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