X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3d80589a2aac0323ee57911de9151a16b3c759de;hb=cb51e62fe2166b236ef488e0a8f35081fcd71388;hp=fae2b7597ec10ca45093e7a9347c8cfe726dd022;hpb=5014beeca83ef54a5740388c443d85f532a34db6;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index fae2b75..3d80589 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -305,6 +305,15 @@ 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; + } + if (isJS) { isJavaAppletTag = aparser.isApplet(); @@ -336,13 +345,7 @@ 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! @@ -398,7 +401,13 @@ 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"); @@ -849,11 +858,11 @@ 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()); - } + } + checkOutputFile(aparser, af, format); + while (aparser.getSize() > 0) + { + System.out.println("Unknown arg: " + aparser.nextValue()); } } } @@ -1043,6 +1052,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi // 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 +1643,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public String getSelectedSequencesFrom(AlignFrameI alf) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return getSelectedSequencesFrom(alf, null); } @@ -1643,6 +1658,10 @@ 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 +1674,7 @@ 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 +1682,10 @@ 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 +1698,7 @@ 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 +1711,10 @@ 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 +1722,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String getSelectedSequencesAsAlignment(String format, String suffix) { - return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(), + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); } @@ -1703,6 +1730,10 @@ 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 +1752,10 @@ 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 +1775,10 @@ 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 +1816,10 @@ 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 +1833,55 @@ 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 +1893,10 @@ 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 +1911,10 @@ 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 +1923,80 @@ 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 +2031,11 @@ 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 +2051,10 @@ 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 +2062,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String getSelectedSequencesAsAlignment(String format, boolean suffix) { - return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(), + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); } @@ -1975,6 +2070,10 @@ 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); }