ssm.addStructureMapping(sm2);
StructureMappingcommandSet[] commands = ChimeraCommands
- .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+ .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel, false);
assertEquals(1, commands.length);
assertEquals(1, commands[0].commands.length);
String theCommand = commands[0].commands[0];