Added a flag for tracking whether Coherence was actually computed. If it
wasn't computed we skip plotting.
Organized the imports. Removed unused imports.
Used Eclipse's formatting tool to correct line spacing and indentation.
Our problem was the vague error messages and nullpointer, so I addressed
those.

The readNoiseFile already had loggers and everything for a nonexistant
file. I added a check for null and if it was null change the value of
fileName to "". This removes the null pointer exception and let the
existing error handling take over.

Where it had NHNMFile = get("nhnm-modelfile"); I added a check for null
and it logs which file is missing. There was already a logger there, so
I didn't have to change too much.


After testing, this is how it behaves when noise model files are
missing.

If either NHNM or NLNM model files are missing:
The thread no longer dies. It sends exceptions to the logger and dumps
an explanation and stack traces to the screen.

If NHNM is missing:
When it calls if(getNHNM().isValid()) it is not valid so it skips
plotting that line. NLNM is still calculated.

If NLNM is missing:
The still keeps going, it just doesn't compute NLNM. This will be
visible in DQA since that column will be missing values. It will also be
recorded in the logs.
Organized imports in NLNMDeviation
Used Eclipse's auto format to fix indentation and spacing issues.
Removed unused variable and associated comments from computeMetric in
NLNMDeviation.
If plotting Difference metrics it would error if seedscan didn't
recompute everything. This change adds a flag like in Coherence to fix
this.
Fixed indentations, autoformatted, and removed unused imports.
Merge pull request #11 from asl-usgs/jamesdev

Merging Coherence, Difference, NLNM metric changes
merging changes from master