import java.util.Locale;
import java.util.Map;
+import javax.swing.SwingUtilities;
+
import jalview.analysis.AlignmentUtils;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Jalview.ExitCode;
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
- long progress = -1;
+ final long progress = System.currentTimeMillis();
boolean first = true;
boolean progressBarSet = false;
first = false;
if (!headless && desktop != null)
{
- desktop.setProgressBar(
- MessageManager.getString(
- "status.processing_commandline_args"),
- progress = System.currentTimeMillis());
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ desktop.setProgressBar(
+ MessageManager.getString(
+ "status.processing_commandline_args"),
+ progress);
+
+ }
+ });
progressBarSet = true;
}
}
boolean showSSAnnotations = avm.getFromSubValArgOrPref(
Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
"STRUCT_FROM_PDB", true);
- af.setAnnotationsVisibility(showSSAnnotations, true, false);
// Show sequence annotations?
boolean showAnnotations = avm.getFromSubValArgOrPref(
Arg.SHOWANNOTATIONS, av.getSubVals(), null,
"SHOW_ANNOTATIONS", true);
- af.setAnnotationsVisibility(showAnnotations, false, true);
- // show temperature factor annotations?
- if (avm.getBoolean(Arg.NOTEMPFAC))
+ boolean hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
+ final AlignFrame _af = af;
+ // many of jalview's format/layout methods are only thread safe on the
+ // swingworker thread.
+ // all these methods should be on the alignViewController so it can
+ // coordinate such details
+ try
{
- // do this better (annotation types?)
- List<String> hideThese = new ArrayList<>();
- hideThese.add("Temperature Factor");
- hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(), hideThese, null,
- false, false);
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ _af.setAnnotationsVisibility(showSSAnnotations, true,
+ false);
+
+ _af.setAnnotationsVisibility(showAnnotations, false, true);
+
+ // show temperature factor annotations?
+ if (hideTFrows)
+ {
+ // do this better (annotation types?)
+ List<String> hideThese = new ArrayList<>();
+ hideThese.add("Temperature Factor");
+ hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ _af.getCurrentView().getAlignment(), hideThese,
+ null, false, false);
+ }
+ }
+ });
+ } catch (Exception x)
+ {
+ Console.warn(
+ "Unexpected exception adjusting annotation row visibility.",
+ x);
}
// wrap alignment? do this last for formatting reasons
{
Console.debug(
"Opening '" + openFile + "' in existing alignment frame");
+
DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
? DataSourceType.URL
: DataSourceType.FILE;
+
FileLoader fileLoader = new FileLoader(!headless);
fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
false);
// open the structure (from same PDB file or given PDBfile)
if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
+
AlignFrame af = afMap.get(id);
if (avm.containsArg(Arg.STRUCTURE))
{
commandArgsProvided = true;
- for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
+ for (
+
+ ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
argParser.setStructureFilename(null);
String val = av.getValue();
AppJmol jmol = (AppJmol) sview;
jmol.makePDBImage(structureImageFile, imageType, renderer,
userBis);
- Console.debug("Finished Rendering image to "
+ Console.info("Exported structure image to "
+ structureImageFile);
// RESTORE SESSION AFTER EXPORT IF NEED BE
if (sessionToRestore != null)
{
- Console.debug("Restoring session from "
- + sessionToRestore);
-
- sview.getBinding().restoreSession(sessionToRestore.getAbsolutePath());
+ Console.debug(
+ "Restoring session from " + sessionToRestore);
+
+ sview.getBinding().restoreSession(
+ sessionToRestore.getAbsolutePath());
}
} catch (ImageOutputException ioexec)
continue;
} finally
{
- try {
+ try
+ {
this.colourAlignFrame(af, originalColourScheme);
} catch (Exception t)
{
- addError("Unexpected error when restoring colourscheme to alignment after temporary change for export.",t);
+ addError(
+ "Unexpected error when restoring colourscheme to alignment after temporary change for export.",
+ t);
}
}
}
if (wrap)
{
+
AlignFrame af = afMap.get(id);
if (af != null)
{
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
{
- AlignFrame af = afMap.get(id);
- for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
- .findAnnotation(PDBChain.class.getName().toString()))
- {
- AnnotationColourGradient acg = new AnnotationColourGradient(aa,
- af.alignPanel.av.getGlobalColourScheme(), 0);
- acg.setSeqAssociated(true);
- af.changeColour(acg);
- Console.info("Changed colour " + acg.toString());
- }
+ AlignFrame af = afMap.get(id);
+ for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+ .findAnnotation(PDBChain.class.getName().toString()))
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+ af.alignPanel.av.getGlobalColourScheme(), 0);
+ acg.setSeqAssociated(true);
+ af.changeColour(acg);
+ Console.info("Changed colour " + acg.toString());
+ }
}
*/
ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
- if (af == null)
+ if (avm != null && !avm.containsArg(Arg.GROOVY))
{
- addWarn("Did not have an alignment window for id=" + id);
+ // nothing to do
return;
}
+ if (af == null)
+ {
+ addWarn("Groovy script does not have an alignment window. Proceeding with caution!");
+ }
+
if (avm.containsArg(Arg.GROOVY))
{
- String groovyscript = avm.getValue(Arg.GROOVY);
- if (groovyscript != null)
+ for (ArgValue groovyAv : avm.getArgValueList(Arg.GROOVY))
{
- // Execute the groovy script after we've done all the rendering stuff
- // and before any images or figures are generated.
- Console.info("Executing script " + groovyscript);
- Jalview.getInstance().executeGroovyScript(groovyscript, af);
+ String groovyscript = groovyAv.getValue();
+ if (groovyscript != null)
+ {
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ Console.info("Executing script " + groovyscript);
+ Jalview.getInstance().executeGroovyScript(groovyscript, af);
+ }
}
}
}
ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
+ if (avm != null && !avm.containsArg(Arg.IMAGE))
+ {
+ // nothing to do
+ return true;
+ }
+
if (af == null)
{
- addWarn("Did not have an alignment window for id=" + id);
+ addWarn("Do not have an alignment window to create image from (id="
+ + id + "). Not proceeding.");
return false;
}
ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
+ if (avm != null && !avm.containsArg(Arg.OUTPUT))
+ {
+ // nothing to do
+ return true;
+ }
+
if (af == null)
{
- addWarn("Did not have an alignment window for id=" + id);
+ addWarn("Do not have an alignment window (id=" + id
+ + "). Not proceeding.");
return false;
}
git://source.jalview.org / jalview.git / blobdiff