*/
package jalview.bin;
+import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignFrameI;
import jalview.api.AlignViewportI;
import jalview.api.JalviewApp;
import java.util.Hashtable;
import java.util.Map;
import java.util.Vector;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
protected JSFunctionExec jsFunctionExec;
+ private boolean noCalculation, noMenuBar, noStatus;
+
+ private boolean noAnnotation;
+
+ public boolean getStartCalculations()
+ {
+ return !noCalculation;
+ }
+
+ public boolean getAllowMenuBar()
+ {
+ return !noMenuBar;
+ }
+
+ public boolean getShowStatus()
+ {
+ return !noStatus;
+ }
+
+ public boolean getShowAnnotation()
+ {
+ return !noAnnotation;
+ }
+
public static AlignFrame getCurrentAlignFrame()
{
return getInstance().currentAlignFrame;
*/
public static void main(String[] args)
{
- // setLogging(); // BH - for event debugging in JavaScript
+ // Platform.startJavaLogging();
getInstance().doMain(args);
}
- /**
- * Allow an outside entity to initiate the second half of argument parsing
- * (only).
- *
- * @param args
- * @return null is good
- */
- @Override
- public Object parseArguments(String[] args)
- {
-
- try
- {
- ArgsParser aparser = new ArgsParser(args);
- return parseArguments(aparser, false);
- } catch (Throwable t)
- {
- return t;
- }
- }
-
- private static void logClass(String name)
- {
- // BH - for event debugging in JavaScript
- ConsoleHandler consoleHandler = new ConsoleHandler();
- consoleHandler.setLevel(Level.ALL);
- Logger logger = Logger.getLogger(name);
- logger.setLevel(Level.ALL);
- logger.addHandler(consoleHandler);
- }
@SuppressWarnings("unused")
- private static void setLogging()
- {
-
- /**
- * @j2sIgnore
- *
- */
- {
- System.out.println("not in js");
- }
-
- // BH - for event debugging in JavaScript (Java mode only)
- if (!Platform.isJS())
- /**
- * Java only
- *
- * @j2sIgnore
- */
- {
- Logger.getLogger("").setLevel(Level.ALL);
- logClass("java.awt.EventDispatchThread");
- logClass("java.awt.EventQueue");
- logClass("java.awt.Component");
- logClass("java.awt.focus.Component");
- logClass("java.awt.focus.DefaultKeyboardFocusManager");
- }
-
- }
-
/**
* @param args
*/
{
boolean isJS = Platform.isJS();
- if (!isJS)
+ if (isJS)
+ {
+ Platform.setAppClass(this);
+ }
+ else
{
System.setSecurityManager(null);
}
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");
parseArguments(aparser, true);
}
+ /**
+ * Allow an outside entity to initiate the second half of argument parsing
+ * (only).
+ *
+ * @param args
+ * @return null is good
+ */
+ @Override
+ public Object parseArguments(String[] args)
+ {
+
+ try
+ {
+ ArgsParser aparser = new ArgsParser(args);
+ return parseArguments(aparser, false);
+ } catch (Throwable t)
+ {
+ return t;
+ }
+ }
+
+ /**
+ *
+ * @param aparser
+ * @param isStartup
+ * @return
+ */
private Object parseArguments(ArgsParser aparser, boolean isStartup)
{
boolean isJS = Platform.isJS();
String fileFormat = (isJavaAppletTag
? aparser.getAppletValue("format", null)
: null);
-
FileFormatI format = null;
DataSourceType protocol = null;
}
}
+ String data;
+
if (file != null)
{
+
if (!headless)
{
desktop.setProgressBar(
// TODO ?
}
+ if (aparser.contains(ArgsParser.NOMENUBAR))
+ {
+ noMenuBar = true;
+ System.out.println("CMD [nomenu] executed successfully!");
+ }
+
+ if (aparser.contains(ArgsParser.NOSTATUS))
+ {
+ noStatus = 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 [nocalculation] executed successfully!");
+ }
+
AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file,
protocol, format);
if (af == null)
// TODO: file2 How to implement file2 for the applet spit screen?
- String data = aparser.getValue(ArgsParser.COLOUR, true);
+ data = aparser.getValue(ArgsParser.COLOUR, true);
if (data != null)
{
data.replaceAll("%20", " ");
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!");
}
}
- if (aparser.contains(ArgsParser.NOANNOTATION)
- || aparser.contains(ArgsParser.NOANNOTATION2))
+
+ boolean doUpdateAnnotation = false;
+
+ /**
+ * 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))
{
- 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))
af.getViewport().setSortByTree(false);
if (!af.getViewport().getSortByTree())
{
+ doUpdateAnnotation = true;
System.out
.println("CMD [-nosortbytree] executed successfully!");
}
}
+ if (doUpdateAnnotation)
+ { // BH 2019.07.24
+ af.setMenusForViewport();
+ af.alignPanel.updateLayout();
+ }
data = aparser.getValue(ArgsParser.TREE, true);
if (data != null)
{
+ "] 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());
}
}
}
// 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);
+ }
+
}
+
git://source.jalview.org / jalview.git / blobdiff