IMPLEMENTED

- Problem with a haplotype being rendered improperly for haplotypes 
selection mode. The family_map check of the problematic markers seem to
contain the correct data, it's just the renderer

- min exten and min score do not work properly -- check out rs2817738, which
needs to extend by at least one more, as well as rs9461082 which only highlights a single region, though the min_extension should be two
 --- this is just now an offset of -1 problem in the kinetic_graphics.js function

- implement a JUMP TO marker input box,
- also reDRAW resets the slider positions, which it should'nt do.
- Fix reselecting individuals after coming out of select mode
- Fix block size plotting to be more relevant.
- Select mode should place nodes ontop of darkened rect, and then return them back

EDIT Haplomode to incorporate non-related individuals:
   * Press a button to initiate a selection mode in the main pedview
   * Tick all the members that you want (quick button to toggle all affecteds)
   * Initiate haplomode

   New HMode consists of:
   	 * Lined up individuals (swappable) order
   	 * Tools to highlight a region of SNPs (a messner file can be given)
   	 * Tools to find stretches of homology:
   	         * for single/double alleles across selected individuals
   	         * for single/double alleles across selected indivs, barring other indivs


Window needs an adjuster to be dynamically set to show N markers
 - Adjuster could be a slider that represents all M markers with start and stop bars

- Rewrite resolveblocks method, to incorporate different PAIRS of groups
(instead of pushing everything in one go) -- this will mean changing the
haploblock_Backend as well to push PAIRS.
 - Does it actually need pairs? Surely each allele must be evaluated
   seperately (because crossover is independent of a gametes sister allele)
   - Maybe I'm just pushing the wrong groups? Need to explore for that subset again.


Fix scrolling when Align mode is initiated.



Fix haplo color blocks, especially for those between rs4148618 and rs2279900 [DONE]

Haplotypes should have their own layer for quicker rendering:  [ DONE -- no significant improvement in anims]
	On entering haplomode:
	- Move current pedigree objects from main_layer to haplo_layer
	- Transition to alignment
	- render haplotypes on hapo_layer

	On leaving haplomode:
	- unload haplotypes
	- Transition out of alignment
	- move current pedigree from haplo_layer to main_layer
	- haplo_layer.clear()


Haplotypes should always be aligned [Done]


Drag and scroll haplotypes:
	- window = 20 												[ DONE --]
	- A view of about window haplotypes at any time,            [ DONE ]
	  with the next window loaded in with a scroll up and
	  the old window scrolled out of view and unloaded



Xlinked scenario for haplotype reconstruction (two alleles to  choose from, not 4) [DONE]
  -- implemented inheritance patterns, now need to display it using the X_Dom scenario




At the moment haplotypes are stored in an Object array of {data:0(1 or 2), pointer:}.
    -- This is wasteful of course, since
			a) data is not contiguous across indices
			b) data is 64-bit for 2-bit data
	-- A solution would be to use a JS byte-array, but you would need to implement an associative pointer array too for each data array. [DONE]

	  -- Do now or do later? It genuinely might not matter.




- Need to reset graphics and containers when using the container from something else, going back to main menu, and then resuming. -- partially implemented
- Better loading of pedfile graphics from file
- Selection  


 - Modes:
    - Create mode:
       - Add individuals -> tree
       - produce ped file (generate)
    - Present mode:
       - Read in pedfile with genotypes
    - Share mode:
       - Generate url


 - Annotations of SNPs


 - Share session between users
 - Detect if session is
 - (give option to password) sessions
 - Impl:
   - MySQL to store JSON stringified and lzcompressed with session keys set by user.
   - Save?
     -> Prompt name (add filler if not unique)
     -> key[name] = {entire family_map with person data and db_annoations}