question: private static void applyBonferroniCorrection ( PhyloTree tree ) { int numberOfUpCases = 0 ; int numberOfDownCases = 0 ; for ( Node v = tree . getFirstNode ( ) ; v != null ; v = v . getNext ( ) ) { NodeData vd = ( NodeData ) v . getData ( ) ; if ( vd . getDownPValue ( ) != Double . NaN && vd . getDownPValue ( ) != - 1 && v . getOutDegree ( ) > 1 ) numberOfDownCases ++ ; if ( vd . getUpPValue ( ) != Double . NaN && vd . getUpPValue ( ) != - 1 && v . getInDegree ( ) > 0 ) numberOfUpCases ++ ; } if ( numberOfDownCases == 0 ) numberOfDownCases = 1 ; if ( numberOfUpCases == 0 ) numberOfUpCases = 1 ; for ( Node v = tree . getFirstNode ( ) ; v != null ; v = v . getNext ( ) ) { NodeData vd = ( NodeData ) v . getData ( ) ; if ( vd . getUpPValue ( ) != Double . NaN && vd . getUpPValue ( ) != - 1 && v . getInDegree ( ) > 0 ) vd . setUpPValue ( Math . min ( 1 , vd . getUpPValue ( ) * numberOfUpCases ) ) ; if ( vd . getDownPValue ( ) != Double . NaN && vd . getDownPValue ( ) != - 1 && v . getOutDegree ( ) > 1 ) vd . setDownPValue ( Math . min ( 1 , vd . getDownPValue ( ) * numberOfDownCases ) ) ; } }
target:  apply the Bonferroni correction