X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=5d82015cacd1e6b8b79fa93259eb4ecedb74e542;hb=14bfc6fb57f123b815f08dbf5b35544abd33b3af;hp=f59c37f16cae5d38c3848d231c4e168a08e9f57c;hpb=a3d82d30b2bc55f250bbf1c94975308407e8aae7;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index f59c37f..5d82015 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -86,6 +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; @@ -148,6 +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; @@ -312,6 +315,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi || "true".equals(System.getProperty("java.awt.headless"))) { headless = true; + setSynchronous(true); } if (isJS) @@ -346,7 +350,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi System.exit(0); } - // anything else! final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS); @@ -402,11 +405,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi try { if (!isJS && Platform.isWin()) - { + { UIManager.setLookAndFeel( headless ? "javax.swing.plaf.metal.MetalLookAndFeel" : UIManager.getSystemLookAndFeelClassName()); -// UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); + // UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } } catch (Exception ex) { @@ -460,7 +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 @@ -527,6 +544,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } parseArguments(aparser, true); + System.err.println(TERMINATOR_LINE); } /** @@ -859,7 +877,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi groovyscript = null; } } - checkOutputFile(aparser, af, format); + createOutputFiles(aparser, af, format); while (aparser.getSize() > 0) { System.out.println("Unknown arg: " + aparser.nextValue()); @@ -1040,19 +1058,34 @@ 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); + // System.out.println("format " + outputFormat); if (outputFormat.equalsIgnoreCase("png")) { @@ -1643,6 +1676,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public String getSelectedSequencesFrom(AlignFrameI alf) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return getSelectedSequencesFrom(alf, null); } @@ -1654,6 +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); } @@ -1666,7 +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); } @@ -1674,6 +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); } @@ -1686,7 +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 @@ -1699,6 +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); } @@ -1706,7 +1755,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String getSelectedSequencesAsAlignment(String format, String suffix) { - return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(), + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); } @@ -1714,6 +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); } @@ -1732,6 +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); } @@ -1751,6 +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); } @@ -1788,6 +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); } @@ -1801,43 +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 @@ -1849,6 +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); } @@ -1863,6 +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); } @@ -1871,56 +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 @@ -1955,7 +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); } @@ -1971,6 +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); } @@ -1978,7 +2095,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String getSelectedSequencesAsAlignment(String format, boolean suffix) { - return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(), + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); } @@ -1986,6 +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); } @@ -2067,5 +2188,82 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi // + " " + 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