X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=0ec9ee0e685c5e38f347014808b105283af6f945;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=cb2b469de9a1929909536d97f5ff9e09bf43fb59;hpb=4b0220906ff60a04786c3f3eb95fa306407f27c7;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index cb2b469..0ec9ee0 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,32 +20,50 @@
*/
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;
@@ -63,17 +81,17 @@ import java.security.PermissionCollection;
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.SwingUtilities;
import javax.swing.UIManager;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
+import netscape.javascript.JSObject;
/**
* Main class for Jalview Application
@@ -90,18 +108,17 @@ import groovy.util.GroovyScriptEngine;
* @author $author$
* @version $Revision$
*/
-public class Jalview
+public class Jalview implements ApplicationSingletonI, JalviewJSApi
{
public static Jalview getInstance()
{
- Instance i = Instance.getInstance();
- return (i.jalview == null ? i.jalview = new Jalview() : i.jalview);
+ return (Jalview) ApplicationSingletonProvider
+ .getInstance(Jalview.class);
}
- public Jalview()
+ private Jalview()
{
- Instance.getInstance().jalview = this;
}
static
@@ -124,6 +141,36 @@ public class Jalview
public String appletResourcePath;
+ JalviewAppLoader appLoader;
+
+ protected JSFunctionExec jsFunctionExec;
+
+ private boolean noCalculation, noMenuBar, noStatus;
+
+ private boolean noAnnotation;
+
+ public static final String TERMINATOR_LINE = "Jalview argument parsing complete.";
+
+ 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;
@@ -229,57 +276,24 @@ public class Jalview
*/
public static void main(String[] args)
{
- // setLogging(); // BH - for event debugging in JavaScript
- new Jalview().doMain(args);
+ // Platform.startJavaLogging();
+ getInstance().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)
{
- if (!Platform.isJS())
+ boolean isJS = Platform.isJS();
+ if (isJS)
+ {
+ Platform.setAppClass(this);
+ }
+ else
{
System.setSecurityManager(null);
}
@@ -294,7 +308,17 @@ public class Jalview
String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
Cache.loadProperties(usrPropsFile);
- if (Platform.isJS())
+
+ if (aparser.contains(ArgsParser.NODISPLAY)
+ || aparser.contains(ArgsParser.NOGUI)
+ || aparser.contains(ArgsParser.HEADLESS)
+ || "true".equals(System.getProperty("java.awt.headless")))
+ {
+ headless = true;
+ setSynchronous(true);
+ }
+
+ if (isJS)
{
isJavaAppletTag = aparser.isApplet();
if (isJavaAppletTag)
@@ -325,13 +349,6 @@ public class Jalview
showUsage();
System.exit(0);
}
- if (aparser.contains(ArgsParser.NODISPLAY)
- || aparser.contains(ArgsParser.NOGUI)
- || aparser.contains(ArgsParser.HEADLESS)
- || "true".equals(System.getProperty("java.awt.headless")))
- {
- headless = true;
- }
// anything else!
@@ -363,7 +380,7 @@ public class Jalview
else
{
System.out.println("Executing setprop argument: " + defs);
- if (Platform.isJS())
+ if (isJS)
{
Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
}
@@ -387,7 +404,13 @@ public class Jalview
try
{
- UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ if (!isJS && Platform.isWin())
+ {
+ UIManager.setLookAndFeel(
+ headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
+ : UIManager.getSystemLookAndFeelClassName());
+ // UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ }
} catch (Exception ex)
{
System.err.println("Unexpected Look and Feel Exception");
@@ -435,18 +458,32 @@ public class Jalview
* configure 'full' SO model if preferences say to,
* else use the default (SO Lite)
*/
- if (Cache.getDefault("USE_FULL_SO", false))
+ if (Cache.getDefault(Preferences.USE_FULL_SO, false))
{
- SequenceOntologyFactory.setInstance(new SequenceOntology());
+ SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
- if (!headless)
+ if (headless)
+ {
+ // If this is not tested, then
+
+ if (aparser.contains(ArgsParser.NOUSAGESTATS))
+ {
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+ if (aparser.contains(ArgsParser.NOQUESTIONNAIRE))
+ {
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
+ }
+
+ }
+ else
{
- desktop = new Desktop();
+ desktop = Desktop.getInstance();
desktop.setInBatchMode(true); // indicate we are starting up
desktop.setVisible(true);
- if (!Platform.isJS())
+ if (!isJS)
/**
* Java only
*
@@ -477,7 +514,7 @@ public class Jalview
}
else
{
- if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ if (Cache.getProperty(Preferences.NOQUESTIONNAIRES) == null)
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
@@ -506,111 +543,85 @@ public class Jalview
}
}
- String data = null;
- FileFormatI format = null;
- DataSourceType protocol = null;
- FileLoader fileLoader = new FileLoader(!headless);
+ parseArguments(aparser, true);
+ System.err.println(TERMINATOR_LINE);
+ }
+
+ /**
+ * 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();
+ Desktop desktop = (headless ? null : Desktop.getInstance());
// script to execute after all loading is
// completed one way or another
// extract groovy argument and execute if necessary
- String groovyscript = aparser.getValue(ArgsParser.GROOVY, true);
+ 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;
if (file == null && desktop == null)
{
System.out.println("No files to open!");
System.exit(1);
}
- String vamsasImport = aparser.getValue(ArgsParser.VDOC);
- String vamsasSession = aparser.getValue(ArgsParser.VSESS);
- if (vamsasImport != null || vamsasSession != null)
+ boolean haveImport = false;// checkStartVamas(aparser);
+ // Finally, deal with the remaining input data.
+ long progress = -1;
+ if (file == null && isJavaAppletTag)
{
- 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)
+ // Maybe the sequences are added as parameters
+ StringBuffer data = new StringBuffer("PASTE");
+ int i = 1;
+ while ((file = aparser.getAppletValue("sequence" + i, null)) != 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());
- }
+ data.append(file.toString() + "\n");
+ i++;
}
- if (vamsasSession != null)
+ if (data.length() > 5)
{
- 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();
- }
+ file = data.toString();
}
}
- long progress = -1;
- // Finally, deal with the remaining input data.
+
+ String data;
+
if (file != null)
{
+
if (!headless)
{
desktop.setProgressBar(
@@ -618,9 +629,8 @@ public class Jalview
.getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
- System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!Platform.isJS())
+ if (!isJS)
/**
* ignore in JavaScript -- can't just check file existence - could load
* it?
@@ -646,21 +656,83 @@ public class Jalview
try
{
- format = new IdentifyFile().identify(file, protocol);
+ format = (isJavaAppletTag && fileFormat != null
+ ? FileFormats.getInstance().forName(fileFormat)
+ : null);
+ if (format == null)
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ }
} catch (FileFormatException e1)
{
// TODO ?
}
- AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
- format);
+ 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);
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);
if (data != null)
{
@@ -705,6 +777,13 @@ public class Jalview
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))
{
@@ -714,13 +793,30 @@ public class Jalview
System.out.println("CMD [-sortbytree] executed successfully!");
}
}
- if (aparser.contains(ArgsParser.NOANNOTATION)
- || aparser.contains(ArgsParser.NOANNOTATION2))
+
+ boolean doUpdateAnnotation = false;
+
+ /**
+ * we do this earlier in JalviewJS because of a complication with
+ * SHOWOVERVIEW
+ *
+ * For now, just fixing this in JalviewJS.
+ *
+ *
+ * @j2sIgnore
+ *
+ */
{
- af.getViewport().setShowAnnotation(false);
- if (!af.getViewport().isShowAnnotation())
+ if (aparser.contains(ArgsParser.NOANNOTATION)
+ || aparser.contains(ArgsParser.NOANNOTATION2))
{
- System.out.println("CMD no-annotation executed successfully!");
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ doUpdateAnnotation = true;
+ System.out
+ .println("CMD no-annotation executed successfully!");
+ }
}
}
if (aparser.contains(ArgsParser.NOSORTBYTREE))
@@ -728,10 +824,16 @@ public class Jalview
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);
if (data != null)
{
@@ -752,114 +854,34 @@ public class Jalview
// TODO - load PDB structure(s) to alignment JAL-629
// (associate with identical sequence in alignment, or a specified
// sequence)
- if (groovyscript != null)
- {
- // 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;
- }
-
if (isJavaAppletTag)
{
loadAppletParams(aparser, af);
}
- else
+ else if (!isJS)
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
-
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
- {
- // PNG filename
- // SVG filename
- // HTML filename
- // biojsmsa filename
- String outputFormat = aparser.nextValue();
- 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!!");
- }
-
- }
-
- while (aparser.getSize() > 0)
+ if (groovyscript != null)
{
- System.out.println("Unknown arg: " + aparser.nextValue());
+ // 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;
}
}
+ createOutputFiles(aparser, af, format);
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
+ }
}
}
AlignFrame startUpAlframe = null;
@@ -867,8 +889,7 @@ public class Jalview
// And the user
// ////////////////////
- if (!Platform.isJS() && !headless && file == null
- && vamsasImport == null
+ if (!isJS && !headless && file == null && !haveImport
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
/**
* Java only
@@ -911,8 +932,8 @@ public class Jalview
}
}
- startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
- format);
+ startUpAlframe = new FileLoader(!headless)
+ .LoadFileWaitTillLoaded(file, protocol, format);
// extract groovy arguments before anything else.
}
@@ -940,6 +961,112 @@ public class Jalview
}
desktop.setInBatchMode(false);
}
+
+ return null;
+ }
+
+ /**
+ * Writes an output file for each format (if any) specified in the
+ * command-line arguments. Supported formats are currently
+ *