scriptability
regression tests
Pass-by-value should be avoided for objects.
Chemical treatment as base class for fragmentation and cleavage ?
Update usermanual with Catalogue 1 in the xpm module.
Should be possible to paste in to m/z,z pair lists without drag and dropping.
Should be possible to remove selected items from a m/z,z pair list
It should be possible to define the formula of a monomer on the basis of distinct groups (subformulas) which bear a name so that they can be referred to by name when defining fragmentation patterns. This would give enormous flexibility to define real patterns amongst monomers that fragment, like for example saying loose the side chain, or proton loss in ribose, or oxidation in ring...
Verify that fragmentation computes the proper masses of fragments depending on the ionization.
Upon fragmentation, the ionization rule should be re-read from the XpertEdit window so that ionizations might change live. For example, switch from negative to positive mode in mass spec of oligonucleotides.
The definition of the fragmentation pattern might need some variable like "add the ionization rule".
Determine nucac base composition, based on the mass
Fragment oligomers should be distinct : those getting charged via formula and the other ones via explicit ionization.
sequence.cpp@681 -- Index cannot be less than 0.

cleave a selected sequence as for fragmentations


