Hit alignment coloring not visible in image files

Hello, I am using your sample code for hit alignment coloring.

private void run() throws Exception {

        Molecule query = MolImporter.importMol(QUERY);

        Molecule target = MolImporter.importMol(TARGET);

        Molecule display = getDisplayMol(query, target, getDisplayOptions());



        DisplayUtil.showMolecule(query, 0, "Query");

        DisplayUtil.showMolecule(target, 1, "Target");

        DisplayUtil.showMolecule(display, 2, "Colored target");

}

In the opened JFrame there are visible nice coloring of red and green for the display molecule. 

The problem is that I cannot figure out how to transform display molecule into image (jpeg) file that would still contain red and green coloring.

If I use MolExporter methods exportToBinFormat or exportToObject, I get black and white image of the display molecule. Is there a way to get image with hit coloring?

            byte[] d4 = (byte[])MolExporter.exportToObject(display, "jpeg:w300,h300");

            FileOutputStream fos = new FileOutputStream(path);

            fos.write(d4);

            fos.close();

Hi,

 You are almost done, just add setcolors parameter in export:

byte[] d4 = (byte[])MolExporter.exportToObject(display, "jpeg:w300,h300,setcolors");

I tested this solution with JChem 6.2, but this should work with older releases as well.

Regards,
István Őri 

PS.: You can read more about image export parameters at https://www.chemaxon.com/marvin/help/formats/images-doc.html