Multiple Structure Alignment Example doesn't work

[pwrose]

• MultipleAlignment result = algorithm.align(atomArrays);

--> should this line read: MultipleAlignment result = multiple.align(atomArrays);

• System.out.println(MultipleAlignmentWriter.toFASTA(result));

--> after fixing the previous statement, the toFASTA method throws an exception.

• MultipleAlignmentDisplay.display(result); --> display method does not exists

[lafita]

The classes that use Jmol were renamed to contain Jmol in its name, so this class is now called MultipleAlignmentJmolDisplay. I will update the example and also fix the type with algorithm/multiple.

I would recommend that you use the DemoMultipleMC classes inside the demo package in both the biojava-structure and the biojava-structure-gui modules, since they are up to day and should work without errors.

Thank you for reporting the errors in the example.

[lafita]

The toFASTA method was throwing a NullPointer because the StructureIdentifiers were not set in the example, so the headers of the FASTA alignment format were null. It is fixed now.