package jalview.bin;
import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignFrameI;
import jalview.api.AlignViewportI;
import jalview.api.JalviewApp;
import jalview.api.StructureSelectionManagerProvider;
* @param args
* open <em>filename</em>
*/
+ @SuppressWarnings("unused")
public static void main(String[] args)
{
- // Platform.startJavaLogging();
+ if (false)
+ {
+ Platform.startJavaLogging();
+ }
getInstance().doMain(args);
}
* 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)
"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)
{
}
}
}
+
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;
}
/**
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)
{
* .AlignFrame, java.lang.String)
*/
@Override
- public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
+ public String getSelectedSequencesFrom(AlignFrame alf, String sep)
{
if (alf == null)
{
}
@Override
- public void highlightIn(AlignFrameI alf, String sequenceId,
+ public void highlightIn(AlignFrame alf, String sequenceId,
String position, String alignedPosition)
{
if (alf == null)
}
@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)
}
@Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String sep)
{
if (alf == null)
}
@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)
{
}
@Override
- public String orderAlignmentBy(AlignFrameI alf, String order,
+ public String orderAlignmentBy(AlignFrame alf, String order,
String undoName, String sep)
{
if (alf == null)
}
@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)
{
}
@Override
- public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+ public boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay)
{
if (alf == null)
}
@Override
- public String getFeaturesFrom(AlignFrameI alf, String format)
+ public String getFeaturesFrom(AlignFrame alf, String format)
{
if (alf == null)
{
}
@Override
- public String getAnnotationFrom(AlignFrameI alf)
+ public String getAnnotationFrom(AlignFrame alf)
{
if (alf == null)
{
return appLoader.getAnnotationFrom(alf);
}
- @Override
- public AlignFrameI newView()
- {
- return newViewFrom(null, null);
- }
-
- @Override
- public AlignFrameI newView(String name)
- {
- return newViewFrom(null, name);
- }
-
- @Override
- public AlignFrameI newViewFrom(AlignFrameI alf)
- {
- return newViewFrom(alf, null);
- }
+ // @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 AlignFrameI newViewFrom(AlignFrameI alf, String name)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.newViewFrom(alf, name);
- }
+ // @Override
+ // public AlignFrame newViewFrom(AlignFrame alf, String name)
+ // {
+ // if (alf == null)
+ // {
+ // alf = getCurrentAlignFrame();
+ // }
+ // 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)
}
@Override
- public void scrollViewToIn(AlignFrameI alf, String topRow,
+ public void scrollViewToIn(AlignFrame alf, String topRow,
String leftHandColumn)
{
if (alf == null)
}
@Override
- public void scrollViewToRowIn(AlignFrameI alf, String topRow)
+ public void scrollViewToRowIn(AlignFrame alf, String topRow)
{
if (alf == null)
{
}
@Override
- public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
+ public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
{
if (alf == null)
{
}
@Override
- public String getFeatureGroupsOn(AlignFrameI alf)
+ public String getFeatureGroupsOn(AlignFrame alf)
{
if (alf == null)
{
}
@Override
- public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
{
if (alf == null)
{
}
@Override
- public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+ public void setFeatureGroupStateOn(AlignFrame alf, String groups,
boolean state)
{
if (alf == null)
}
@Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, boolean suffix)
{
if (alf == null)
}
@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
git://source.jalview.org / jalview.git / blobdiff