X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=5d82015cacd1e6b8b79fa93259eb4ecedb74e542;hb=14bfc6fb57f123b815f08dbf5b35544abd33b3af;hp=28d029c1ac68d23c33fc0d31bd7d62f279c7e2a5;hpb=7d52ef194d39e75fed7730041da25c48e456cf8c;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 28d029c..5d82015 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,6 +20,7 @@ */ package jalview.bin; +import jalview.api.AlignCalcWorkerI; import jalview.api.AlignFrameI; import jalview.api.AlignViewportI; import jalview.api.JalviewApp; @@ -85,6 +86,7 @@ import java.util.Map; import java.util.Vector; import javax.swing.LookAndFeel; +import javax.swing.SwingUtilities; import javax.swing.UIManager; import groovy.lang.Binding; @@ -147,6 +149,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi private boolean noAnnotation; + public static final String TERMINATOR_LINE = "Jalview argument parsing complete."; + public boolean getStartCalculations() { return !noCalculation; @@ -304,6 +308,16 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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(); @@ -335,13 +349,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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! @@ -397,7 +404,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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"); @@ -450,7 +463,21 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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 @@ -517,6 +544,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } parseArguments(aparser, true); + System.err.println(TERMINATOR_LINE); } /** @@ -640,14 +668,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi // 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; @@ -757,6 +777,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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)) { @@ -849,11 +876,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi + "] 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()); } } } @@ -1031,18 +1058,35 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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 + * + * 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)); @@ -1632,6 +1676,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public String getSelectedSequencesFrom(AlignFrameI alf) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return getSelectedSequencesFrom(alf, null); } @@ -1643,6 +1691,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public String getSelectedSequencesFrom(AlignFrameI alf, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getSelectedSequencesFrom(alf, sep); } @@ -1655,7 +1707,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public void highlight(String sequenceId, String position, String alignedPosition) { - highlightIn(getCurrentAlignFrame(), sequenceId, position, + highlightIn(null, sequenceId, position, alignedPosition); } @@ -1663,6 +1715,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public void highlightIn(AlignFrameI alf, String sequenceId, String position, String alignedPosition) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } appLoader.highlightIn(alf, sequenceId, position, alignedPosition); } @@ -1675,7 +1731,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public void select(String sequenceIds, String columns, String sep) { - selectIn(getCurrentAlignFrame(), sequenceIds, columns, sep); + selectIn(null, sequenceIds, columns, sep); } @Override @@ -1688,6 +1744,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public void selectIn(AlignFrameI alf, String sequenceIds, String columns, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } appLoader.selectIn(alf, sequenceIds, columns, sep); } @@ -1695,7 +1755,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String getSelectedSequencesAsAlignment(String format, String suffix) { - return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(), + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); } @@ -1703,6 +1763,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, String format, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep); } @@ -1721,6 +1785,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public String getAlignmentOrderFrom(AlignFrameI alf, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getAlignmentOrderFrom(alf, sep); } @@ -1740,6 +1808,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String orderAlignmentBy(AlignFrameI alf, String order, String undoName, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.orderAlignmentBy(alf, order, undoName, sep); } @@ -1777,6 +1849,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public void loadAnnotationFrom(AlignFrameI alf, String annotation) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } appLoader.loadAnnotationFrom(alf, annotation); } @@ -1790,43 +1866,55 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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 @@ -1838,6 +1926,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public AlignFrameI newViewFrom(AlignFrameI alf, String name) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.newViewFrom(alf, name); } @@ -1852,6 +1944,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public boolean addPdbFile(AlignFrameI alFrame, String sequenceId, String pdbEntryString, String pdbFile) { + if (alFrame == null) + { + alFrame = getCurrentAlignFrame(); + } return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString, pdbFile); } @@ -1860,56 +1956,80 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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 @@ -1944,7 +2064,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public Object openTreePanel(AlignFrame af, String treeType, String modelName) - { + { // JalviewJS api + if (af == null) + { + af = getCurrentAlignFrame(); + } return CalculationChooser.openTreePanel(af, treeType, modelName, null); } @@ -1960,6 +2084,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public Object openPcaPanel(AlignFrame af, String modelName) { + if (af == null) + { + af = getCurrentAlignFrame(); + } return CalculationChooser.openPcaPanel(af, modelName, null); } @@ -1967,7 +2095,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String getSelectedSequencesAsAlignment(String format, boolean suffix) { - return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(), + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); } @@ -1975,6 +2103,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, String format, boolean suffix) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, "" + suffix); } @@ -2050,5 +2182,88 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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