package jalview.bin;
+import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.net.URISyntaxException;
import jalview.io.exceptions.ImageOutputException;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.StructureCommandI;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
import jalview.util.FileUtils;
import jalview.util.HttpUtils;
import jalview.util.ImageMaker;
}
- // 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))
commandArgsProvided = true;
for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
+ argParser.setStructureFilename(null);
String val = av.getValue();
SubVals subVals = av.getSubVals();
int argIndex = av.getArgIndex();
+ Arg.STRUCTURE.argString() + "=" + val);
continue;
}
+ String structureFilename = null;
File structureFile = null;
if (subVals.getContent() != null
&& subVals.getContent().length() != 0)
{
- structureFile = new File(subVals.getContent());
+ structureFilename = subVals.getContent();
Console.debug("Using structure file (from argument) '"
- + structureFile.getAbsolutePath() + "'");
+ + structureFilename + "'");
+ structureFile = new File(structureFilename);
}
- // TRY THIS
- /*
- * PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE,
- * selectedSequence, true, Desktop.instance);
- *
- * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new
- * SequenceI[] { selectedSequence });
- *
- */
/* THIS DOESN'T WORK */
else if (seq.getAllPDBEntries() != null
&& seq.getAllPDBEntries().size() > 0)
{
structureFile = new File(
seq.getAllPDBEntries().elementAt(0).getFile());
- Console.debug("Using structure file (from sequence) '"
- + structureFile.getAbsolutePath() + "'");
+ if (structureFile != null)
+ {
+ Console.debug("Using structure file (from sequence) '"
+ + structureFile.getAbsolutePath() + "'");
+ }
+ structureFilename = structureFile.getAbsolutePath();
}
- if (structureFile == null)
+ if (structureFilename == null || structureFile == null)
{
addWarn("Not provided structure file with '" + val + "'");
continue;
Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
+ argParser.setStructureFilename(structureFilename);
+
// open structure view
AlignmentPanel ap = af.alignPanel;
if (headless)
if (structureViewer == null)
{
- addError("Failed to import and open structure view for file '"
- + structureFile + "'.");
+ if (!StringUtils.equalsIgnoreCase(sViewerName, "none"))
+ {
+ addError("Failed to import and open structure view for file '"
+ + structureFile + "'.");
+ }
continue;
}
try
for (ArgValue structureImageArgValue : avm
.getArgValueList(Arg.STRUCTUREIMAGE))
{
- String structureImageFilename = structureImageArgValue
- .getValue();
+ String structureImageFilename = argParser.makeSubstitutions(
+ structureImageArgValue.getValue(), id, true);
if (structureViewer != null && structureImageFilename != null)
{
SubVals structureImageSubVals = null;
BitmapImageSizing userBis = ImageMaker
.parseScaleWidthHeightStrings(scale, width, height);
+ /////
+ // DON'T TRY TO EXPORT IF VIEWER IS UNSUPPORTED
+ 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);
.getColourScheme(af);
this.colourAlignFrame(af, imageColour);
- // TODO MAKE THIS VIEWER INDEPENDENT!!
- switch (StructureViewer.getViewerType())
+ /////
+ // custom image background colour
+
+ String bgcolourstring = avm.getValueFromSubValOrArg(
+ structureImageArgValue, Arg.BGCOLOUR,
+ structureImageSubVals);
+ Color bgcolour = null;
+ if (bgcolourstring != null && bgcolourstring.length() > 0)
{
- case JMOL:
- JalviewStructureDisplayI sview = structureViewer
- .getJalviewStructureDisplay();
- if (sview instanceof AppJmol)
+ bgcolour = ColorUtils.parseColourString(bgcolourstring);
+ if (bgcolour == null)
{
- AppJmol jmol = (AppJmol) sview;
- try
- {
- boolean success = this.checksBeforeWritingToFile(avm,
- subVals, false, structureImageFilename,
- "structure image", isError);
- if (!success)
- {
- continue;
- }
-
- Console.debug(
- "Rendering image to " + structureImageFile);
- jmol.makePDBImage(structureImageFile, imageType,
- renderer, userBis);
- Console.debug("Finished Rendering image to "
- + structureImageFile);
-
- } catch (ImageOutputException ioexc)
- {
- addError("Unexpected error whilst exporting image to "
- + structureImageFile, ioexc);
- isError = true;
- continue;
- }
+ Console.warn(
+ "Background colour string '" + bgcolourstring
+ + "' not recognised -- using default");
+ }
+ }
+
+ JalviewStructureDisplayI sview = structureViewer
+ .getJalviewStructureDisplay();
+ File sessionToRestore = null;
+
+ List<StructureCommandI> extraCommands = new ArrayList<>();
+
+ if (extraCommands.size() > 0 || bgcolour != null)
+ {
+ try
+ {
+ sessionToRestore = sview.saveSession();
+ } catch (Throwable t)
+ {
+ Console.warn(
+ "Unable to save temporary session file before custom structure view export operation.");
}
- break;
- default:
- addWarn("Cannot export image for structure viewer "
- + structureViewer.getViewerType() + " yet");
+ }
+
+ ////
+ // Do temporary ops
+
+ if (bgcolour != null)
+ {
+ 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
+ {
+ // We don't expect class cast exception
+ AppJmol jmol = (AppJmol) sview;
+ jmol.makePDBImage(structureImageFile, imageType, renderer,
+ userBis);
+ 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());
+
+ }
+ } catch (ImageOutputException ioexec)
+ {
+ addError(
+ "Unexpected error when restoring structure viewer session after custom view operations.");
+ isError = true;
continue;
+ } finally
+ {
+ try {
+ this.colourAlignFrame(af, originalColourScheme);
+ } catch (Exception t)
+ {
+ addError("Unexpected error when restoring colourscheme to alignment after temporary change for export.",t);
+ }
}
- this.colourAlignFrame(af, originalColourScheme);
}
}
}
+ argParser.setStructureFilename(null);
}
}
}
git://source.jalview.org / jalview.git / blobdiff