void function ( Map < String , Integer > arg0 , STINode < SNAPPData > arg1 , SNAPPData arg2 ) { arg2 . mx = 1 ; arg2 . nucleotideIndex = arg0 . get ( arg1 . getName ( ) ) ; arg2 . FBottom = new FMatrix ( arg2 . mx ) ; for ( int loc0 = 1 ; loc0 <= arg2 . mx ; loc0 ++ ) { for ( R loc1 : R . loopOver ( loc0 ) ) arg2 . FBottom . set ( loc1 , getFBottomLeaf ( loc0 , loc1 , arg1 ) ) ; } }
perform the initial processing of a leaf . concode_field_sep int nucleotideIndex concode_elem_sep int MAXIMUM_NUMBER_OF_TAXA_FOR_CONVOLUTIONLIB concode_elem_sep FMatrix FBottom concode_elem_sep ThreadLocal<JNIConvolution> myConvolution concode_elem_sep boolean USING_CONVOLUTIONLIB concode_elem_sep boolean PRINT_DETAILS concode_elem_sep int mx concode_elem_sep FMatrix FTop concode_field_sep double getFBottomLeaf concode_elem_sep double getFBottom concode_elem_sep double getProbabilityOfTree concode_elem_sep void processInternalNode concode_elem_sep FMatrix getFBottomNormal concode_elem_sep FMatrix getFBottomConvolution concode_elem_sep int alleleToColor concode_elem_sep Map<String,Integer> getNucleotideIndexMap concode_elem_sep double getProbabilityObservationGivenTree concode_elem_sep JNIConvolution createConvolution concode_elem_sep void processTopBranchOfNode concode_elem_sep JNIConvolution initialValue concode_elem_sep void processNode