/* global variables */ extern int activeParams[NUM_LINKED][MAX_NUM_DIVS]; /* a table holding the parameter status */ extern int autoClose; /* autoclose */ extern int autoOverwrite; /* Overwrite or append outputfiles when nowarnings=yes */ 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 Comptree comptreeParams; /* holds parameters for comparetree command */ extern char *constraintNames; /* holds names of constraints (| sep. strings) */ extern Calibration constraintCalibration[MAX_NUM_CONSTRAINTS]; /* holds calibration structs of constraints */ extern int dataType; /* type of data */ extern int defChars; /* flag for whether number of characters is known*/ extern int defConstraints; /* flag for whether constraints on tree are read */ 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; /* flag for whether number of taxa is known */ extern Doublet doublet[16]; /* holds information on states for doublets */ extern int echoMB; /* flag used by Manual to prevent echoing */ extern long unsigned int 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 long int 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 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 inSumtBlock; /* 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 isTranslateDef; /* is a translation block defined */ extern int isUserTreeDefined; /* flag indicating whether user tree is found */ 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 MoveType moveTypes[NUM_MOVE_TYPES]; /* holds information on the move types */ extern char missingId; /* missing character Id */ extern Model modelParams[MAX_NUM_DIVS]; /* holds model params for up to 30 partitions */ extern int nBitsInALong; /* number of bits in a long */ extern int noWarn; /* no warnings on overwriting files */ extern int numActiveLocks; /* number of active, locked nodes */ extern int numChar; /* number of characters in character matrix */ extern int numCharSets; /* holds number of character sets */ extern int numColumns; /* number of parameter columns for sump and plot */ extern int numComments; /* number of nested comments */ extern int numCurrentDivisions; /* number of partitions of data */ extern int numDefinedConstraints; /* number of constraints defined */ extern int numDefinedPartitions; /* number of partitions defined */ extern int numMoveTypes; /* the number of move types */ extern int numOpenExeFiles; /* number of execute files open */ extern int numPartitions; /* number of current partitions */ extern int numRows; /* number of parameter rows for sump and plot */ extern int numTaxa; /* number of taxa in character matrix */ extern int numTaxaSets; /* holds number of taxa sets */ extern int outGroupNum; /* number of outgroup taxon */ extern ParmInfo paramTable[]; /* information on parameters */ extern char *partitionNames; /* hold names of partitions (first is "default") */ extern MrBFlt *parameterValues; /* vector holding sump or plot parameters */ extern int partitionNum; /* number of current partition */ extern Plot plotParams; /* holds parameters for plot command */ extern int printAncStates[MAX_NUM_DIVS]; /* divisions to print anc states for */ extern int quitOnError; /* quit on error? */ extern int readWord; /* should we read a word next? */ extern ReassembleInfo reassembleParams; /* holds parameters for reassemble command */ extern MrBFlt relConstraintProbs[30]; /* relative probs. of trees with constraint */ extern int replaceLogFile; /* should logfile be replace/appended to */ extern long int runIDSeed; /* seed used only for generating run ID [stamp] */ extern char spacer[10]; /* holds blanks for printing indentations */ extern long int swapSeed; /* seed used only for determining which to swap */ extern Sump sumpParams; /* holds parameters for sump command */ extern Sumt sumtParams; /* holds parameters for sumt command */ extern char stamp[11]; /* holds a unique identifier for each analysis */ extern char *taxaNames; /* holds name of taxa */ extern TaxaInformation *taxaInfo; /* holds critical information about taxa */ extern int *tempSet; /* temporarily holds defined character set */ extern char *taxaSetNames; /* holds names of taxa sets */ extern int theAmbigChar; /* int containing ambiguous character */ extern char *transFrom; /* translation block information */ extern char *transTo; /* translation block information */ extern int longIntegerSize; /* size of an long integer */ extern int userBrlensDef; /* are the branch lengths on user tree defined */ extern int userLevel; /* the level of the user */ extern Tree *userTree; /* user tree */ extern int userLevel; /* user level */ # 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[4]; /* likelihood/prior/heat vals of me */ extern MrBFlt partnerStateInfo[4]; /* likelihood/prior/heat vals of partner */ # endif