SeqTools package to-do lists

Blixem

• Issues
  • Variations: the variations track is experimental code and will need to be improved, in particular in its handling of overlapping features.
  • Feature-series: this functionality was disabled when Blixem and Dotter were re-written at version 4. We should consider whether this is still a useful feature and, if so, whether to use the original SFS file format or to switch to GFF. The SFS file format is documented here.
  • 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.
  • DNA search: this currently just jumps to the start of the DNA section that was found; we should also highlight the found DNA in the reference 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 yellow line in a match sequence) in Blixem, e.g. by hovering over it with the mouse.
  • When you hover over an exon in the exon view in Blixem (when bumped), it would be nice if info about the exon were shown in the toolbar feedback area.
  • 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.
  • When calling Dotter from Blixem, start Dotter with the crosshair placed at the currently-selected coords in Blixem (if applicable).
  • Cosmetic: the %ID labels on the big picture grid should be right-aligned.
  • Button tooltips: the zoom buttons in the big-picture should have tooltips.

Dotter

• Issues
  • There is a 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.
  
  
• Enhancements
  • Undo function (RT:214316).
  • Search-for-residues function (RT:212364).