*/
package jalview.bin;
-import jalview.api.AlignFrameI;
+import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.JalviewApp;
import jalview.api.StructureSelectionManagerProvider;
public class Jalview implements ApplicationSingletonI, JalviewJSApi
{
+ // for testing those nasty messages you cannot ever find.
+ // static
+ // {
+ // System.setOut(new PrintStream(new ByteArrayOutputStream())
+ // {
+ // @Override
+ // public void println(Object o)
+ // {
+ // if (o != null)
+ // {
+ // System.err.println(o);
+ // }
+ // }
+ //
+ // });
+ // }
public static Jalview getInstance()
{
return (Jalview) ApplicationSingletonProvider
private boolean noCalculation, noMenuBar, noStatus;
+ private boolean noAnnotation;
+
public boolean getStartCalculations()
{
return !noCalculation;
return !noStatus;
}
+ public boolean getShowAnnotation()
+ {
+ return !noAnnotation;
+ }
public static AlignFrame getCurrentAlignFrame()
{
* @param args
* open <em>filename</em>
*/
+ @SuppressWarnings("unused")
public static void main(String[] args)
{
- // Platform.startJavaLogging();
+ if (false)
+ {
+ Platform.startJavaLogging();
+ }
getInstance().doMain(args);
}
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();
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");
* configure 'full' SO model if preferences say to,
* else use the default (SO Lite)
*/
- if (Cache.getDefault(Preferences.USE_FULL_SO, false))
+ // BH NOTE 2020.06.01 Jalview-JS/develop has this true for Java, false for
+ // JavaScript
+ if (Cache.getDefault(Preferences.USE_FULL_SO, !isJS))
{
SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
try
{
ArgsParser aparser = new ArgsParser(args);
- return parseArguments(aparser, false);
+ parseArguments(aparser, false);
+ return null;
} catch (Throwable t)
{
return t;
*
* @param aparser
* @param isStartup
- * @return
+ * @return null, indicating no error
*/
- private Object parseArguments(ArgsParser aparser, boolean isStartup)
+ private void parseArguments(ArgsParser aparser, boolean isStartup)
{
boolean isJS = Platform.isJS();
System.out.println("No files to open!");
System.exit(1);
}
- boolean haveImport = checkStartVamas(aparser);
// Finally, deal with the remaining input data.
long progress = -1;
if (file == null && isJavaAppletTag)
// 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;
"CMD [-open2 " + file2 + "] executed successfully!");
}
}
-
setCurrentAlignFrame(af);
- // TODO: file2 How to implement file2 for the applet spit screen?
-
data = aparser.getValue(ArgsParser.COLOUR, true);
if (data != null)
{
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());
}
}
}
+
AlignFrame startUpAlframe = null;
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
- if (!isJS && !headless && file == null && !haveImport
+ if (!isJS && !headless && file == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
/**
* Java only
desktop.setInBatchMode(false);
}
- return null;
}
- private boolean checkStartVamas(ArgsParser aparser)
- {
- String vamsasImport = aparser.getValue(ArgsParser.VDOC);
- String vamsasSession = aparser.getValue(ArgsParser.VSESS);
- if (vamsasImport == null && vamsasSession == null)
- {
- return false;
- }
- if (desktop == null || headless)
- {
- System.out.println(
- "Headless vamsas sessions not yet supported. Sorry.");
- System.exit(1);
- }
- boolean haveImport = (vamsasImport != null);
- if (haveImport)
- {
- // if we have a file, start a new session and import it.
- boolean inSession = false;
- try
- {
- DataSourceType viprotocol = AppletFormatAdapter
- .checkProtocol(vamsasImport);
- if (viprotocol == DataSourceType.FILE)
- {
- inSession = desktop.vamsasImport(new File(vamsasImport));
- }
- else if (viprotocol == DataSourceType.URL)
- {
- inSession = desktop.vamsasImport(new URL(vamsasImport));
- }
-
- } catch (Exception e)
- {
- System.err.println("Exeption when importing " + vamsasImport
- + " as a vamsas document.");
- e.printStackTrace();
- }
- if (!inSession)
- {
- System.err.println("Failed to import " + vamsasImport
- + " as a vamsas document.");
- }
- else
- {
- System.out.println("Imported Successfully into new session "
- + desktop.getVamsasApplication().getCurrentSession());
- }
- }
- if (vamsasSession != null)
- {
- if (vamsasImport != null)
- {
- // close the newly imported session and import the Jalview specific
- // remnants into the new session later on.
- desktop.vamsasStop_actionPerformed(null);
- }
- // now join the new session
- try
- {
- if (desktop.joinVamsasSession(vamsasSession))
- {
- System.out.println(
- "Successfully joined vamsas session " + vamsasSession);
- }
- else
- {
- System.err.println("WARNING: Failed to join vamsas session "
- + vamsasSession);
- }
- } catch (Exception e)
- {
- System.err.println(
- "ERROR: Failed to join vamsas session " + vamsasSession);
- e.printStackTrace();
- }
- if (vamsasImport != null)
- {
- // the Jalview specific remnants can now be imported into the new
- // session at the user's leisure.
- Cache.log.info(
- "Skipping Push for import of data into existing vamsas session.");
- // TODO:
- // enable
- // this
- // when
- // debugged
- // desktop.getVamsasApplication().push_update();
- }
- }
- 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));
imageName = imageFile.getName();
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
htmlSVG.exportHTML(file);
-
System.out.println("Creating HTML image: " + file);
continue;
}
* .AlignFrame)
*/
@Override
- public String getSelectedSequencesFrom(AlignFrameI alf)
+ public String getSelectedSequencesFrom(AlignFrame alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return getSelectedSequencesFrom(alf, null);
}
* .AlignFrame, java.lang.String)
*/
@Override
- public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
+ public String getSelectedSequencesFrom(AlignFrame 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);
}
@Override
- public void highlightIn(AlignFrameI alf, String sequenceId,
+ public void highlightIn(AlignFrame 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)
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns)
{
selectIn(alf, sequenceIds, columns, null);
}
@Override
- public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
+ public void selectIn(AlignFrame 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);
}
@Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
}
}
@Override
- public String getAlignmentOrderFrom(AlignFrameI alf)
+ public String getAlignmentOrderFrom(AlignFrame alf)
{
return getAlignmentFrom(alf, null);
}
@Override
- public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getAlignmentOrderFrom(alf, sep);
}
}
@Override
- public String orderAlignmentBy(AlignFrameI alf, String order,
+ public String orderAlignmentBy(AlignFrame alf, String order,
String undoName, String sep)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.orderAlignmentBy(alf, order, undoName, sep);
}
}
@Override
- public String getAlignmentFrom(AlignFrameI alf, String format)
+ public String getAlignmentFrom(AlignFrame alf, String format)
{
return getAlignmentFrom(alf, format, null);
}
}
@Override
- public String getAlignmentFrom(AlignFrameI alf, String format,
+ public String getAlignmentFrom(AlignFrame alf, String format,
String suffix)
{
return appLoader.getAlignmentFrom(alf, format, suffix);
}
@Override
- public void loadAnnotationFrom(AlignFrameI alf, String annotation)
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.loadAnnotationFrom(alf, annotation);
}
}
@Override
- public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+ public boolean loadFeaturesFrom(AlignFrame 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)
+ public String getFeaturesFrom(AlignFrame 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)
+ public String getAnnotationFrom(AlignFrame alf)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getAnnotationFrom(alf);
}
- @Override
- public AlignFrameI newView()
- {
- return newViewFrom(getCurrentAlignFrame(), null);
- }
-
- @Override
- public AlignFrameI newView(String name)
- {
- return newViewFrom(getCurrentAlignFrame(), name);
- }
+ // @Override
+ // public AlignFrame newView()
+ // {
+ // return newViewFrom(null, null);
+ // }
+ //
+ // @Override
+ // public AlignFrame newView(String name)
+ // {
+ // return newViewFrom(null, name);
+ // }
+ //
+ // @Override
+ // public AlignFrame newViewFrom(AlignFrame alf)
+ // {
+ // return newViewFrom(alf, null);
+ // }
+
+ // @Override
+ // public AlignFrame newViewFrom(AlignFrame alf, String name)
+ // {
+ // if (alf == null)
+ // {
+ // alf = getCurrentAlignFrame();
+ // }
+ // return appLoader.newViewFrom(alf, name);
+ // }
@Override
- public AlignFrameI newViewFrom(AlignFrameI alf)
- {
- return newViewFrom(alf, null);
- }
-
- @Override
- public AlignFrameI newViewFrom(AlignFrameI alf, String name)
- {
- return appLoader.newViewFrom(alf, name);
- }
-
- @Override
- public AlignFrameI loadAlignment(String text, String title)
+ public AlignFrame loadAlignment(String text, String title)
{
return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT, title);
}
@Override
- public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
+ if (alFrame == null)
+ {
+ alFrame = getCurrentAlignFrame();
+ }
return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
pdbFile);
}
@Override
- public void scrollViewToIn(AlignFrameI alf, String topRow,
+ public void scrollViewToIn(AlignFrame alf, String topRow,
String leftHandColumn)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
}
@Override
- public void scrollViewToRowIn(AlignFrameI alf, String topRow)
+ public void scrollViewToRowIn(AlignFrame alf, String topRow)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
appLoader.scrollViewToRowIn(alf, topRow);
}
@Override
- public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
+ public void scrollViewToColumnIn(AlignFrame 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)
+ public String getFeatureGroupsOn(AlignFrame 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)
+ public String getFeatureGroupsOfStateOn(AlignFrame 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(AlignFrame 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);
}
@Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, boolean suffix)
{
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
"" + suffix);
}
}
@Override
- public void setMouseoverListener(AlignFrameI af, String listener)
+ public void setMouseoverListener(AlignFrame af, String listener)
{
// TODO Auto-generated method stub
}
@Override
- public void setSelectionListener(AlignFrameI af, String listener)
+ public void setSelectionListener(AlignFrame af, String listener)
{
// TODO Auto-generated method stub
}
@Override
- public void removeJavascriptListener(AlignFrameI af, String listener)
+ public void removeJavascriptListener(AlignFrame af, String listener)
{
// TODO Auto-generated method stub
}
+ @Override
+ public void showOverview()
+ {
+ currentAlignFrame.overviewMenuItem_actionPerformed(null);
+ }
+
+ public void notifyWorker(AlignCalcWorkerI worker, String status)
+ {
+ // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+ // + " " + status);
+ }
}
git://source.jalview.org / jalview.git / blobdiff