*/
package jalview.bin;
+import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignFrameI;
import jalview.api.AlignViewportI;
import jalview.api.JalviewApp;
import java.util.Vector;
import javax.swing.LookAndFeel;
+import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import groovy.lang.Binding;
private boolean noCalculation, noMenuBar, noStatus;
+ private boolean noAnnotation;
+
+ public static final String TERMINATOR_LINE = "Jalview argument parsing complete.";
+
public boolean getStartCalculations()
{
return !noCalculation;
return !noStatus;
}
+ public boolean getShowAnnotation()
+ {
+ return !noAnnotation;
+ }
public static AlignFrame getCurrentAlignFrame()
{
String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
Cache.loadProperties(usrPropsFile);
+
+ 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();
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!
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");
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 = Desktop.getInstance();
desktop.setInBatchMode(true); // indicate we are starting up
}
parseArguments(aparser, true);
+ System.err.println(TERMINATOR_LINE);
}
/**
// TODO ?
}
- if (aparser.contains(ArgsParser.SHOWOVERVIEW))
- {
- jalview.bin.Cache.setPropertyNoSave(Preferences.SHOW_OVERVIEW,
- "true");
-
- System.out.println("CMD [showoverview] executed successfully!");
- }
-
if (aparser.contains(ArgsParser.NOMENUBAR))
{
noMenuBar = 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 [-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))
{
System.out.println("CMD [-sortbytree] executed successfully!");
}
}
-
+
boolean doUpdateAnnotation = false;
-
- if (aparser.contains(ArgsParser.NOANNOTATION)
- || aparser.contains(ArgsParser.NOANNOTATION2))
+ /**
+ * 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))
{
- doUpdateAnnotation = true;
- 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))
+ "] executed successfully!");
groovyscript = null;
}
- checkOutputFile(aparser, af, format);
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
- }
+ }
+ createOutputFiles(aparser, af, format);
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
}
}
}
return haveImport;
}
- private void checkOutputFile(ArgsParser aparser, AlignFrame af,
+ /**
+ * Writes an output file for each format (if any) specified in the
+ * command-line arguments. Supported formats are currently
+ * <ul>
+ * <li>png</li>
+ * <li>svg</li>
+ * <li>html</li>
+ * <li>biojsmsa</li>
+ * <li>imgMap</li>
+ * <li>eps</li>
+ * </ul>
+ * A format parameter should be followed by a parameter specifying the output
+ * file name. {@code imgMap} parameters should follow those for the
+ * corresponding alignment image output.
+ *
+ * @param aparser
+ * @param af
+ * @param format
+ */
+ private void createOutputFiles(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();
+ // System.out.println("format " + outputFormat);
+
if (outputFormat.equalsIgnoreCase("png"))
{
af.createPNG(new File(file));
@Override
public String getSelectedSequencesFrom(AlignFrameI alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return getSelectedSequencesFrom(alf, null);
}
@Override
public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesFrom(alf, sep);
}
public void highlight(String sequenceId, String position,
String alignedPosition)
{
- highlightIn(getCurrentAlignFrame(), sequenceId, position,
+ highlightIn(null, sequenceId, position,
alignedPosition);
}
public void highlightIn(AlignFrameI alf, String sequenceId,
String position, String alignedPosition)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
}
@Override
public void select(String sequenceIds, String columns, String sep)
{
- selectIn(getCurrentAlignFrame(), sequenceIds, columns, sep);
+ selectIn(null, sequenceIds, columns, sep);
}
@Override
public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.selectIn(alf, sequenceIds, columns, sep);
}
public String getSelectedSequencesAsAlignment(String format,
String suffix)
{
- return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+ return getSelectedSequencesAsAlignmentFrom(null,
format, suffix);
}
public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
}
@Override
public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getAlignmentOrderFrom(alf, sep);
}
public String orderAlignmentBy(AlignFrameI alf, String order,
String undoName, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.orderAlignmentBy(alf, order, undoName, sep);
}
@Override
public void loadAnnotationFrom(AlignFrameI alf, String annotation)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.loadAnnotationFrom(alf, annotation);
}
public boolean loadFeaturesFrom(AlignFrameI alf, String features,
boolean autoenabledisplay)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
}
@Override
public String getFeatures(String format)
{
- return getFeaturesFrom(getCurrentAlignFrame(), format);
+ return getFeaturesFrom(null, format);
}
@Override
public String getFeaturesFrom(AlignFrameI alf, String format)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getFeaturesFrom(alf, format);
}
@Override
public String getAnnotation()
{
- return getAnnotationFrom(getCurrentAlignFrame());
+ return getAnnotationFrom(null);
}
@Override
public String getAnnotationFrom(AlignFrameI alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getAnnotationFrom(alf);
}
@Override
public AlignFrameI newView()
{
- return newViewFrom(getCurrentAlignFrame(), null);
+ return newViewFrom(null, null);
}
@Override
public AlignFrameI newView(String name)
{
- return newViewFrom(getCurrentAlignFrame(), name);
+ return newViewFrom(null, name);
}
@Override
@Override
public AlignFrameI newViewFrom(AlignFrameI alf, String name)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.newViewFrom(alf, name);
}
public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
+ if (alFrame == null)
+ {
+ alFrame = getCurrentAlignFrame();
+ }
return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
pdbFile);
}
public void scrollViewToIn(AlignFrameI alf, String topRow,
String leftHandColumn)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
}
@Override
public void scrollViewToRowIn(AlignFrameI alf, String topRow)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToRowIn(alf, topRow);
}
@Override
public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToColumnIn(alf, leftHandColumn);
}
@Override
public String getFeatureGroups()
{
- return getFeatureGroupsOn(getCurrentAlignFrame());
+ return getFeatureGroupsOn(null);
}
@Override
public String getFeatureGroupsOn(AlignFrameI alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getFeatureGroupsOn(alf);
}
@Override
public String getFeatureGroupsOfState(boolean visible)
{
- return getFeatureGroupsOfStateOn(getCurrentAlignFrame(), visible);
+ return getFeatureGroupsOfStateOn(null, visible);
}
@Override
public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getFeatureGroupsOfStateOn(alf, visible);
}
@Override
- public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
- boolean state)
- {
- setFeatureGroupStateOn(alf, groups, state);
+ public void setFeatureGroupState(String groups, boolean state)
+ { // JalviewLite API
+ setFeatureGroupStateOn(null, groups, state);
}
@Override
- public void setFeatureGroupState(String groups, boolean state)
+ public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+ boolean state)
{
- appLoader.setFeatureGroupStateOn(getCurrentAlignFrame(), groups, state);
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.setFeatureGroupStateOn(alf, groups, state);
}
@Override
@Override
public Object openTreePanel(AlignFrame af, String treeType,
String modelName)
- {
+ { // JalviewJS api
+ if (af == null)
+ {
+ af = getCurrentAlignFrame();
+ }
return CalculationChooser.openTreePanel(af, treeType, modelName, null);
}
@Override
public Object openPcaPanel(AlignFrame af, String modelName)
{
+ if (af == null)
+ {
+ af = getCurrentAlignFrame();
+ }
return CalculationChooser.openPcaPanel(af, modelName, null);
}
public String getSelectedSequencesAsAlignment(String format,
boolean suffix)
{
- return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+ return getSelectedSequencesAsAlignmentFrom(null,
format, suffix);
}
public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, boolean suffix)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
"" + suffix);
}
}
+ @Override
+ public void showOverview()
+ {
+ currentAlignFrame.overviewMenuItem_actionPerformed(null);
+ }
+
+ public void notifyWorker(AlignCalcWorkerI worker, String status)
+ {
+ // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+ // + " " + status);
+ }
+
+ /**
+ * flag to allow selected Runnable and Thread processes to run synchronously
+ *
+ * JAL-3563
+ *
+ */
+ private static boolean isSynchronous = false;
-}
+ /**
+ * Set Jalview to run selected processes synchronously in test and headless
+ * environments.
+ *
+ * JAL-3563
+ *
+ * @param b
+ * @author Bob Hanson
+ */
+ public static void setSynchronous(boolean b)
+ {
+ isSynchronous = b;
+ }
+
+ /**
+ * Allows optional synchronous running of a Runnable that would otherwise use
+ * SwingUtilities.invokeLater.
+ *
+ * JAL-3563
+ *
+ * @param t
+ * @author Bob Hanson
+ */
+ public static boolean isSynchronous()
+ {
+ return isSynchronous;
+ }
+
+ /**
+ * Allows optional synchronous running of a Runnable that would otherwise use
+ * SwingUtilities.invokeLater.
+ *
+ * JAL-3563
+ *
+ * @param t
+ * @author Bob Hanson
+ */
+ public static void execRunnable(Runnable r)
+ {
+ if (isSynchronous())
+ {
+ r.run();
+ }
+ else
+ {
+ SwingUtilities.invokeLater(r);
+ }
+ }
+
+ /**
+ * Allows optional synchronous running of a thread that would otherwise be run
+ * using start().
+ *
+ * JAL-3563
+ *
+ * @param t
+ * @author Bob Hanson
+ */
+ public static void execThread(Thread t)
+ {
+ if (isSynchronous())
+ {
+ t.run();
+ }
+ else
+ {
+ t.start();
+ }
+ }
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff