Track Symbol Definitions

##5.3.3 Track Symbol Definitions (Required) StochHMM digitizes the character or word to an integer value. Track symbol definitions requires a name and symbols(characters or strings) used by the track. A track can have up to 255 discrete symbols, all symbols must be explicitly defined. Characters or Strings of a track are not limited to 1 character, but can be any size. See USER track below.

If there are ambiguous characters, see Section 5.3.4 Ambigious Symbol Definitions.

If a track is a real number track, instead of symbols use REAL_NUMBER If a track is determined by a function at runtime using another track, a function name can be provided along with a scaling factor.

TRACK SYMBOL DEFINITIONS
======================================================
SEQ:	A,C,G,T      
SIDD:	siddAnalysis:	SEQ	SCALE:	0.9
USER:	AA,1,2,NN   
PWM:	REAL_NUMBER

Here we have defined 4 different tracks for this model

SEQ is an alphanumerical track with four characters A,C,G, and T.

SIDD is a REAL_NUMBER track but is defined by a user-defined function called siddAnalysis. siddAnalysis: SEQ means that the siddAnalysis function will use the SEQ sequence data to determine the SIDD track values. The values provided by siddAnalysis will multiplied by the SCALE number. Here we’ll multiply every value by 0.9.

TODO: If a user defined weighting function is defined then the weights section must be defined before the track section of the model.

At runtime siddAnalysis will use SEQ sequence to determine the SIDD track values.

USER is an alphanumerical track with 4 symbols: AA, 1, 2, and NN.

PWM is a REAL_NUMBER track