- <!-- JAL-4160,JAL-629 --> New command line argument framework allowing flexible batch processing, figure generation, and import of structures, pae matrices and other sequence associated data
- <!-- JAL-4121 --> Assume --headless when jalview is run with a command line argument that generates output
- <!-- JAL-4160,JAL-629 --> New command line argument framework allowing flexible batch processing, figure generation, and import of structures, pae matrices and other sequence associated data
- <!-- JAL-4121 --> Assume --headless when jalview is run with a command line argument that generates output