Moved filling of  fNRegions from parameter to before the fRegionValue array
is defined. The code had been using default fNRegions=4 regardless
of vaule  of  h_num_regions in parameter file.

Modified so that the fGoodPosAdcPulseTime, fGoodNegAdcPulseTime
  or fGoodAdcPulseTime is set to kBig

Modified THcShowerRawHit::SetReference to takeADC signals

Modified THcTrigRawHit::SetReference to take ADC signals

Modified THcShowerArray::ProcessHits so that fAdcTdcOffset add to frAdcPulseTime

Modified THcShowerArray::ReadDatabase so that defaults for fAdcThreshold etc
  are before gHcParms->LoadParmValues

Fix typo in previous commit's THcCherenkov.cxx

Include methods for FADC conversions and apply to non-raw data objects in THcRawAdcHit

Add raw pulse time data object to Cherenkov detector classes

Add raw pulse time data object to shower detector classes

Add raw pulse time data object to hodoscope detector class

   Gets rid of vars.push_back(RVarDef ... stuff

Also do some whitespace cleanup

New parameters are added.  hallc_replay of 3/31/2017 or later is needed.

As of now, the size of the TClonesArray objects are hard-coded in the
respective header files. This is not okay in the long run. Ideally,
the size of the TClonesArrays should be defined by the parameter which
dictates how many readout detectors exist for the respective
detector. I tried doing this in the Init method however, podd
complained regarding the size of the TClonesArrays in the DEF-file
histograms. I was unsuccessful in my first attempt. This should be
addressed in the future even though things work for now.

Add array fADC_hit that is a flag if there is a hit in the ADC
fADC_hit is set in Decode method
The FADC has a threshold on accepting ADC hit
Modified CoarseProcess method to eliminate old FASTBUS bias in the analysis

The calls to `Find()` need to be wrapped in checks if returned pointer is null.
Otherwise a further call to get value produces SegFault. The `LoadParmValues()`
does not suffer from this, since it throws error if non-optional parameter is
not found. The error message also tells which parameter is missing.

I still left three calls to `Find()` in `THcAnalyzer.cxx`. They are wrapped in
checks and some other things...

 - Added new leafs to the hodoscope tree.
 - Added new leafs to the aerogel tree.
 - Added new leafs to cerenkov tree.
 - Added new leafs to the shower tree.

Left all the old leafs in there. Will need a careful cleanup...

This makes the code nicer and with less duplication in logic.

Along with that I had to correct all the call sites to the RawHodoHit in all the
classes that use it.

  Don't check if UInt_t's are >=0
  Remove unused/repeated variables
  Cast enums to Int_t in switch statements
  Initialize temp variables

  Otherwise InitHistlist doesn't have the detector map
  and can't do setup of reference time stuff or sanity checks on the
  detector mapping

Some detector classes lacked the ability to get the appropriate
Apparatus character and were only working for HMS.

  May want to use a hit class that doesn't inherit from THcHodoscope
  as the Cerenkov is not using Neg tubes or TDCs.

  Modify THcFormula and THcParmList to match changes to THaFormula
     (needed for reports)
  Small changes in THcInterface and detector classes for compatibility
     with new OO decoder and podd 1.6

  Don't start variables that are not member variables with f
  Declare temporary variables as locally as possible
  Remove some unused member variables from THcHodoscope.h

      Declare loop variables in the for statement
      Go back to UInt_t for some variables
      Don't prefix non-member variables with f

  Adds tests to THcHodoscope fiducial tracking efficiency
  Adds tests to THcCherenkov for Cerenkov efficiency

  For the most part this is making sure that the loop variable in
  a for loop is of the same type as the variable that it is compared
  against (Often a UInt_t).

This reverts commit e9ce1040.

Conflicts:
	src/THcHallCSpectrometer.cxx

  For the most part this is making sure that the loop variable in
  a for loop is of the same type as the variable that it is compared
  against (Often a UInt_t).

  Use InitArrays method in THcCherenkov and THcAerogel
  Null out all array pointers in the InitArrays method and
  call that method from all constructors so that it is always
  safe to delete these arrays.

Class for an Cherenkov detector consisting of two PMT's.
Fourth pull request. January 30 2014.
No need to cahnge the Map file.
New parameter hcer_tot_pmts = 2 is added to the hcana.param file
This code is for the coarse process of THcCherenkov class.
Names of all the variables are in lower case.

Variable Name   Description
phototubes      Nuber of Cherenkov photo tubes
adc             Raw ADC values
adc_p           Pedestal Subtracted ADC values
npe             Number of Photo electrons
npesum          Sum of Number of Photo electrons
ncherhit        Number of Hits(Cherenkov)

We have added a new parameter hcer_tot_pmts = 2 in hcana.param file.
It is equal to total number of PMTs in Cherenkov detector. With this
update, the THcCherenkov coarse process is complete. We have Raw adc,
pedestal subtracted adc, number of photo electrons and hits histograms
in the output root file for gas Cherenkov detector.