Sequence editor
From BioclipseWiki
The proposal is to have a new editor, similar to the BioJava SequenceView but with a lot more functionality. Probably implemented as a Multi Page Editor (MPE).
Features:
- Different types of sequences (DNA, RNA, Protein, Custom)
- Cut and paste
- Individual and multi selection of residues
- Alignment handling
- Coloring of residues
- Graphs like conservation (if alignment)
- Feature highlighting
Please add more features and ideas here.
masak writes freely on the above features
- Different types of sequences (DNA, RNA, Protein, Custom)
- We already have pretty good Protein sequence support -- the examples I've been using when testing the have been protein FASTA files. DNA and RNA are not readable yet, but it's easy to add them. I'd be happy to accept real-world data files with DNA or RNA in them.
- Cut and paste
- (And copy, I presume.) Both cut and paste are edit operations, something which we don't support yet. Partly because it's not clear how.
- Individual and multiple selection of residues
- Right now one can make a rectangular box. This box can then be dragged around. I've had loose thoughts on expanding this to permitting multiple boxes (say, by holding down Cmd/Ctrl while dragging a new box). Right now I'm also concerned that the box as rendered in wrap mode is a bit too confusing.
- Alignment handling
- We support calling out to a third-party alignment algorithm (using web services) to align the sequence.
- Coloring of residues
- Check. Right now it's hard-coded; we should probably think of adding more color schemes for various things. Ideas welcome.
- Graphs like conservation (if alignment)
- I have no idea what this means.
- Feature highlighting
- Yes, that would be cool. Also dependent on examples.
