Use the ij.IJ.runMacro(String)
method.
Here is an example:
import ij.IJ;
import ij.plugin.PlugIn;
public class Run_Macro implements PlugIn {
@Override
public void run(final String arg) {
final String macro =
"run(\"Clown (14K)\");\n" +
"run(\"Make Binary\");\n";
IJ.runMacro(macro);
}
}
A word of warning about obfuscation, though: Java is notoriously easy to decompile.