Data Structures
Here are the data structures with brief descriptions:
oCancestralStateSmall helper data structure for printing out/downstream use of marginal ancestral probability vectors
oCbestlistList of topologies
oCbInf
oCbranchInfoBranch length information
oCcheckPointStateCheckpointing states
oCconnectRELL
oCconntypConnection within a topology
oCent???
oChashtable???Hash tables
oCiL
oCinfoA brief line
oClinkageDataLinkage of partitions
oClinkageList
oCnniMoveStores data related to a NNI move
oCnoderecTree node record
oCpartitionLengthsThis is used to look up some hard-coded data for each data type
oCpartitionList
oCpartitionType
oCpInfoPartition information structure
oCpllAlignmentDataGeneric structure for storing a multiple sequence alignment
oCpllHashItem
oCpllHashTable
oCpllInstanceTree topology
oCpllInstanceAttr
oCpllLexToken
oCpllNewickNodeInfoInformation describing the parsed newick tree nodes
oCpllNewickTreeIntermediate structure for storing a newick tree
oCpllPartitionInfo
oCpllPartitionRegion
oCpllQueue
oCpllQueueItem
oCpllRearrangeAttrStructure holding attributes for searching possible tree rearrangements
oCpllRearrangeInfo
oCpllRearrangeList
oCpllRollbackInfo
oCpllStack
oCratecPer-site Rate category entry: likelihood per-site and CAT rate applied ???
oCrecompVectorsStores the recomputation-state of likelihood vectors
oCstringEnt
oCstringHashtable
oCthreadData
oCtopolSingle Topology
oCtopolRELL
oCtopolRELL_LIST
oCtraversalCounter
oCtraversalDataTraversal descriptor
\CtraversalInfoTraversal descriptor entry