Data Fields
pllInstance Struct Reference

Tree topology. More...

#include <pll.h>

+ Collaboration diagram for pllInstance:

Data Fields

int * ti
float maxMegabytesMemory
float vectorRecomFraction
boolean useRecom
double stlenTime
boolean fastScaling
boolean saveMemory
int startingTree
long randomNumberSeed
double * lhs
double * patrat
double * patratStored
int * rateCategory
int * aliaswgt
boolean manyPartitions
boolean grouped
boolean constrained
int threadID
volatile int numberOfThreads
unsigned char * y_ptr
double lower_spacing
double upper_spacing
double * ancestralVector
char * secondaryStructureInput
traversalData td [1]
int maxCategories
int categories
double coreLZ [PLL_NUM_BRANCHES]
int multiStateModel
boolean curvatOK [PLL_NUM_BRANCHES]
int bDeep
unsigned char ** yVector
int secondaryStructureModel
int originalCrunchedLength
int * secondaryStructurePairs
double fracchange
double lhCutoff
double lhAVG
unsigned long lhDEC
unsigned long itCount
int numberOfInvariableColumns
int weightOfInvariableColumns
int rateHetModel
double startLH
double endLH
double likelihood
node ** nodep
nodeptr nodeBaseAddress
int mxtips
int * constraintVector
int numberOfSecondaryColumns
boolean searchConvergenceCriterion
int ntips
int nextnode
boolean bigCutoff
boolean partitionSmoothed [PLL_NUM_BRANCHES]
boolean partitionConverged [PLL_NUM_BRANCHES]
boolean rooted
boolean doCutoff
double gapyness
char ** nameList
char * tree_string
char * tree0
char * tree1
int treeStringLength
unsigned int bestParsimony
unsigned int * parsimonyScore
double bestOfNode
nodeptr removeNode
nodeptr insertNode
double zqr [PLL_NUM_BRANCHES]
double currentZQR [PLL_NUM_BRANCHES]
double currentLZR [PLL_NUM_BRANCHES]
double currentLZQ [PLL_NUM_BRANCHES]
double currentLZS [PLL_NUM_BRANCHES]
double currentLZI [PLL_NUM_BRANCHES]
double lzs [PLL_NUM_BRANCHES]
double lzq [PLL_NUM_BRANCHES]
double lzr [PLL_NUM_BRANCHES]
double lzi [PLL_NUM_BRANCHES]
unsigned int ** bitVectors
unsigned int vLength
int optimizeRateCategoryInvocations
checkPointState ckp
boolean thoroughInsertion
boolean useMedian
int bestTrav
int max_rearrange
int stepwidth
int initial
boolean initialSet
int mode
boolean perGeneBranchLengths
boolean permuteTreeoptimize
boolean compressPatterns
double likelihoodEpsilon
boolean useCheckpoint

Detailed Description

Tree topology.

Apart from the topology this structure contains several fields that act like global variables in raxml

Field Documentation

int* pllInstance::aliaswgt

weight by pattern

int pllInstance::bDeep

yVectors are 0: shallow-copy, or 1: deep-copy of alignment

int pllInstance::bestTrav

best rearrangement radius

boolean pllInstance::constrained

No idea what this is, but is always set to PLL_FALSE

int* pllInstance::constraintVector
What is this?
double pllInstance::fracchange

Average substitution rate

boolean pllInstance::grouped

No idea what this is, but is always set to PLL_FALSE

hashtable* pllInstance::h

hashtable for ML convergence criterion

int pllInstance::initial

user defined rearrangement radius which also sets bestTrav if initialSet is set

boolean pllInstance::initialSet

set bestTrav according to initial

nodeptr pllInstance::insertNode

the node where insertion should take place . Together with removeNode represents an SPR move

double* pllInstance::lhs

Array to store per-site log likelihoods of originalCrunchedLength (compressed) sites

double pllInstance::likelihood

last likelihood value evaluated for the current topology

int pllInstance::max_rearrange

max. rearrangemenent radius

float pllInstance::maxMegabytesMemory

User says how many MB in main memory should be used

int pllInstance::mode

candidate for removal

int pllInstance::mxtips

Number of tips in the topology

char** pllInstance::nameList

list of tips names (read from the phylip file)

node** pllInstance::nodep

pointer to the list of nodes, which describe the current topology

int pllInstance::originalCrunchedLength

Length of alignment after removing duplicate sites in each partition

double* pllInstance::patrat

rates per pattern

boolean pllInstance::permuteTreeoptimize

randomly select subtrees for SPR moves

nodeptr pllInstance::removeNode

the node that has been removed. Together with insertNode represents an SPR move

recompVectors* pllInstance::rvec

this data structure tracks which vectors store which nodes

node* pllInstance::start

starting node by default for full traversals (must be a tip contained in the tree we are operating on)

int pllInstance::stepwidth

step in rearrangement radius

boolean pllInstance::thoroughInsertion

true if the neighbor branches should be optimized when a subtree is inserted (slower)

char* pllInstance::tree_string

the newick representaion of the topology

boolean pllInstance::useRecom

ON if we apply recomputation of ancestral vectors

float pllInstance::vectorRecomFraction

vectorRecomFraction ~= 0.8 * maxMegabytesMemory

unsigned char** pllInstance::yVector

list of raw sequences (parsed from the alignment)

The documentation for this struct was generated from the following file: