Data processing bug fixes

There were some problems with assinging the correct pdb and resolution to files.
This fixes those issues so we always have consitent and clear data.
Code cleaning
Call addDefinitions in correct context

We should call addDefinitions in the context of the heatmap itself. This change
fixes things so we now do that.
Check if there is no resolution and store null

This occurs when dealing with modeled exemplars. Without doing this we end up
showing a black square instead of the grey colored square for things that are
missing. This commit should prevent such things from happening.
Show NA when no resolution

We shouldn't show null or undefined as a resolution, instead NA is better for
the user. This make such a change.
Remove extra whitespace
Switch row/column ordering

I was using a column first ordering, when I should be row first. This flips that
ordering making things easier to read and understand. Or at least more consitent
with how we normally do things.
Use a handlebars template for hovering

This makes altering and building the popup easier for me. There's a problem in
that if someone tries to hover before the request is done to load the template
then nothing will be shown. This is not ideal and can be worked around I'm sure.
Template tinkering
Store sequence id in item data

Before the item map was only {sequence: data} and the data object did not
include the sequence attribute. I've fixed that so it now also includes the
sequence as part of it.
Check if we have 3D coordinates for all items

This will be useful later on when we have to display 3D coordinates. This way we
can prevent sending out bad requests and I can then remove logic dealing with
such things. In addition, it is easier to display to the user that there are no
3D coordinates for this base pair.
Update gitignore
Some things shouldn't be +x
Add place to mark if rows have no 3D

Not all things have 3D information associated with them. In these cases we will
mark the rows so people know this. This may not be the best way to this, but I
will use it for now.
More things to -x
Clean up my HTML a bit

Just change some spaces and add a missing action attribute for the form.
Reorganizing

I'm reorganizing the code so it is easier to update the displays. This involves
moving bits around to try and reduce the complexity and duplication.
Draw a grey square if no exemplar exists
Use new jsmol tools
Remove old tools and outline new script