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);
}
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
Console.info("Writing " + file);
-
+ try {
switch (type)
{
break;
case "biojs":
+ Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
try
{
BioJsHTMLOutput.refreshVersionInfo(
}
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);
+ af.createEPS(file, name);
break;
case "imagemap":
- af.createImageMap(file, name);
Console.debug("Creating ImageMap file: " + fileName);
+ af.createImageMap(file, name);
break;
default:
+ "' not known. Ignoring");
break;
}
+ } catch (Exception ioex) {
+ Console.warn("Unexpected error during export",ioex);
+ }
}
}
return true;