*/
package jalview.bin;
+import java.awt.GraphicsEnvironment;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
import jalview.api.AlignCalcWorkerI;
-import jalview.api.JalviewJSApp;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
-//import netscape.javascript.JSObject;
/**
* Main class for Jalview Application <br>
Cache.loadProperties(usrPropsFile); // must do this before
+ boolean allowServices = true;
+
if (isJS)
{
j2sAppletID = Platform.getAppID(null);
showUsage();
System.exit(0);
}
- // ?>>
+ // BH note: Only -nodisplay is official; others are deprecated?
if (aparser.contains("nodisplay") || aparser.contains("nogui")
- || aparser.contains("headless"))
+ || aparser.contains("headless")
+ || GraphicsEnvironment.isHeadless())
+ {
+ if (!isJS) {
+ // BH Definitely not a good idea in JavaScript;
+ // probably should not be here for Java, either.
+ System.setProperty("java.awt.headless", "true");
+ }
+ headless = true;
+ }
+ if (GraphicsEnvironment.isHeadless())
{
- System.setProperty("java.awt.headless", "true");
headless = true;
}
// <<?
// anything else!
final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
- if (jabawsUrl != null)
+ allowServices = !("none".equals(jabawsUrl));
+ if (allowServices && jabawsUrl != null)
{
try
{
}
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"));
try
System.exit(0);
}
- desktop = null;
-
if (!isJS)
/** @j2sIgnore */
{
SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
+
+ desktop = null;
if (!headless)
{
desktop = Desktop.getInstance();
* @j2sIgnore
*/
{
- desktop.startServiceDiscovery();
+ if (allowServices)
+ desktop.startServiceDiscovery();
if (!aparser.contains("nousagestats"))
{
startUsageStats(desktop);
}
/**
- * Parse all command-line String[] arguments as well as all JavaScript-derived parameters from Info.
+ * Parse all command-line String[] arguments as well as all JavaScript-derived
+ * parameters from Info.
*
- * We allow for this method to be run from JavaScript. Basically allowing simple scripting.
+ * We allow for this method to be run from JavaScript. Basically allowing
+ * simple scripting.
*
* @param aparser
* @param isStartup
System.exit(1);
}
+ setDisplayParameters(aparser);
+
// time to open a file.
long progress = -1;
FileLoader fileLoader = new FileLoader(!headless);
FileFormatI format = null;
// Finally, deal with the remaining input data.
- JalviewJSApp jsApp = null;
AlignFrame af = null;
- if (file != null)
+ JalviewJSApp jsApp = (isJS ? new JalviewJSApp(this, aparser) : null);
+
+ if (file == null)
+ {
+ if (isJS)
+ {
+ // JalviewJS allows sequence1 sequence2 ....
+
+ }
+ else if (!headless && Cache.getDefault("SHOW_STARTUP_FILE", true))
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+
+ // We'll only open the default file if the desktop is visible.
+ // And the user
+ // ////////////////////
+
+ file = Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org")
+ + "/examples/exampleFile_2_7.jar");
+ if (file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ {
+ // hardwire upgrade of the startup file
+ file.replace("_2_3.jar", "_2_7.jar");
+ // and remove the stale setting
+ Cache.removeProperty("STARTUP_FILE");
+ }
+
+ protocol = DataSourceType.FILE;
+
+ if (file.indexOf("http:") > -1)
+ {
+ protocol = DataSourceType.URL;
+ }
+
+ if (file.endsWith(".jar"))
+ {
+ format = FileFormat.Jalview;
+ }
+ else
+ {
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e)
+ {
+ // TODO what?
+ }
+ }
+ af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
+ }
+ }
+ else
{
if (!headless)
{
}
}
}
+
String fileFormat = (isJS
? (String) aparser.getAppletValue("format", null, true)
: null);
// 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!");
- }
-
af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, protocol,
format);
if (af == null)
{
- System.out.println("error");
+ System.out.println("jalview error - AlignFrame was not created");
}
else
{
}
setCurrentAlignFrame(af);
- String data = aparser.getValue(ArgsParser.COLOUR, true);
- if (data != null)
- {
- data.replaceAll("%20", " ");
-
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
- af.getViewport(), af.getViewport().getAlignment(), data);
-
- if (cs != null)
- {
- System.out.println(
- "CMD [-color " + data + "] executed successfully!");
- }
- af.changeColour(cs);
- }
-
- // Must maintain ability to use the groups flag
- data = aparser.getValue(ArgsParser.GROUPS, true);
- if (data != null)
- {
- af.parseFeaturesFile(data,
- AppletFormatAdapter.checkProtocol(data));
- // System.out.println("Added " + data);
- System.out.println(
- "CMD groups[-" + data + "] executed successfully!");
- }
- data = aparser.getValue(ArgsParser.FEATURES, true);
- if (data != null)
- {
- af.parseFeaturesFile(data,
- AppletFormatAdapter.checkProtocol(data));
- // System.out.println("Added " + data);
- System.out.println(
- "CMD [-features " + data + "] executed successfully!");
- }
- data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
- if (data != null)
- {
- af.loadJalviewDataFile(data, null, null, null);
- // System.out.println("Added " + data);
- System.out.println(
- "CMD [-annotations " + data + "] executed successfully!");
- }
-
- // JavaScript feature
-
- 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))
- {
- 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(ArgsParser.NOANNOTATION)
- || aparser.contains(ArgsParser.NOANNOTATION2))
- {
- af.getViewport().setShowAnnotation(false);
- if (!af.getViewport().isShowAnnotation())
- {
- doUpdateAnnotation = true;
- System.out
- .println("CMD no-annotation executed successfully!");
- }
- }
- }
-
- if (aparser.contains(ArgsParser.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);
- if (data != null)
- {
- try
- {
- NewickFile nf = new NewickFile(data,
- AppletFormatAdapter.checkProtocol(data));
- af.getViewport()
- .setCurrentTree(af.showNewickTree(nf, data).getTree());
- System.out.println(
- "CMD [-tree " + data + "] executed successfully!");
- } catch (IOException ex)
- {
- System.err.println("Couldn't add tree " + data);
- ex.printStackTrace(System.err);
- }
- }
- // TODO - load PDB structure(s) to alignment JAL-629
- // (associate with identical sequence in alignment, or a specified
- // sequence)
-
+ setFrameDependentProperties(aparser, af);
+
if (isJS)
{
- jsApp = new JalviewJSApp(aparser);
- jsApp.load(af);
+ jsApp.initFromParams(af);
}
else
/**
+ "] executed successfully!");
groovyscript = null;
}
- createOutputFiles(aparser, af, format);
}
- }
- }
- else
- {
- if (!isJS && !headless && Cache.getDefault("SHOW_STARTUP_FILE", true))
- /**
- * Java only
- *
- * @j2sIgnore
- */
- {
-
- // We'll only open the default file if the desktop is visible.
- // And the user
- // ////////////////////
-
- file = Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
- + "/examples/exampleFile_2_7.jar");
- if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar"))
- {
- // hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
- // and remove the stale setting
- Cache.removeProperty("STARTUP_FILE");
- }
-
- protocol = DataSourceType.FILE;
-
- if (file.indexOf("http:") > -1)
- {
- protocol = DataSourceType.URL;
- }
-
- if (file.endsWith(".jar"))
- {
- format = FileFormat.Jalview;
- }
- else
- {
- try
- {
- format = new IdentifyFile().identify(file, protocol);
- } catch (FileFormatException e)
- {
- // TODO what?
- }
+ if (!isJS || !isStartup) {
+ createOutputFiles(aparser, format);
}
-
- af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
-
}
}
// extract groovy arguments before anything else.
}
desktop.setInBatchMode(false);
}
-
- if (isJS && isStartup)
- {
+
+ if (jsApp != null) {
jsApp.callInitCallback();
}
}
+ /**
+ * Set general display parameters irrespective of file loading or headlessness.
+ *
+ * @param aparser
+ */
+ private void setDisplayParameters(ArgsParser aparser)
+ {
+ 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!");
+ }
+ }
+
+
+ private void setFrameDependentProperties(ArgsParser aparser,
+ AlignFrame af)
+ {
+ String data = aparser.getValue(ArgsParser.COLOUR, true);
+ if (data != null)
+ {
+ data.replaceAll("%20", " ");
+
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
+
+ if (cs != null)
+ {
+ System.out.println(
+ "CMD [-color " + data + "] executed successfully!");
+ }
+ af.changeColour(cs);
+ }
+
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue(ArgsParser.GROUPS, true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD groups[-" + data + "] executed successfully!");
+ }
+ data = aparser.getValue(ArgsParser.FEATURES, true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD [-features " + data + "] executed successfully!");
+ }
+ data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
+ if (data != null)
+ {
+ af.loadJalviewDataFile(data, null, null, null);
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD [-annotations " + data + "] executed successfully!");
+ }
+
+ // JavaScript feature
+
+ 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))
+ {
+ 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 (noAnnotation)
+ {
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ doUpdateAnnotation = true;
+ }
+ }
+ }
+
+ if (aparser.contains(ArgsParser.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);
+ if (data != null)
+ {
+ try
+ {
+ NewickFile nf = new NewickFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ af.getViewport()
+ .setCurrentTree(af.showNewickTree(nf, data).getTree());
+ System.out.println(
+ "CMD [-tree " + data + "] executed successfully!");
+ } catch (IOException ex)
+ {
+ System.err.println("Couldn't add tree " + data);
+ ex.printStackTrace(System.err);
+ }
+ }
+ // TODO - load PDB structure(s) to alignment JAL-629
+ // (associate with identical sequence in alignment, or a specified
+ // sequence)
+
+ }
/**
* Writes an output file for each format (if any) specified in the
* corresponding alignment image output.
*
* @param aparser
- * @param af
* @param format
*/
- private void createOutputFiles(ArgsParser aparser, AlignFrame af,
- FileFormatI format)
+ private void createOutputFiles(ArgsParser aparser, FileFormatI format)
{
+ AlignFrame af = currentAlignFrame;
while (aparser.getSize() >= 2)
{
String outputFormat = aparser.nextValue();
System.out.println(
"Creating image map: " + imageFile.getAbsolutePath());
continue;
- }
- if (!Platform.isJS()) /** @j2sIgnore */
- {
- // skipping outputFormat?
- System.out.println("Unknown arg: " + outputFormat);
- fname = new File(aparser.nextValue()).getAbsolutePath();
- af.saveAlignment(fname, format);
- if (af.isSaveAlignmentSuccessful())
+ default:
+ // fall through - try to parse as an alignment data export format
+ FileFormatI outFormat = null;
+ try
+ {
+ outFormat = FileFormats.getInstance().forName(outputFormat);
+ } catch (Exception formatP)
+ {
+ }
+ if (outFormat == null)
+ {
+ System.out.println("Couldn't parse " + outputFormat
+ + " as a valid Jalview format string.");
+ continue;
+ }
+ if (!outFormat.isWritable())
{
System.out.println(
- "Written alignment in " + format + " format to " + fname);
+ "This version of Jalview does not support alignment export as "
+ + outputFormat);
+ continue;
+ }
+ // record file as it was passed to Jalview so it is recognisable to the CLI
+ // caller
+ String file;
+ fname = new File(file = aparser.nextValue()).getAbsolutePath();
+ // JBPNote - yuck - really wish we did have a bean returned from this which gave
+ // success/fail like before !
+ af.saveAlignment(fname, outFormat);
+ if (!af.isSaveAlignmentSuccessful())
+ {
+ System.out.println("Written alignment in " + outputFormat
+ + " format to " + file);
+ continue;
}
else
{
- System.out.println("Error writing file " + fname + " in " + format
- + " format!!");
+ System.out.println("Error writing file " + file + " in "
+ + outputFormat + " format!!");
}
}
- break;
}
+ // ??? Should report - 'ignoring' extra args here...
while (aparser.getSize() > 0)
{
- System.out.println("Unknown arg: " + aparser.nextValue());
+ System.out.println("Ignoring extra argument: " + aparser.nextValue());
}
}
// System.out.println("Jalview worker " + worker.getClass().getSimpleName()
// + " " + status);
}
-
+
+
+ private static boolean isInteractive = true;
+
+ public static boolean isInteractive()
+ {
+ return isInteractive;
+ }
+
+ public static void setInteractive(boolean tf)
+ {
+ isInteractive = tf;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff