CMD [showoverview] executed successfully!");
- }
-
// set or clear the sortbytree flag.
- if (aparser.contains(ArgsParser.SORTBYTREE))
+ if (aparser.contains("sortbytree"))
{
af.getViewport().setSortByTree(true);
if (af.getViewport().getSortByTree())
System.out.println("CMD [-sortbytree] executed successfully!");
}
}
-
- boolean doUpdateAnnotation = false;
-
- /**
- * we do this earlier in JalviewJS because of a complication with
- * SHOWOVERVIEW
- *
- * For now, just fixing this in JalviewJS.
- *
- *
- * @j2sIgnore
- *
- */
+ if (aparser.contains("no-annotation"))
{
- if (aparser.contains(ArgsParser.NOANNOTATION)
- || aparser.contains(ArgsParser.NOANNOTATION2))
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
{
- af.getViewport().setShowAnnotation(false);
- if (!af.getViewport().isShowAnnotation())
- {
- doUpdateAnnotation = true;
- System.out
- .println("CMD no-annotation executed successfully!");
- }
+ System.out.println("CMD no-annotation executed successfully!");
}
}
- if (aparser.contains(ArgsParser.NOSORTBYTREE))
+ if (aparser.contains("nosortbytree"))
{
af.getViewport().setSortByTree(false);
if (!af.getViewport().getSortByTree())
{
- doUpdateAnnotation = true;
System.out
.println("CMD [-nosortbytree] executed successfully!");
}
}
- if (doUpdateAnnotation)
- { // BH 2019.07.24
- af.setMenusForViewport();
- af.alignPanel.updateLayout();
- }
- data = aparser.getValue(ArgsParser.TREE, true);
+ data = aparser.getValue("tree", true);
if (data != null)
{
try
// TODO - load PDB structure(s) to alignment JAL-629
// (associate with identical sequence in alignment, or a specified
// sequence)
- if (isJavaAppletTag)
+ if (groovyscript != null)
{
- loadAppletParams(aparser, af);
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, af);
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
+ groovyscript = null;
}
- else if (!isJS)
- /**
- * Java only
- *
- * @j2sIgnore
- */
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
{
- if (groovyscript != null)
+ String outputFormat = aparser.nextValue();
+ file = aparser.nextValue();
+
+ if (outputFormat.equalsIgnoreCase("png"))
{
- // Execute the groovy script after we've done all the rendering
- // stuff
- // and before any images or figures are generated.
- System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, af);
- System.out.println("CMD groovy[" + groovyscript
- + "] executed successfully!");
- groovyscript = null;
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("svg"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ System.out.println("Creating SVG image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("html"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(file);
+
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ {
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
+ System.out
+ .println("Creating BioJS MSA Viwer HTML file: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("eps"))
+ {
+ File outputFile = new File(file);
+ System.out.println(
+ "Creating EPS file: " + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
+ continue;
+ }
+
+ af.saveAlignment(file, format);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println("Written alignment in " + format
+ + " format to " + file);
}
- checkOutputFile(aparser, af, format);
- while (aparser.getSize() > 0)
+ else
{
- System.out.println("Unknown arg: " + aparser.nextValue());
+ System.out.println("Error writing file " + file + " in "
+ + format + " format!!");
}
+
+ }
+
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
}
}
}
// And the user
// ////////////////////
- if (!isJS && !headless && file == null && !haveImport
+ if (!Platform.isJS() && !headless && file == null
+ && vamsasImport == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
/**
* Java only
}
}
- startUpAlframe = new FileLoader(!headless)
- .loadFileWaitTillLoaded(file, protocol, format);
+ startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ format);
// extract groovy arguments before anything else.
}
}
desktop.setInBatchMode(false);
}
-
- return null;
}
- private boolean checkStartVamas(ArgsParser aparser)
- {
- String vamsasImport = aparser.getValue(ArgsParser.VDOC);
- String vamsasSession = aparser.getValue(ArgsParser.VSESS);
- if (vamsasImport == null && vamsasSession == null)
- {
- return false;
- }
- if (desktop == null || headless)
- {
- System.out.println(
- "Headless vamsas sessions not yet supported. Sorry.");
- System.exit(1);
- }
- boolean haveImport = (vamsasImport != null);
- if (haveImport)
- {
- // if we have a file, start a new session and import it.
- boolean inSession = false;
- try
- {
- DataSourceType viprotocol = AppletFormatAdapter
- .checkProtocol(vamsasImport);
- if (viprotocol == DataSourceType.FILE)
- {
- inSession = desktop.vamsasImport(new File(vamsasImport));
- }
- else if (viprotocol == DataSourceType.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();
- }
- }
- return haveImport;
- }
-
- private void checkOutputFile(ArgsParser aparser, AlignFrame af,
- FileFormatI format)
- {
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
- {
- // PNG filename
- // SVG filename
- // HTML filename
- // biojsmsa filename
- String outputFormat = aparser.nextValue();
- String file = aparser.nextValue();
- if (outputFormat.equalsIgnoreCase("png"))
- {
- af.createPNG(new File(file));
- imageName = (new File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("svg"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- af.createSVG(imageFile);
- System.out.println("Creating SVG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("html"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(file);
-
- System.out.println("Creating HTML image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("biojsmsa"))
- {
- if (file == null)
- {
- System.err.println("The output html file must not be null");
- return;
- }
- try
- {
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
- {
- e.printStackTrace();
- }
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(file);
- System.out.println("Creating BioJS MSA Viwer HTML file: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("eps"))
- {
- File outputFile = new File(file);
- System.out.println(
- "Creating EPS file: " + outputFile.getAbsolutePath());
- af.createEPS(outputFile);
- continue;
- }
-
- af.saveAlignment(file, format);
- if (af.isSaveAlignmentSuccessful())
- {
- System.out.println(
- "Written alignment in " + format + " format to " + file);
- }
- else
- {
- System.out.println("Error writing file " + file + " in " + format
- + " format!!");
- }
-
- }
- }
-
- private static void showUsage()
+ private static void showUsage()
{
System.out.println(
"Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- PromptUserConfig prompter = new PromptUserConfig(
- Desktop.getDesktopPane(), "USAGESTATS",
- "Jalview Usage Statistics",
+ PromptUserConfig prompter = new 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)",
}
try
{
- Map<String, Object> vbinding = new HashMap<>();
+ Map<String, java.lang.Object> vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
}
}
+ public static boolean isHeadlessMode()
+ {
+ String isheadless = System.getProperty("java.awt.headless");
+ if (isheadless != null && isheadless.equalsIgnoreCase("true"))
+ {
+ return true;
+ }
+ return false;
+ }
+
public AlignFrame[] getAlignFrames()
{
return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
*/
public void quit()
{
- if (jsFunctionExec != null)
- {
- jsFunctionExec.tidyUp();
- jsFunctionExec = null;
- }
-
if (desktop != null)
{
desktop.quit();
}
}
- /**
- * Get the SwingJS applet ID and combine that with the frameType
- *
- * @param frameType
- * "alignment", "desktop", etc., or null
- * @return
- */
- public static String getAppID(String frameType)
- {
- String id = Cache.getProperty("Info.j2sAppletID");
- if (id == null)
- {
- id = "jalview";
- }
- return id + (frameType == null ? "" : "-" + frameType);
- }
-
- /**
- * Handle all JalviewLite applet parameters
- *
- * @param aparser
- * @param af
- */
- private void loadAppletParams(ArgsParser aparser, AlignFrame af)
- {
- JalviewApp app = new JalviewApp()
- {
-
- // TODO BH 2019
- //
- // These are methods that are in JalviewLite that various classes call
- // but are not in JalviewLiteJsApi. Or, even if they are, other classes
- // call
- // them to JalviewLite directly. Some may not be necessary, but they have
- // to
- // be at least mentioned here, or the classes calling them should
- // reference
- // JalviewLite itself.
-
- private boolean alignPDBStructures; // From JalviewLite; not implemented
-
- private Hashtable<String, Hashtable<String, String[]>> jsmessages;
-
- private Hashtable<String, int[]> jshashes;
-
- @Override
- public String getParameter(String name)
- {
- return aparser.getAppletValue(name, null);
- }
-
- @Override
- public boolean getDefaultParameter(String name, boolean def)
- {
- String stn;
- return ((stn = getParameter(name)) == null ? def
- : "true".equalsIgnoreCase(stn));
- }
-
- /**
- * Get the applet-like document base even though this is an application.
- */
- @Override
- public URL getDocumentBase()
- {
- return Platform.getDocumentBase();
- }
-
- /**
- * Get the applet-like code base even though this is an application.
- */
- @Override
- public URL getCodeBase()
- {
- return Platform.getCodeBase();
- }
-
- @Override
- public AlignViewportI getViewport()
- {
- return af.getViewport();
- }
-
- /**
- * features
- *
- */
- @Override
- public boolean parseFeaturesFile(String filename,
- DataSourceType protocol)
- {
- return af.parseFeaturesFile(filename, protocol);
- }
-
- /**
- * scorefile
- *
- */
- @Override
- public boolean loadScoreFile(String sScoreFile) throws IOException
- {
- af.loadJalviewDataFile(sScoreFile, null, null, null);
- return true;
- }
-
- /**
- * annotations, jpredfile, jnetfile
- *
- */
- @Override
- public void updateForAnnotations()
- {
- af.updateForAnnotations();
- }
-
- @Override
- public void loadTree(NewickFile fin, String treeFile)
- throws IOException
- {
- // n/a -- already done by standard Jalview command line processing
- }
-
- @Override
- public void setAlignPdbStructures(boolean defaultParameter)
- {
- alignPDBStructures = true;
- }
-
- @Override
- public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
- String[] chains, DataSourceType protocol)
- {
- StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs);
- }
-
- @Override
- public void setFeatureGroupState(String[] groups, boolean state)
- {
- af.setFeatureGroupState(groups, state);
- }
-
- @Override
- public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
- String[][] chains, String[] protocols)
- {
- System.err.println(
- "Jalview applet interface alignedStructureView not implemented");
- }
-
- @Override
- public void newFeatureSettings()
- {
- System.err.println(
- "Jalview applet interface newFeatureSettings not implemented");
- }
-
- private Vector<Runnable> jsExecQueue;
-
- @Override
- public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
- {
- jsFunctionExec = exec;
- return (jsExecQueue == null ? (jsExecQueue = new Vector<>())
- : jsExecQueue);
- }
-
- @Override
- public AppletContext getAppletContext()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public boolean isJsfallbackEnabled()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public JSObject getJSObject()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
- {
- // TODO Q: what exactly is this? BH
- return null;
- }
-
- @Override
- public void updateColoursFromMouseOver(Object source,
- MouseOverStructureListener mouseOverStructureListener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public Object[] getSelectionForListener(SequenceGroup seqsel,
- ColumnSelection colsel, HiddenColumns hidden,
- SelectionSource source, Object alignFrame)
- {
- return appLoader.getSelectionForListener(getCurrentAlignFrame(),
- seqsel, colsel, hidden, source, alignFrame);
- }
-
- @Override
- public String arrayToSeparatorList(String[] array)
- {
- return appLoader.arrayToSeparatorList(array);
- }
-
- @Override
- public Hashtable<String, int[]> getJSHashes()
- {
- return (jshashes == null ? (jshashes = new Hashtable<>())
- : jshashes);
- }
-
- @Override
- public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
- {
- return (jsmessages == null ? (jsmessages = new Hashtable<>())
- : jsmessages);
- }
-
- @Override
- public Object getFrameForSource(VamsasSource source)
- {
- if (source != null)
- {
- AlignFrame af;
- if (source instanceof jalview.gui.AlignViewport
- && source == (af = getCurrentAlignFrame()).getViewport())
- {
- // should be valid if it just generated an event!
- return af;
- }
- // TODO: ensure that if '_af' is specified along with a handler
- // function, then only events from that alignFrame are sent to that
- // function
- }
- return null;
- }
-
- @Override
- public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
- {
- return new jalview.gui.FeatureRenderer((AlignmentPanel) vp);
- }
-
- };
-
- appLoader = new JalviewAppLoader(true);
- appLoader.load(app);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
- */
- @Override
- public String getSelectedSequences()
- {
- return getSelectedSequencesFrom(getCurrentAlignFrame());
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
- */
- @Override
- public String getSelectedSequences(String sep)
- {
- return getSelectedSequencesFrom(getCurrentAlignFrame(), sep);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
- * .AlignFrame)
- */
- @Override
- public String getSelectedSequencesFrom(AlignFrameI alf)
- {
- return getSelectedSequencesFrom(alf, null);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
- * .AlignFrame, java.lang.String)
- */
- @Override
- public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
- {
- return appLoader.getSelectedSequencesFrom(alf, sep);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
- * .AlignFrame, java.lang.String)
- */
- @Override
- public void highlight(String sequenceId, String position,
- String alignedPosition)
- {
- highlightIn(getCurrentAlignFrame(), sequenceId, position,
- alignedPosition);
- }
-
- @Override
- public void highlightIn(AlignFrameI alf, String sequenceId,
- String position, String alignedPosition)
- {
- appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
- }
-
- @Override
- public void select(String sequenceIds, String columns)
- {
- selectIn(getCurrentAlignFrame(), sequenceIds, columns, null);
- }
-
- @Override
- public void select(String sequenceIds, String columns, String sep)
- {
- selectIn(getCurrentAlignFrame(), sequenceIds, columns, sep);
- }
-
- @Override
- public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
- {
- selectIn(alf, sequenceIds, columns, null);
- }
-
- @Override
- public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
- String sep)
- {
- appLoader.selectIn(alf, sequenceIds, columns, sep);
- }
-
- @Override
- public String getSelectedSequencesAsAlignment(String format,
- String suffix)
- {
- return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
- format, suffix);
- }
-
- @Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
- String format, String sep)
- {
- return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
- }
-
- @Override
- public String getAlignmentOrder()
- {
- return getAlignmentFrom(getCurrentAlignFrame(), null);
- }
-
- @Override
- public String getAlignmentOrderFrom(AlignFrameI alf)
- {
- return getAlignmentFrom(alf, null);
- }
-
- @Override
- public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
- {
- return appLoader.getAlignmentOrderFrom(alf, sep);
- }
-
- @Override
- public String orderBy(String order, String undoName)
- {
- return orderBy(order, undoName, null);
- }
-
- @Override
- public String orderBy(String order, String undoName, String sep)
- {
- return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep);
- }
-
- @Override
- public String orderAlignmentBy(AlignFrameI alf, String order,
- String undoName, String sep)
- {
- return appLoader.orderAlignmentBy(alf, order, undoName, sep);
- }
-
- @Override
- public String getAlignment(String format)
- {
- return getAlignmentFrom(null, format, null);
- }
-
- @Override
- public String getAlignmentFrom(AlignFrameI alf, String format)
- {
- return getAlignmentFrom(alf, format, null);
- }
-
- @Override
- public String getAlignment(String format, String suffix)
- {
- return getAlignmentFrom(getCurrentAlignFrame(), format, suffix);
- }
-
- @Override
- public String getAlignmentFrom(AlignFrameI alf, String format,
- String suffix)
- {
- return appLoader.getAlignmentFrom(alf, format, suffix);
- }
-
- @Override
- public void loadAnnotation(String annotation)
- {
- loadAnnotationFrom(getCurrentAlignFrame(), annotation);
- }
-
- @Override
- public void loadAnnotationFrom(AlignFrameI alf, String annotation)
- {
- appLoader.loadAnnotationFrom(alf, annotation);
- }
-
- @Override
- public void loadFeatures(String features, boolean autoenabledisplay)
- {
- loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay);
- }
-
- @Override
- public boolean loadFeaturesFrom(AlignFrameI alf, String features,
- boolean autoenabledisplay)
- {
- return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
- }
-
- @Override
- public String getFeatures(String format)
- {
- return getFeaturesFrom(getCurrentAlignFrame(), format);
- }
-
- @Override
- public String getFeaturesFrom(AlignFrameI alf, String format)
- {
- return appLoader.getFeaturesFrom(alf, format);
- }
-
- @Override
- public String getAnnotation()
- {
- return getAnnotationFrom(getCurrentAlignFrame());
- }
-
- @Override
- public String getAnnotationFrom(AlignFrameI alf)
- {
- return appLoader.getAnnotationFrom(alf);
- }
-
- @Override
- public AlignFrameI newView()
- {
- return newViewFrom(getCurrentAlignFrame(), null);
- }
-
- @Override
- public AlignFrameI newView(String name)
- {
- return newViewFrom(getCurrentAlignFrame(), name);
- }
-
- @Override
- public AlignFrameI newViewFrom(AlignFrameI alf)
- {
- return newViewFrom(alf, null);
- }
-
- @Override
- public AlignFrameI newViewFrom(AlignFrameI alf, String name)
- {
- return appLoader.newViewFrom(alf, name);
- }
-
- @Override
- public AlignFrameI loadAlignment(String text, String title)
- {
- return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT, title);
- }
-
- @Override
- public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
- String pdbEntryString, String pdbFile)
- {
- return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
- pdbFile);
- }
-
- @Override
- public void scrollViewToIn(AlignFrameI alf, String topRow,
- String leftHandColumn)
- {
- appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
- }
-
- @Override
- public void scrollViewToRowIn(AlignFrameI alf, String topRow)
- {
- appLoader.scrollViewToRowIn(alf, topRow);
- }
-
- @Override
- public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
- {
- appLoader.scrollViewToColumnIn(alf, leftHandColumn);
- }
-
- @Override
- public String getFeatureGroups()
- {
- return getFeatureGroupsOn(getCurrentAlignFrame());
- }
-
- @Override
- public String getFeatureGroupsOn(AlignFrameI alf)
- {
- return appLoader.getFeatureGroupsOn(alf);
- }
-
- @Override
- public String getFeatureGroupsOfState(boolean visible)
- {
- return getFeatureGroupsOfStateOn(getCurrentAlignFrame(), visible);
- }
-
- @Override
- public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
- {
- return appLoader.getFeatureGroupsOfStateOn(alf, visible);
- }
-
- @Override
- public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
- boolean state)
- {
- setFeatureGroupStateOn(alf, groups, state);
- }
-
- @Override
- public void setFeatureGroupState(String groups, boolean state)
- {
- appLoader.setFeatureGroupStateOn(getCurrentAlignFrame(), groups, state);
- }
-
- @Override
- public String getSeparator()
- {
- return appLoader.getSeparator();
- }
-
- @Override
- public void setSeparator(String separator)
- {
- appLoader.setSeparator(separator);
- }
-
- @Override
- public String getJsMessage(String messageclass, String viewId)
- {
- // see http://www.jalview.org/examples/jalviewLiteJs.html
- return null;
- }
-
- /**
- * Open a new Tree panel on the desktop statically. Params are standard (not
- * set by Groovy). No dialog is opened.
- *
- * @param af
- * @param treeType
- * @param modelName
- * @return null, or the string "label.you_need_at_least_n_sequences" if number
- * of sequences selected is inappropriate
- */
- @Override
- public Object openTreePanel(AlignFrame af, String treeType,
- String modelName)
- {
- return CalculationChooser.openTreePanel(af, treeType, modelName, null);
- }
-
- /**
- * public static method for JalviewJS API to open a PCAPanel without
- * necessarily using a dialog.
- *
- * @param af
- * @param modelName
- * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
- * if number of sequences selected is inappropriate
- */
- @Override
- public Object openPcaPanel(AlignFrame af, String modelName)
- {
- return CalculationChooser.openPcaPanel(af, modelName, null);
- }
-
- @Override
- public String getSelectedSequencesAsAlignment(String format,
- boolean suffix)
- {
- return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
- format, suffix);
- }
-
- @Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
- String format, boolean suffix)
- {
- return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
- "" + suffix);
- }
-
- @Override
- public String arrayToSeparatorList(String[] array)
- {
- return appLoader.arrayToSeparatorList(array);
- }
-
- @Override
- public String[] separatorListToArray(String list)
- {
- return appLoader.separatorListToArray(list);
- }
-
- //// probably not needed in JalviewJS -- From when Jmol and Jalview did not
- //// have a direct connection?
-
- @Override
- public void setMouseoverListener(String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setMouseoverListener(AlignFrameI af, String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setSelectionListener(String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setSelectionListener(AlignFrameI af, String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setStructureListener(String listener, String modelSet)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void removeJavascriptListener(AlignFrameI af, String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void mouseOverStructure(String pdbResNum, String chain,
- String pdbfile)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void showOverview()
+ public static AlignFrame getCurrentAlignFrame()
{
- currentAlignFrame.overviewMenuItem_actionPerformed(null);
+ return Jalview.currentAlignFrame;
}
- public void notifyWorker(AlignCalcWorkerI worker, String status)
+ public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
- // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
- // + " " + status);
+ Jalview.currentAlignFrame = currentAlignFrame;
}
-
}
-
git://source.jalview.org / jalview.git / blobdiff