Data Fields
pllInstance Struct Reference

Tree topology. More...

#include <pll.h>

+ Collaboration diagram for pllInstance:

Data Fields

int * ti
 
recompVectorsrvec
 
float maxMegabytesMemory
 
float vectorRecomFraction
 
boolean useRecom
 
traversalCountertravCounter
 
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
 
stringHashtablenameHash
 
char * secondaryStructureInput
 
traversalData td [1]
 
int maxCategories
 
int categories
 
double coreLZ [PLL_NUM_BRANCHES]
 
branchInfobInf
 
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
 
nodestart
 
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
 
hashtableh
 
int optimizeRateCategoryInvocations
 
checkPointState ckp
 
boolean thoroughInsertion
 
boolean useMedian
 
pllStackrearrangeHistory
 
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.

Todo:
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
Todo:
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: