SeqTools package to-do lists
Blixem
- Issues
- Multiple row selections: using the up/down arrow keys to move the row selection doesn't always work if there are adjacent rows from the same match sequence.
- Printing: the pfetch window should have a print option.
- Enhancements
- It would be nice to be able to view the sequence data for an insertion (a vertical purple line in a match sequence) in Blixem, e.g. by hovering over it with the mouse.
- Bumping the gene model section should be improved so that different featuresets can be bumped separately. It would also be good to show information about the features in this section in the feedback area when you mouse-over them.
- When running Dotter on a large range it takes a long time to start up and there is no indication that anything is happening; it would be good to have a status bar of some description, and a cancel button. When running from Blixem, we should report if Dotter fails to start.
- Better Blixem<->Dotter interactions, ideally full two-way communications, or at least when calling Dotter from Blixem it would be good to start Dotter with the crosshair placed at the currently-selected coords in Blixem (if applicable).
Dotter
- Issues
- There is an intermittent bug where the dot-plot can appear blacked-out if the plot is very wide and you zoom in (say to about half of the default compression factor).
- Enhancements
- If you hit the boundary of one sequence when moving along a diagonal in Dotter and continue to press the movement keys (,.[]), then it stops moving on the one sequence but continues to move along the other, i.e. it goes off the diagonal. It would be nicer if it stopped moving altogether.
Belvu
- Issues
- Printing: the pfetch window should have a print option; so should the Annotations window.
- In the colour-by-conservation colour schemes, the foreground colour is tied to the background colour. This means that if the same background colour is specified more than once, the foreground colours are ambiguous.
- Colours dialog: the dialog for editing the residue colours used to have a section at the bottom showing residues grouped by colour. This has not been implemented in the new Belvu yet.
- For short alignments, the initial window size is too large.
- There is a bug with changing the font size on Mac OS X, where the highlighting does not line up correctly with the text if the font size is not a multiple of 4.
- Enhancements