Fix Covariate constructor and GLM intervalNr calculation#15
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The Covariate(Double[], String) constructor was setting the values field directly but not populating valuesInput. This caused two problems: 1. Calling initAndValidate() after the constructor would overwrite the values array with an empty array (since valuesInput was empty) 2. XML serialization would not include the covariate values The fix ensures valuesInput is populated in the constructor, making the object properly initialized and serializable. Fixes #14
The hardcoded -2 in intervalNr calculation only worked when firstlargerzero=1 (i.e., when rateShifts starts with 0.0). Changed to -firstlargerzero-1 which correctly computes the last valid interval index for any rateShifts configuration, including single-epoch models with rateShifts=[Infinity]. Fixes getCoalescentRate(), getNe(), and getMig() methods.
CovariateTest covers the Covariate(Double[], String) constructor populating valuesInput so that initAndValidate does not clobber values. GLMTest covers single-epoch GLM rate lookups (firstlargerzero == 0), the case where the old hardcoded intervalNr = dim - 2 produced -1 and the downstream Ne/migration covariate lookup threw ArrayIndexOutOfBounds.
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Summary
Covariate(Double[], String)constructor to also populatevaluesInputintervalNrcalculation for single-epoch modelsFix 1: Covariate constructor (fixes #14)
The constructor was setting the
valuesfield directly but not populatingvaluesInput. This caused:initAndValidate()to overwritevalueswith an empty arrayFix 2: GLM intervalNr calculation (fixes #16)
The hardcoded
-2inintervalNrcalculation only worked whenfirstlargerzero=1(i.e., when rateShifts starts with 0.0).Changed to
-firstlargerzero-1which correctly computes the last valid interval index for any rateShifts configuration, including single-epoch models withrateShifts=[Infinity].Fixes
getCoalescentRate(),getNe(), andgetMig()methods.