artpoon/sealign

SeALign is an attempt to port Andrew Rambaut's Se-Al alignment editor to HTML5 Canvas and Javascript

sealign's Issues

Refactor JS functions into canvas state prototype

Dragging selection off-panel needs to activate scroll

Interface enhancements

• shift-click for scrolling alignment in window, as an alternative to using scrollbars
• depressing key modifiers should change cursor on canvas (like open hand on shift, and hand grip for shift-click)

Vertical scroll needs to be in reverse

Handle position should default to top. Since this corresponds to the max level, need to apply the slider value by deleting it from the maximum value - this will scroll through sequences in the alignment up and down as expected.

Selection is not attached to bases, does not move with alignment on scroll

Export alignment

• Apply alignment operations to original sequence strings
• export in different formats (NEXUS, FASTA)

Alignment operations

Every interaction with the alignment canvas should be stored as an operation. The possible operations are:

• open gap in a sequence
• close gap in sequence
• delete a range of bases in a sequence
• open a gap in a range of sequences (block or columns)
• delete gaps in a range of sequences (block or columns)
• reposition a sequence relative to the alignment (opening/closing leading and trailing gaps)

Selecting objects, groups

• mouse-over bases should draw a box around that base
• clicking on a single base should select that base for repositioning
• click and drag on a continuous range of bases in a sequence to select group
• click and drag on a range of bases across sequences (in a block) to select group
• command-click and drag to select entire sequence (like in Se-Al)
• option-click and drag to select entire columns of an alignment (like in Se-Al)

Translate sequences

• Flip between nucleotide and amino acid sequences
• shift alignment reading frame
• Flip to codon alignment like in Se-Al

Unrecognized characters, like gap ("-") take colour of base before it

Alignment canvas bases do not match mouse coordinate system

Highlighted base does not change when mouse moves past the boundary of one into another.
For some reason, the canvas seems to match up to the coordinate system when I have the JavaScript console inset to the window.