import java.awt.Color;
import java.io.File;
import java.io.IOException;
-import java.lang.reflect.Field;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
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;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
-import jalview.ext.jmol.JalviewJmolBinding;
-import jalview.ext.jmol.JmolCommands;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
import jalview.gui.AppJmol;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.structure.StructureCommandI;
-import jalview.structure.StructureCommandsI;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
}
- // report errors
- Console.warn(
- "The following errors and warnings occurred whilst processing files:\n"
- + errorsToString());
+ // report errors - if any
+ String errorsRaised = errorsToString();
+ if (errorsRaised.trim().length() > 0)
+ {
+ Console.warn(
+ "The following errors and warnings occurred whilst processing files:\n"
+ + errorsRaised);
+ }
// gui errors reported in Jalview
if (argParser.getBoolean(Arg.QUIT))
}
}
+
// Show secondary structure annotations?
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);
+
+ 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
+ {
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ _af.setAnnotationsVisibility(showSSAnnotations, true,
+ false);
- // show temperature factor annotations?
- if (avm.getBoolean(Arg.NOTEMPFAC))
+ _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)
{
- // 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);
+ Console.warn(
+ "Unexpected exception adjusting annotation row visibility.",
+ x);
}
// wrap alignment? do this last for formatting reasons
/////
// DON'T TRY TO EXPORT IF VIEWER IS UNSUPPORTED
- if (viewerType!=ViewerType.JMOL) {
+ if (viewerType != ViewerType.JMOL)
+ {
addWarn("Cannot export image for structure viewer "
+ viewerType.name() + " yet");
continue;
/////
// Apply the temporary colourscheme to the linked alignment
// TODO: enhance for multiple linked alignments.
-
+
String imageColour = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.IMAGECOLOUR,
structureImageSubVals);
Color bgcolour = null;
if (bgcolourstring != null && bgcolourstring.length() > 0)
{
- try
- {
- //
- // FIXME: Why not use ColorUtils.parseColourString(bgcolourstring) - this is consistent and backwards compatible
- //
- if (bgcolourstring.charAt(0) == '#')
- {
- bgcolour = Color.decode(bgcolourstring);
- }
- else
- {
- Field field = Color.class.getField(bgcolourstring);
- bgcolour = (Color) field.get(null);
- }
- } catch (IllegalArgumentException | NoSuchFieldException
- | SecurityException | IllegalAccessException nfe)
+ bgcolour = ColorUtils.parseColourString(bgcolourstring);
+ if (bgcolour == null)
{
Console.warn(
"Background colour string '" + bgcolourstring
+ "' not recognised -- using default");
- //bgcolour = Color.black;
}
}
.getJalviewStructureDisplay();
File sessionToRestore = null;
-
- List<StructureCommandI> extraCommands=new ArrayList<>();
-
- if (extraCommands.size() > 0 || bgcolour!=null)
+
+ List<StructureCommandI> extraCommands = new ArrayList<>();
+
+ if (extraCommands.size() > 0 || bgcolour != null)
{
- try {
+ try
+ {
sessionToRestore = sview.saveSession();
} catch (Throwable t)
{
- Console.warn("Unable to save temporary session file before custom structure view export operation.");
+ Console.warn(
+ "Unable to save temporary session file before custom structure view export operation.");
}
}
-
+
////
- // Do temporary ops
+ // Do temporary ops
+
+ if (bgcolour != null)
+ {
+ sview.getBinding().setBackgroundColour(bgcolour);
+ }
+
+ sview.getBinding().executeCommands(extraCommands, false,
+ "Executing Custom Commands");
- sview.getBinding().setBackgroundColour(bgcolour);
-
- sview.getBinding().executeCommands(extraCommands, false, "Executing Custom Commands");
-
// and export the view as an image
boolean success = this.checksBeforeWritingToFile(avm,
subVals, false, structureImageFilename,
"structure image", isError);
-
+
if (!success)
{
continue;
}
- Console.debug(
- "Rendering image to " + structureImageFile);
- //
- // TODO - extend StructureViewer / Binding with makePDBImage so we can do this with every viewer
- //
-
- try {
+ Console.debug("Rendering image to " + structureImageFile);
+ //
+ // TODO - extend StructureViewer / Binding with makePDBImage so
+ // we can do this with every viewer
+ //
+
+ try
+ {
// We don't expect class cast exception
AppJmol jmol = (AppJmol) sview;
- jmol.makePDBImage(structureImageFile, imageType,
- renderer, userBis);
- Console.debug("Finished Rendering image to "
+ jmol.makePDBImage(structureImageFile, imageType, renderer,
+ userBis);
+ Console.info("Exported structure image to "
+ structureImageFile);
-
+
// RESTORE SESSION AFTER EXPORT IF NEED BE
if (sessionToRestore != null)
{
- sview.getBinding().openSession(sessionToRestore.getCanonicalPath());
+ Console.debug(
+ "Restoring session from " + sessionToRestore);
+
+ sview.getBinding().restoreSession(
+ sessionToRestore.getAbsolutePath());
+
}
- } catch (ImageOutputException ioexc)
+ } catch (ImageOutputException ioexec)
{
- addError("Unexpected error whilst exporting image to "
- + structureImageFile, ioexc);
+ addError(
+ "Unexpected error when restoring structure viewer session after custom view operations.");
isError = true;
continue;
- }
- catch (IOException ioexec)
+ } finally
{
- addError("Unexpected error when restoring structure viewer session after custom view operations.");
- isError = true;
- continue;
- }
- finally
- {
- this.colourAlignFrame(af, originalColourScheme);
+ try
+ {
+ this.colourAlignFrame(af, originalColourScheme);
+ } catch (Exception t)
+ {
+ addError(
+ "Unexpected error when restoring colourscheme to alignment after temporary change for export.",
+ t);
+ }
}
}
}
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