[Biojava-l] GUI (and other) changes

[Keith James]

I've made quite a lot of changes to the RulerRenderer so that it can
now have ticks pointing either up or down and numbering is now
displayed when in the vertical orientation.

SymbolSequenceRenderer has had a lot of changes too as it was cutting
off a residue in vertical mode. As getMaxCharBounds() is not behaving
quite as I expect, there are still some (documented) fudges. Ideally
I'd like to go to using GlyphVectors so that we can get full control
and do rendering of peptides by physico-chemical properties, bases
coloured by methylation state etc.

I've added a bunch of classes

src/org/biojava/bio/gui/sequence/PairwiseDiagonalRenderer.java
src/org/biojava/bio/gui/sequence/PairwiseRenderContext.java
src/org/biojava/bio/gui/sequence/PairwiseSequencePanel.java
src/org/biojava/bio/gui/sequence/PairwiseSequenceRenderer.java
src/org/biojava/bio/gui/sequence/PairwiseOverlayRenderer.java
src/org/biojava/bio/gui/sequence/CrosshairRenderer.java

which are designed for displaying relationships between two
sequences. The similarity is abstracted to "Location X on Sequence P
relates to Location Y on Sequence Q" in the same way Bioperl handles
it. The way this is depicted is up to the renderer, so could be a
dotplot style like or equally a side-by-side plot like ACT or Lion's
genomeSCOUT (tm). I've tried to reuse as much of the SequenceRenderer
code as I can, so PairwiseRenderContext extends SequenceRenderContext
with methods for the second sequence. In fact, much of the techie
details were plagiarised from existing work where I couldn't logically
reuse or extend.

I've got an interactive viewer for pairwise similarity data conforming
to the BlastLikeDataSetCollection.dtd in its final stages and these
classes provide much of its its core functionality. Next up should be
an n-way comparison viewer using the same framework. I should be able
to release the pairwise viewer (GPL) before Christmas.

I had to add what is basically a copy of Bioperl's
SimilarityPairFeature as Homology/HomologyFeature (which can have n
related sequences) was a bit heavyweight. One class is missing; the
builder in the ssbind package which makes them. It needs a bit more
work.

Enjoy,

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK