Andreas Prlic comments

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                                            Andreas Prlic

"Karyotype" views

I took the old Dalliance 0.7 code base and added a couple of new features. Now it can show an ideogram of one or all chromosomes. For now it is...

Add support for parsing Sanger sequencing files (ABI, SCF)

Is there a faster usage method for the "countCompounds()" method?

I agree it would be nice to have some utility methods for that, something along the lines of what @tolgap is suggesting. Should fit well to the already existing set...

New StructuralAlignment Algorithms

I am not sure about the licensing situation for the other algorithms, before any of these would be implemented we would need to verify that they are under LGPL, or...

Generalize StructureAlignment Visualization

Open up Symmetry visualization API (quaternary and internal)

I agree to everything you say. I need both 1) and 2) plus in general we should try to generalize alignment viewers so we can use others such as PV...

Add ability to create a Profile from a multiple sequence alignment file

We need more people providing pull requests for the sequence aspects of BioJava.

Extend Genbank parser to provide references to publications

A contribution like that would be great..

NullPointerException when StructureIdentifiers are not set in MultipleAlignment

My vote is for solution 3 as the default.

Better support for symmetry in the Structure model

What about different implementations of Structure (and the other interfaces?). I never intended that there would be only one StructureImpl, ChainImpl, etc. and there could be alternative implementations that provide...