/* global variables */ extern int abortMove; /* flag determining whether to abort move */ extern int *activeParams[NUM_LINKED]; /* a table holding the parameter status */ extern int *activeParts; /* partitions changes should apply to */ extern int autoClose; /* autoclose */ extern int autoOverwrite; /* Overwrite or append outputfiles when nowarnings=yes */ extern int chainHasAdgamma; /* indicates if chain has adgamma HMMs */ extern Chain chainParams; /* holds parameters for Markov chain */ extern CharInformation *charInfo; /* holds critical information about characters */ extern char **charSetNames; /* holds names of character sets */ extern int *compCharPos; /* char position in compressed matrix */ extern int *compColPos; /* column position in compressed matrix */ extern SafeLong *compMatrix; /* compressed character matrix */ extern int compMatrixRowSize; /* row size of compressed matrix */ extern Comptree comptreeParams; /* holds parameters for comparetree command */ extern char **constraintNames; /* holds names of constraints */ extern SafeLong **definedConstraint; /* holds information about defined constraints */ extern SafeLong **definedConstraintTwo; /* bitfields representing second taxa sets of defined constraints (used for PARTIAL constraints) */ extern SafeLong **definedConstraintPruned; /* bitfields representing taxa sets of defined constraints after delited taxa are removed */ extern SafeLong **definedConstraintTwoPruned; /* bitfields representing second taxa sets of defined constraints after delited taxa are removed(used for PARTIAL constraints) */ extern int dataType; /* type of data */ extern Calibration defaultCalibration; /* default model settings */ extern ModelParams defaultModel; /* default model settings */ extern int defChars; /* flag for whether number of characters is known*/ extern int defMatrix; /* flag for whether matrix is successfull read */ extern int defPairs; /* flag for whether constraints on tree are read */ extern int defPartition; /* flag for whether character partition is read */ extern int defTaxa; /* are taxon labels defined ? */ extern Doublet doublet[16]; /* holds information on states for doublets */ extern int echoMB; /* flag used by Manual to prevent echoing */ extern SafeLong expecting; /* variable denoting expected token type */ extern int fileNameChanged; /* has file name been changed? */ extern int foundNewLine; /* whether a new line has been found */ extern char gapId; /* gap character Id */ extern SafeLong globalSeed; /* seed that is initialized at start up */ extern char **headerNames; /* string to hold headers in sump and plot */ extern int inComment; /* flag for whether input stream is commented */ extern int inferAncStates; /* should ancestral states be inferred (y/n) */ extern int inferSiteOmegas; /* should site omega values be inferred (y/n) */ extern int inferSiteRates; /* should site rates be inferred (y/n) */ extern int inferPosSel; /* should positive selection be inferred (y/n) */ extern char inputFileName[100]; /* input (NEXUS) file name */ extern int inTreesBlock; /* are we in the sumt block */ extern int inValidCommand; /* a useful flag set whenever you enter a cmd */ extern int isInAmbig, isInPoly; /* flags whether we are within () or {} */ extern int isMixed; /* flags whether dataset is mixed */ extern int inMrbayesBlock; /* flag for whether we are in a mrbayes block */ extern int *intValues; /* integer values of parameters */ extern int isTaxsetDef; /* is a taxon set defined */ extern int isTranslateDef; /* is a translation block defined */ extern int isTranslateDiff; /* is translate different from current taxaset? */ extern int *linkTable[NUM_LINKED]; /* how parameters are linked across parts */ extern int localOutGroup; /* outgroup for non-excluded taxa */ extern char **localTaxonNames; /* points to names of non-excluded taxa */ extern FILE *logFileFp; /* file pointer to log file */ extern char logFileName[100]; /* name of the log file */ extern int logToFile; /* should screen output be logged to a file */ extern char manFileName[100]; /* name of man file */ extern char matchId; /* mach character Id */ extern int *matrix; /* matrix containing original data */ extern int matrixHasPoly; /* flag for whether matrix has polymorphisms */ extern int memAllocs[NUM_ALLOCS]; /* allocated memory flags */ extern int mode; /* mode of program (interactive/noninteractive) */ extern char **modelIndicatorParams; /* model indicator params */ extern char ***modelElementNames; /* names for component models */ extern MCMCMove **moves; /* vector of applicable moves */ extern MoveType moveTypes[NUM_MOVE_TYPES]; /* holds information on the move types */ extern char missingId; /* missing character Id */ extern Tree **mcmcTree; /* pointers to mcmc trees */ extern Model *modelParams; /* holds model params for partitions */ extern ModelInfo *modelSettings; /* stores important info on model params */ extern int nBitsInALong; /* number of bits in a SafeLong */ extern Calibration *nodeCalibration; /* holds information about node calibrations */ extern int noWarn; /* no warnings on overwriting files */ extern int nPThreads; /* number of pthreads to use */ extern int numActiveLocks; /* number of active, locked nodes */ extern int numApplicableMoves; /* number of moves applicable to parameters */ extern int numChar; /* number of characters in character matrix */ extern int numCharSets; /* holds number of character sets */ extern int numComments; /* number of nested comments */ extern int numCompressedChars; /* number of compressed characters */ extern int numCurrentDivisions; /* number of partitions of data */ extern int numDefinedConstraints; /* number of constraints defined */ extern enum ConstraintType *definedConstraintsType; /* Store type of constraint */ extern int numDefinedPartitions; /* number of partitions defined */ extern int numDefinedSpeciespartitions; /* number of species partitions defined */ extern int numGlobalChains; /* number of global chains */ extern int numLocalTaxa; /* number of non-excluded taxa */ extern int numLocalChar; /* number of non-excluded characters */ extern int numMoveTypes; /* the number of move types */ extern int numOpenExeFiles; /* number of execute files open */ extern int numParams; /* number of parameters in model */ extern int numDivisions; /* number of current divisions */ extern int numPrintParams; /* number of substitution model parameters to print */ extern int numPrintTreeParams; /* number of tree model parameters to print */ extern CLFlt *numSitesOfPat; /* no. sites of each pattern */ extern int numSpecies; /* number of species in current speciespartition */ extern int numTaxa; /* number of taxa in character matrix */ extern int numTaxaSets; /* holds number of taxa sets */ extern int numTopologies; /* number of topologies for one chain and state */ extern int numTranslates; /* number of taxa in active translate block */ extern int numTrees; /* number of trees for one chain and state */ extern int numUserTrees; /* number of defined user trees */ extern int *numVars; /* number of variables in setting arrays */ extern int *origChar; /* index from compressed char to original char */ extern int outGroupNum; /* number of outgroup taxon */ extern ParmInfo paramTable[]; /* information on parameters */ extern MrBFlt *paramValues; /* values of parameters */ extern int **partitionId; /* holds information about defined partitions */ extern char **partitionNames; /* hold names of partitions (first is "default") */ extern MrBFlt *parameterValues; /* vector holding sump or plot parameters */ extern Param *params; /* vector of parameters in model */ extern int partitionNum; /* index of current partition */ extern Plot plotParams; /* holds parameters for plot command */ extern int precision; /* precision of samples and summary stats */ extern int *printAncStates; /* divisions to print anc states for */ extern int quitOnError; /* quit on error? */ extern int readComment; /* should we read comment (looking for &)? */ extern int readWord; /* should we read a word next? */ extern ReassembleInfo reassembleParams; /* holds parameters for reassemble command */ extern int replaceLogFile; /* should logfile be replace/appended to */ extern SafeLong runIDSeed; /* seed used only for generating run ID [stamp] */ extern SafeLong safeLongWithAllBitsSet; /* a SafeLong with all bits set, for bit ops */ extern int setUpAnalysisSuccess; /* Set to YES if analysis is set without error */ extern int scientific; /* use scientific format for samples ? */ extern ShowmovesParams showmovesParams; /* holds parameters for Showmoves command */ extern char spacer[10]; /* holds blanks for printing indentations */ extern NameSet *speciesNameSets; /* hold species name sets, one for each speciespartition */ extern int **speciespartitionId; /* holds info about defined speciespartitions */ extern char **speciespartitionNames; /* hold names of speciespartitions (first is "default") */ extern int speciespartitionNum; /* index of current species partition */ extern char stamp[11]; /* holds a unique identifier for each analysis */ extern SafeLong swapSeed; /* seed used only for determining which to swap */ extern int state[MAX_CHAINS]; /* state of chain */ extern MrBFlt *stdStateFreqs; /* std char state frequencies */ extern int *stdType; /* compressed std char type: ord, unord, irrev */ extern Sump sumpParams; /* holds parameters for sump command */ extern char sumpToken[]; /* string holding a .p file token */ extern char *sumpTokenP; /* pointer to a .p file token */ extern Sumt sumtParams; /* holds parameters for sumt command */ extern Sumss sumssParams; /* holds parameters for sumss command */ extern char stamp[11]; /* holds a unique identifier for each analysis */ extern int stdStateFreqsRowSize; /* row size for stdStateFreqs */ extern int *sympiIndex; /* sympi state freq index for multistate chars */ extern TaxaInformation *taxaInfo; /* holds critical information about taxa */ extern char **taxaNames; /* holds name of taxa */ extern char **taxaSetNames; /* holds names of taxa sets */ extern SafeLong **taxaSet; /* holds information about defined taxasets */ extern int *tempActiveConstraints; /* info on the active constraints in prset */ extern int *tempLinkUnlink[NUM_LINKED]; /* for changing parameter linkage */ extern int *tempLinkUnlinkVec; /* for changing parameter linkage */ extern MrBFlt *tempNum; /* vector of numbers used for setting arrays */ extern int *tempSet; /* temporarily holds defined character set */ extern int theAmbigChar; /* int containing ambiguous character */ extern int *tiIndex; /* compressed std char ti index */ extern Calibration *tipCalibration; /* holds tip calibrations */ extern char **transFrom; /* translation block information */ extern char **transTo; /* translation block information */ extern int userBrlensDef; /* are the branch lengths on user tree defined */ extern int userLevel; /* the level of the user */ extern PolyTree *userTree[]; /* array of user trees */ extern char workingDir[100]; /* working directory */ #if defined (BEAGLE_ENABLED) extern int tryToUseBEAGLE; /* try to use the BEAGLE library */ extern long beagleFlags; /* BEAGLE requirement flags */ extern int* beagleResource; /* BEAGLE resource list */ extern int beagleResourceCount; /* BEAGLE resource list length */ extern int beagleInstanceCount; /* total number of BEAGLE instances */ extern int beagleScalingScheme; /* BEAGLE dynamic scaling */ extern int beagleScalingFrequency; /* BEAGLE rescaling frequency */ extern int recalcScalers; /* shoud we recalculate scalers for one of divisions for current state YES/NO */ #endif #if defined (THREADS_ENABLED) extern int tryToUseThreads; /* try to use pthreads with BEAGLE library */ #endif /* Aamodel parameters */ extern MrBFlt aaJones[20][20]; /* rates for Jones model */ extern MrBFlt aaDayhoff[20][20]; /* rates for Dayhoff model */ extern MrBFlt aaMtrev24[20][20]; /* rates for mtrev24 model */ extern MrBFlt aaMtmam[20][20]; /* rates for mtmam model */ extern MrBFlt aartREV[20][20]; /* rates for rtREV model */ extern MrBFlt aaWAG[20][20]; /* rates for WAG model */ extern MrBFlt aacpREV[20][20]; /* rates for aacpREV model */ extern MrBFlt aaVt[20][20]; /* rates for VT model */ extern MrBFlt aaBlosum[20][20]; /* rates for Blosum62 model */ extern MrBFlt jonesPi[20]; /* stationary frequencies for Jones model */ extern MrBFlt dayhoffPi[20]; /* stationary frequencies for Dayhoff model */ extern MrBFlt mtrev24Pi[20]; /* stationary frequencies for mtrev24 model */ extern MrBFlt mtmamPi[20]; /* stationary frequencies for mtmam model */ extern MrBFlt rtrevPi[20]; /* stationary frequencies for rtREV model */ extern MrBFlt wagPi[20]; /* stationary frequencies for WAG model */ extern MrBFlt cprevPi[20]; /* stationary frequencies for aacpREV model */ extern MrBFlt vtPi[20]; /* stationary frequencies for VT model */ extern MrBFlt blosPi[20]; /* stationary frequencies for Blosum62 model */ #if defined (PRINT_RATEMULTIPLIERS_CPP) extern FILE *rateMultfp; #endif #if defined (MPI_ENABLED) extern int proc_id; /* process ID (0, 1, ..., num_procs-1) */ extern int num_procs; /* number of active processors */ extern MrBFlt myStateInfo[7]; /* likelihood/prior/heat/ran/moveInfo vals of me */ extern MrBFlt partnerStateInfo[7]; /* likelihood/prior/heat/ran/moveInfo vals of partner */ #endif #if defined (FAST_LOG) extern CLFlt scalerValue[]; extern CLFlt logValue[]; #endif