[Biojava-l] Multiple Sequence Alignment Viewer

[Kalle Näslund]

Nathan Whitehouse wrote:

>Dear all,
>
>  I've used biojava on and off for some time, and I've
>always found it useful.
>
>  I'm not sure how to proceed with my current problem,
>though I'm sure someone has done it already.
>  
>  I basically need a way to visualize a set of
>sequences which need to be aligned.
>
>  Can anybody point me in the right direction on this?
>  Is there an easy tool to visualize multiple
>alignments? 
> 
>
Hi!

Biojava can render alignments, its just that its not immediately obvious 
how =P

The "simple" approach is to take the Sequences you want to render, and 
insert
them into a SimpleAlignment object. The next step is to take a 
TranslatedSequencePanel
and connect your Alignment to it.

What you need to do next is to setup the renderers that will render your 
alignment.
Start with a MultiLineRenderer. To the MultiLineRenderer you connect one 
AlignmentRenderer
for each sequence in the alignment. Each AlignmentRenderer should have 
the label of the sequence
it should render set on it. And in the end you connect a 
SymbolSequenceRenderer to each
AlignmentRenderer. So, for an Alignment with three sequences,labeled  
seq1,seq2 and seq3,
the renderer tree would look like this.

                      AlignmentRenderer --- SymbolSequenceRenderer
                    / label=labelForSeq1
                   /
                  /
MultilineRenderer --- AlignmentRenderer --- SymbolSequenceRenderer
                  \   label=labelForSeq2
                   \
                    \
                      AlignmentRenderer --- SymbolSequenceRenderer
                      label=labelForSeq3

( notice that you can reuse the SymbolSequenceRenderer and dont need 
three separate
classes, you can just attach the same Instance to each of the 
AlignmentRenderers.
This is the prefered way if you want all sequences to be rendered the 
same way )

And this setup will give you a basic multiple alignment renderer.


BUT ! If you try this, it will fail, and it will fail because none of 
the Sequence
rendering components in biojava can render SymbolLists ( and in bj an 
Alignment is a
SymbolList ), they all render only Sequence objects. there are two 
solutions to this
that i can come upp with.

The first solution is to modify TranslatedSequencePanel to accept 
SymbolLists
( this is a very easy thing to do, it only requires a few lines of code 
to be
changed, i have done this, and if you find it hard, i cand send you a 
diff of my changes ).

The alternative, witch i havent tried, but i think should work, atleast 
in theory, is to just
create a Sequence, with your Alignment as the SymbolList. And then feed 
it to the
TranslatedSequencePanel.


mvh Kalle