Package list

algo: used algorithms
bone: patched backbone version with jBone and own view type (pluginator) with children support
g: global configuration object
menu: render the menu
model: models in the project
views: all different views to represent the models
- header: views for the header area
- labels: views for the labels area
utils: some common helper libs

msa.coffee

bundles all dependencies & initiliazies the views
pluginator.extend = backbone view with children support
the initialize method is called by Backbone.view (when the user calls the constructor)
g is the global namespace (for the current msa) and also the mediator
the g is initiliazed by parameters given in the constructor
render() -> starts the recursive rendering process

consensuscalc: loops over seqs, residues to build consensus count (for max occupant in column) .. this is a good, simple, concrete example for illustrating code framework usage and patterns
identitycalc: uses consensus, identity = matchedChars / totalChars (excluding gaps)

view: custom patch to run with jBone instead of jQuery
extend: inheritance manager
pluginator: support for children views in a backbone view (extends the Backbone view)

colorator: initializing default color scheme settings "taylor")
columns: all column based data structures (array for tracking hidden columns, conservation precomputed, consensus precomputed (with weights), scaling) ..
config: some settings (e.g. the CORS proxy)
consensus (calls algo/ConsensusCalc)
visOrdering (ordering of different views)
visibility (set of flags for show/hide options)
zoomer (sizes and positions of Dom elements and regions, scroll position and speeds, padding, )

defaultmenu (uses a number of components from "views" ; extremely simple menu construction)
menubuilder ("builds" the menu ( "factory" design pattern use). Some behaviors set here .. styles and timeouts. Also supports submenus)

feature (display item with text, shape, size, color, border. Defaults set)
featurecol (feature collection which can be probed to find all features with a set column (x) offset. I wonder if this covers amino acid code rendering (via DOM))
sequence (data object to hold a sequence .. name/id/seq. Contains an embedded featurecol.)
seqcollection (collection of sequence objects accessed through next and prev. getMaxLength() scans all seq lengths)

alignmentbody (listens to events from zoomer and columns, can be rendered, and vertically resized. queries zoomer.)
canvasfontcache (caches rendered letters (for the amino acid code drawing))
canvasseqblock (calculates appropriate viewport for the main view based on scroll bar and positions letter canvas elements. Handles drag/drop events for residue selection. Also shows any current selections (within row I think). Some "throttling" timing is done for legacy browsers, presumably to prevent expensive repetitive redraw actions)
overviewbox (holds color scheme, drawn rectangle with fillRect (so apparently does not leverage canvasseqblock ... but maybe appropriate since no scroll bar here. But also has selection drag/drop mouse code, and selection rendering code)
stage (links and renders the main subviews: consensus, overview, header, body)

the bar above the alignment block

header/conservationview (uses svg to plot bar chart, captures mouse events over this view)
header/headerblock (displays the scrollbar needed for the main canvas, handles consensus, identity, conservation, markers)
header/markerview (marker is ruler .. show column numbers at intervals .. senses mouse events in markers)

labels/labelblock (a collection of labelrowview objects. talks with zoomer to set alignmentscrolltop, and sends scroll events to the main seqBlock canvas)
labels/labelrowview (data object holding labels and metacell, style set by sass class)
labels/labelview (renders checkbox, id, partition, name (the left hand margin text columns), and captures mouse events (hovers and clicks))
labels/metaview (renders gap count, identity, external URL links (uniprot), captures mouse events (hovers, mouseovers, clicks))