Re: JAVA programmer? (and Win-DomMap, and some GIMP)
If I'm correct you can use the map switch. Give it a color map file to select specific colors (I'm totally clueless about the file format though). Pass that output to the matte channel. You might have to create a temp file for that.
In the docs there's an example about using a matte channel to filter only certain areas of the image.
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