Some methods for the MultipleAlignment DS need to be implemented:

• Store and parse alignments as XML files.
• A MultipleAlignmentGUI, similar to the AlignmentGUI, that accepts multiple structures as inputs.
• CE Text Format output and other Writer features.
• String output of the structure and block transformations, like the method toRotMat() of AFPChain.
• Update the documentation in the Jmol Window (Help menu).
• Implement Structure transformation of flexible alignments (transform BlockSets independently).
• Implement ligand transformation for the Jmol visualization.

Two demos in the structure-gui project can be used to visualize MultipleAlignment examples:

• DemoMultipleAlignmentJmol
• DemoCEMC