import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.FileUtils;
theseArgsWereParsed &= processLinked(id);
processGroovyScript(id);
boolean processLinkedOkay = theseArgsWereParsed;
+
+ // wait around until alignFrame isn't busy
+ AlignFrame af = afMap.get(id);
+ while (af != null && af.getViewport().isCalcInProgress())
+ {
+ try
+ {
+ Thread.sleep(25);
+ } catch (Exception q)
+ {
+ }
+ ;
+ }
+
theseArgsWereParsed &= processImages(id);
if (processLinkedOkay)
theseArgsWereParsed &= processOutput(id);
// close ap
if (avm.getBoolean(Arg.CLOSE))
{
- AlignFrame af = afMap.get(id);
+ af = afMap.get(id);
if (af != null)
{
af.closeMenuItem_actionPerformed(true);
Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
if ("" != colour)
{
- af.changeColour_actionPerformed(colour);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(),
+ colour);
+
+ if (cs == null && !"None".equals(colour))
+ {
+ Console.warn(
+ "Couldn't parse '" + colour + "' as a colourscheme.");
+ }
+ else
+ {
+ af.changeColour(cs);
+ }
Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
}
structureFilepath, tft, paeFilepath, false,
ssFromStructure, false, viewerType);
- if (headless)
+ if (sv == null)
{
- sv.setAsync(false);
+ Console.error("Failed to import and open structure view.");
+ continue;
}
-
+ try
+ {
+ long tries = 1000;
+ while (sv.isBusy() && tries > 0)
+ {
+ Thread.sleep(25);
+ if (sv.isBusy())
+ {
+ tries--;
+ Console.debug(
+ "Waiting for viewer for " + structureFilepath);
+ }
+ }
+ if (tries == 0 && sv.isBusy())
+ {
+ Console.warn(
+ "Gave up waiting for structure viewer to load. Something may have gone wrong.");
+ }
+ } catch (Exception x)
+ {
+ Console.warn("Exception whilst waiting for structure viewer "
+ + structureFilepath, x);
+ }
+ Console.debug(
+ "Successfully opened viewer for " + structureFilepath);
String structureImageFilename = ArgParser.getValueFromSubValOrArg(
avm, av, Arg.STRUCTUREIMAGE, subVals);
if (sv != null && structureImageFilename != null)
}
BitmapImageSizing userBis = ImageMaker
.parseScaleWidthHeightStrings(scale, width, height);
+ // TODO MAKE THIS VIEWER INDEPENDENT!!
switch (StructureViewer.getViewerType())
{
case JMOL:
try
{
- Thread.sleep(1000);
+ Thread.sleep(1000); // WHY ???
} catch (InterruptedException e)
{
// TODO Auto-generated catch block
if (sview instanceof AppJmol)
{
AppJmol jmol = (AppJmol) sview;
- jmol.makePDBImage(structureImageFile, imageType, renderer,
- userBis);
+ try
+ {
+ Console.debug("Rendering image to " + structureImageFile);
+ jmol.makePDBImage(structureImageFile, imageType, renderer,
+ userBis);
+ Console.debug("Finished Rendering image to "
+ + structureImageFile);
+
+ } catch (ImageOutputException ioexc)
+ {
+ Console.warn("Unexpected error whilst exporting image to "
+ + structureImageFile, ioexc);
+ }
+
}
break;
default:
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
Console.info("Writing " + file);
-
- switch (type)
+ try
{
-
- case "svg":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createSVG(file, renderer);
- break;
-
- case "png":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createPNG(file, null, userBis);
- break;
-
- case "html":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(fileName, renderer);
- break;
-
- case "biojs":
- try
+ switch (type)
{
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
- {
- e.printStackTrace();
+
+ case "svg":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createSVG(file, renderer);
+ break;
+
+ case "png":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createPNG(file, null, userBis);
+ break;
+
+ case "html":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fileName, renderer);
+ break;
+
+ case "biojs":
+ Console.debug(
+ "Outputting BioJS MSA Viwer HTML file: " + fileName);
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(fileName);
+ break;
+
+ case "eps":
+ Console.debug("Outputting EPS file: " + fileName);
+ af.createEPS(file, renderer);
+ break;
+
+ case "imagemap":
+ Console.debug("Outputting ImageMap file: " + fileName);
+ af.createImageMap(file, name);
+ break;
+
+ default:
+ Console.warn(Arg.IMAGE.argString() + " type '" + type
+ + "' not known. Ignoring");
+ break;
}
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(fileName);
- Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
- break;
-
- case "eps":
- af.createEPS(file, name);
- Console.debug("Creating EPS file: " + fileName);
- break;
-
- case "imagemap":
- af.createImageMap(file, name);
- Console.debug("Creating ImageMap file: " + fileName);
- break;
-
- default:
- Console.warn(Arg.IMAGE.argString() + " type '" + type
- + "' not known. Ignoring");
- break;
+ } catch (Exception ioex)
+ {
+ Console.warn("Unexpected error during export", ioex);
}
}
}
git://source.jalview.org / jalview.git / blobdiff