17.06.08
4.85 - postExp - allow only branch multiply by 10-7 to avoid "non-prob" values.

1	"computeEB_EXP_siteSpecificGL_zero" - not going to use it...
2	P11forgain into gainLossUtils
3	printLofPosBothModels()
4	simulations()
5	printGainLossProbabilityPerPosPerBranch(...outCount)
6	modified printGainLossBayes
7	rate2multiply = max(rateVal,minimumRate) @gainLoss::computePosteriorExpectationOfChangePerSite
8	if (res > 1 + 1e-10) - res = 1;

18.06.08
5.0 - Ancestral Reconstruct
1. added class and functions - ancestralReconstructStates.cpp
2. fix the printTreeStatesAsBPValues function
3. clean code

    rate4SiteGL
        o 6.0  - encapsulate into class... (operate for each simulated seq. )
        o 6.1   - add GAMMA_PLUS_INV
        o 6.2 
            +  Delete un-needed lines         //NO NEED to update since the _spVVec is sent byRef to be optimized and updated in optimizeGainLossModelVV
            +  ErrorMGS at gainLossOptions for imcompatible options
            + "previousL" instead of "changed=false"
            +  C_eval is computing adhoc "_plogLforMissingData" so it is not sent
        o 6.21 - manyStarts as default, defaults:_userAlphaRate =0.7; _userGain =0.5; _userLoss =2.0;

    gain - freq(1)_Q * r_Q
        o 7.0  - with "_gainLossRateAreFreq" - 0<gain<1 and loss = 1-gain.
        This formulation should be more accorate
        o 7.1 - sumlations with different models
            + basic "non-model" - GENERAL_GAMMA_FIXED_CATEGORIES (lib changed)
            + switch changed to dynamic cast at get/set ALpha/Beta - @gainLossUtil


    classes: gainLoss4site, computeCountsGL, coEvol
        o 8.0  - encapsulate into class, enable coEvol
            + new modified functions at gainLoss.cpp - startGainLoss4Site,startComputePosteriorExpectationOfChange,
                startSimulateSequences,simulateSequences,
            + gainLossAlphabet.cpp at phyLib
            + startZeroSequenceContainerGL from sequenceContainer methods
            + all bblEM functionality with _logLforMissingData is tested
        o 8.1 - modify thd gainLossDist (spVVec) - the purpose: the value of gain4site will ce calculated as the multiplication of (general)rate and gain.
        
        
        