Ctakes ytex conceptgraph

[jlpainter]

This patch makes the following code cleanup and mathematical corrections to the kernel metrics as well as the max-depth calculation for a concept graph:

Correct the construction of the initial concept graph whereby the dummy root node has a depth value of zero which was creating wildly unreasonable max-depths for individual graphs.

IntrinsicLCHMetric contained a mathematical error where the formula misinterpreted that it should be -1 times the log and instead had an implementation that was 1 minus the log. In addition, the way the concept graph is computed, there is a dummy root node created which inflated the depth of the nodes by (2) - this is now corrected and the output matches exactly to values computed by the Perl UMLS::Similarity LCH computation

LCHMetric contained a mathematical error where the formula misinterpreted that it should be -1 times the log and instead had an implementation that was 1 minus the log. The LCH metric also contained the same depth error as LCH intrinsic and this has been corrected.

JaccardMetric could have had a divide by zero if the ic1 + ic2 was equal to the lcsIC. Added a check to insure this does not happen.

The LinMetric code has been cleaned up to be more readable

Wu-Palmer Metric also suffered from a mis-calculation of node depth due to the dummy node. This code was also cleaned up to be more readable and to more accurately reflect the computations in the Perl UMLS::Similarity wup.pm module.