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command.c
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/*
* MrBayes 3
*
* (c) 2002-2023
*
* John P. Huelsenbeck
* Dept. Integrative Biology
* University of California, Berkeley
* Berkeley, CA 94720-3140
*
* Fredrik Ronquist
* Swedish Museum of Natural History
* Box 50007
* SE-10405 Stockholm, SWEDEN
*
* With important contributions by
*
* Paul van der Mark ([email protected])
* Maxim Teslenko ([email protected])
* Chi Zhang ([email protected])
*
* and by many users (run 'acknowledgments' to see more info)
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details (www.gnu.org).
*
*/
#include "bayes.h"
#include "command.h"
#include "mbbeagle.h"
#include "model.h"
#include "mcmc.h"
#include "sumpt.h"
#include "utils.h"
#if defined(__MWERKS__)
#include "SIOUX.h"
#endif
#define NUMCOMMANDS 62 /* The total number of commands in the program */
#define NUMPARAMS 283 /* The total number of parameters */
#define PARAM(i, s, f, l) p->string = s; \
p->fp = f; \
p->valueList = l; \
p++;
#define HIDE 0
#define SHOW 1
/* Debugging options */
#undef SHOW_TOKENS
#undef ECHO_PROCESSED_COMMANDS
/* Local function prototypes */
int AddNameSet(NameSet **nameSetList, int numNameSets, char **nameSet, int numNames);
int AddToSet (int i, int j, int k, int id);
int AllocCharacters (void);
int AllocMatrix (void);
int AllocTaxa (void);
char ChangeCase (char c);
int CharacterCode (char ch, int *charCode, int chType);
int CharacterNumber (int charCode, int chType);
int CheckInitialPartitions (void);
int Dex (TreeNode *p);
int DoAbout (void);
int DoAcknowledgments (void);
int DoBeginParm (char *parmName, char *tkn);
int DoBreaks (void);
int DoBreaksParm (char *parmName, char *tkn);
int DoCalibrate (void);
int DoCalibrateParm (char *parmName, char *tkn);
int DoCharset (void);
int DoCharsetParm (char *parmName, char *tkn);
int DoCharStat (void);
int DoCitations (void);
int DoConstraint (void);
int DoConstraintParm (char *parmName, char *tkn);
int DoCtype (void);
int DoCtypeParm (char *parmName, char *tkn);
int DoDelete (void);
int DoDeleteParm (char *parmName, char *tkn);
int DoDimensions (void);
int DoDimensionsParm (char *parmName, char *tkn);
int DoDisclaimer (void);
int DoEndBlock (void);
int DoExecuteParm (char *parmName, char *tkn);
int DoExclude (void);
int DoExcludeParm (char *parmName, char *tkn);
int DoFormat (void);
int DoFormatParm (char *parmName, char *tkn);
int DoHelp (void);
int DoHelpParm (char *parmName, char *tkn);
int DoInclude (void);
int DoIncludeParm (char *parmName, char *tkn);
int DoLog (void);
int DoLogParm (char *parmName, char *tkn);
int DoManual (void);
int DoManualParm (char *parmName, char *tkn);
int DoMatrix (void);
int DoMatrixParm (char *parmName, char *tkn);
int DoNexusParm (char *parmName, char *tkn);
int DoOutgroup (void);
int DoOutgroupParm (char *parmName, char *tkn);
int DoPairs (void);
int DoPairsParm (char *parmName, char *tkn);
int DoPartition (void);
int DoPartitionParm (char *parmName, char *tkn);
int DoRestore (void);
int DoRestoreParm (char *parmName, char *tkn);
int DoSet (void);
int DoSetParm (char *parmName, char *tkn);
int DoShowBeagle (void);
int DoShowMatrix (void);
int DoShowUserTrees (void);
int DoSpeciespartition (void);
int DoSpeciespartitionParm (char *parmName, char *tkn);
int DoTaxaset (void);
int DoTaxasetParm (char *parmName, char *tkn);
int DoTaxaStat (void);
int DoTaxlabels (void);
int DoTaxlabelsParm (char *parmName, char *tkn);
int DoTranslate (void);
int DoTranslateParm (char *parmName, char *tkn);
int DoTree (void);
int DoTreeParm (char *parmName, char *tkn);
int DoUserTree (void);
int DoUserTreeParm (char *parmName, char *tkn);
int DoVersion (void);
int FindValidParam (char *tk, int *numMatches);
int FreeCharacters (void);
int FreeMatrix (void);
int FreeTaxa (void);
int GetNumPartDivisions (int n);
int GetUserHelp (char *helpTkn);
int IsAmbig (int charCode, int dType);
int IsMissing (int charCode, int dType);
int MBResID (char nuc);
int NucID (char nuc);
void PrintSettings (char *command);
void PrintYesNo (int yn, char s[4]);
int ProtID (char aa);
int SetPartition (int part);
int SetSpeciespartition (int part);
int SetTaxaFromTranslateTable (void);
int StandID (char nuc);
void WhatVariableExp (BitsLong exp, char *st);
MrBFlt WhichCont (int x);
/* globals */
int autoClose; /* autoclose */
int autoOverwrite; /* Overwrite or append outputfiles when nowarnings=yes */
Calibration *calibrationPtr; /* ptr to calibration being set */
CharInformation *charInfo; /* holds critical information about characters */
BitsLong **charSet; /* holds information about defined charsets */
char **charSetNames; /* holds names of character sets */
Comptree comptreeParams; /* holds parameters for comparetree command */
char **constraintNames; /* holds names of constraints */
int dataType; /* type of data */
Calibration defaultCalibration; /* default calibration */
BitsLong **definedConstraint; /* bitfields representing taxa sets of defined constraints */
BitsLong **definedConstraintTwo; /* bitfields representing second taxa sets of defined constraints (used for PARTIAL constraints) */
BitsLong **definedConstraintPruned; /* bitfields representing taxa sets of defined constraints after deleted taxa are removed */
BitsLong **definedConstraintTwoPruned; /* bitfields representing second taxa sets of defined constraints for PARTIAL constraints after deleted*/
/* taxa are removed and for NEGATIVE constraint it contains complements of definedConstraintPruned */
int echoMB; /* flag used by Manual to prevent echoing */
BitsLong expecting; /* variable denoting expected token type */
int foundNewLine; /* whether a new line has been found */
int inComment; /* flag for whether input stream is commented */
int inComparetreeCommand; /* flag set whenever you enter comparetree cmd */
int inferAncStates; /* should ancestral states be inferred (y/n) */
int inferSiteOmegas; /* should site omegas be inferred (y/n) */
int inferSiteRates; /* should site rates be inferred (y/n) */
int inMrbayesBlock; /* flag for whether we are in a mrbayes block */
int inSumtCommand; /* flag set whenever you enter sumt cmd */
int inTreesBlock; /* flag for whether we are in a trees block */
int inValidCommand; /* a useful flag set whenever you enter a cmd */
int isInAmbig, isInPoly; /* flags whether we are within () or {} */
int isTaxsetDef; /* is a taxon set defined */
int isTranslateDef; /* is a translation block defined */
int isTranslateDiff; /* is translate different from current taxaset? */
char logFileName[100]; /* name of the log file */
int logToFile; /* should screen output be logged to a file */
FILE *logFileFp; /* file pointer to log file */
int longIntegerSize; /* size of an unsigned integer */
char manFileName[100]; /* name of the file for the command help info */
int *matrix; /* matrix containing original data */
int matrixHasPoly; /* flag for whether matrix has polymorphisms */
int memAllocs[NUM_ALLOCS]; /* allocated memory flags */
int mode; /* mode of program (interactive/noninteractive) */
Calibration *nodeCalibration; /* holds information about node calibrations */
int noWarn; /* no warnings on overwriting files */
int numChar; /* number of characters in character matrix */
int numCharSets; /* number of character sets */
int numComments; /* counts how deeply nested a comment is */
int numDefinedConstraints; /* number of constraints defined */
int numDefinedPartitions; /* number of partitions defined */
int numDefinedSpeciespartitions; /* number of speciespartitions defined */
int numNamedTaxa; /* number of named taxa during parsing of cmd */
int numOpenExeFiles; /* number of execute files open */
int numSpecies; /* number of species in current speciespartition */
int numTaxa; /* number of taxa in character matrix */
int numTaxaSets; /* number of taxa sets */
int numTranslates; /* number of taxa in active translate block */
int outGroupNum; /* number of outgroup taxon */
ParmInfo paramTable[NUMPARAMS]; /* information on parameters */
char **partitionNames; /* hold names of partitions (first is "default") */
int **partitionId; /* holds information about defined partitions */
int partitionNum; /* index of current partition */
Plot plotParams; /* holds parameters for plot command */
int precision; /* precision of samples and summary stats */
int quitOnError; /* quit on error? */
int replaceLogFile; /* should logfile be replace/appended to */
int scientific; /* use scientific format for samples ? */
char spacer[10]; /* holds blanks for printing indentations */
NameSet *speciesNameSets; /* hold species name sets, one for each speciespartition */
int **speciespartitionId; /* holds info about defined speciespartitions */
char **speciespartitionNames; /* hold names of speciespartitions (first is "default") */
int speciespartitionNum; /* index of current speciespartition */
Sump sumpParams; /* holds parameters for sump command */
Sumt sumtParams; /* holds parameters for sumt command */
Sumss sumssParams; /* holds parameters for sumss command */
TaxaInformation *taxaInfo; /* holds critical information about taxa */
char **taxaNames; /* holds name of taxa */
BitsLong **taxaSet; /* holds information about defined taxasets */
char **taxaSetNames; /* holds names of taxa sets */
int *tempActiveConstraints;/* temporarily holds active constraints size allocated */
enum ConstraintType *definedConstraintsType; /* Store type of constraint */
int *tempSet; /* temporarily holds defined set */
int *tempSetNeg; /* holds bitset of negative set of taxa for partial constraint*/
int theAmbigChar; /* int containing ambiguous character */
Calibration *tipCalibration; /* holds information about node calibrations */
char **transFrom; /* translation block information */
char **transTo; /* translation block information */
int userBrlensDef; /* are the branch lengths on user tree defined */
#if defined (BEAGLE_ENABLED)
int tryToUseBEAGLE; /* try to use the BEAGLE library */
int beagleScalingScheme; /* BEAGLE dynamic scaling */
int beagleScalingFrequency;/* BEAGLE dynamic scaling frequency */
long beagleFlags; /* BEAGLE required resource flags */
int beagleResourceNumber; /* BEAGLE resource number */
int *beagleResource; /* BEAGLE resource choice list */
int beagleResourceCount; /* BEAGLE resource choice list length */
int beagleInstanceCount; /* total number of BEAGLE instances */
#if defined (BEAGLE_V3_ENABLED)
int beagleThreadCount; /* max number of BEAGLE CPU threads */
int beagleAllFloatTips; /* use floating-point representation for all tips */
#endif
#endif
/* local (to this file) */
char *tokenP, token[CMD_STRING_LENGTH], *cmdStr=NULL;
Calibration defaultCalibration = {
"Unconstrained", /* name */
unconstrained, /* prior */
{ -1.0, -1.0, -1.0 }, /* priorParams */
NULL, /* LnPriorProb */
NULL, /* LnPriorRatio */
-1.0, /* min */
-1.0 /* max */
};
CmdType commands[] =
{
/* Information on commands initialization:
1 = Command number (cmdNumber)
2 = Command name (string)
3 = Special command (YES/NO) (specialCmd)
4 = Pointer to finishing function (fp)
5 = Number of valid parameters (numParms)
6 = List of valid parameters (parmList)
7 = Expecting (2^TokenType) (expect) (PARAMETER = 4; SEMICOLON = 32; ALPHA = 16384;
ALPHA | QUESTIONMARK | DASH | NUMBER | ASTERISK | EXCLAMATIONMARK | PERCENT | WEIRD | SEMICOLON = 11715360;
ALPHA | QUESTIONMARK | DASH | NUMBER | ASTERISK | EXCLAMATIONMARK | PERCENT | WEIRD | VERTICALBAR | SEMICOLON | LEFTPAR | RIGHTPAR | LEFTCURL | RIGHTCURL = 649252640;
PARAMETER | SEMICOLON = 36; NUMBER | ALPHA = 49152; ALPHA | SEMICOLON = 16416; EQUALSIGN = 8; NUMBER = 32768)
8 = Description of the command (cmdDescription)
9 = Where should the command be used (cmdUse) (IN_CMD = used from command line or mrbayes block; IN_FILE = used in data block or in tree block)
10 = Should the command be shown when "help" is typed (hiding).
#1 #2 #3 #4 #5 #6 #7 #8 #9 #10
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- */
{ 0, "#", NO, NULL, 1, {0}, 4, "", IN_FILE, HIDE },
{ 1, "About", NO, DoAbout, 0, {-1}, 32, "Describes the program", IN_CMD, SHOW },
{ 2, "Acknowledgments", NO, DoAcknowledgments, 0, {-1}, 32, "Shows program acknowledgments", IN_CMD, SHOW },
{ 3, "Begin", NO, NULL, 6, {1,2,3,201,226,227}, 4, "Denotes beginning of block in file", IN_FILE, SHOW },
{ 4, "Calibrate", NO, DoCalibrate, 1, {119}, 4, "Assigns dates to terminals or interior nodes", IN_CMD, SHOW },
{ 5, "Charset", NO, DoCharset, 1, {15}, 4, "Assigns a group of sites to a set", IN_CMD, SHOW },
{ 6, "Charstat", NO, DoCharStat, 0, {-1}, 32, "Shows status of characters", IN_CMD, SHOW },
{ 7, "Citations", NO, DoCitations, 0, {-1}, 32, "Citation of program, models, and methods", IN_CMD, SHOW },
{ 8, "Comparetree", NO, DoCompareTree, 7, {127,128,129,130,221,222,223}, 36, "Compares the trees from two tree files", IN_CMD, SHOW },
{ 9, "Constraint", NO, DoConstraint, 1, {66}, 4, "Defines a constraint on tree topology", IN_CMD, SHOW },
{ 10, "Ctype", NO, DoCtype, 1, {65}, 4, "Assigns ordering for the characters", IN_CMD, SHOW },
{ 11, "Databreaks", YES, DoBreaks, 1, {93}, 32768, "Defines data breaks for autodiscrete gamma model", IN_CMD, SHOW },
{ 12, "Delete", YES, DoDelete, 1, {47}, 49152, "Deletes taxa from the analysis", IN_CMD, SHOW },
{ 13, "Dimensions", NO, DoDimensions, 2, {4,5}, 4, "Defines size of character matrix", IN_FILE, SHOW },
{ 14, "Disclaimer", NO, DoDisclaimer, 0, {-1}, 32, "Describes program disclaimer", IN_CMD, SHOW },
{ 15, "End", NO, DoEndBlock, 0, {-1}, 32, "Denotes end of a block in file", IN_FILE, SHOW },
{ 16, "Endblock", NO, DoEndBlock, 0, {-1}, 32, "Alternative way of denoting end of a block", IN_FILE, SHOW },
{ 17, "Exclude", YES, DoExclude, 1, {45}, 49152, "Excludes sites from the analysis", IN_CMD, SHOW },
{ 18, "Execute", YES, DoExecute, 1, {12}, 16384, "Executes a file", IN_CMD, SHOW },
{ 19, "Format", NO, DoFormat, 7, {6,7,8,9,10,219,220}, 4, "Defines character format in data block", IN_FILE, SHOW },
{ 20, "Help", YES, DoHelp, 1, {50}, 16416, "Provides detailed description of commands", IN_CMD, SHOW },
{ 21, "Include", YES, DoInclude, 1, {46}, 49152, "Includes sites", IN_CMD, SHOW },
{ 22, "Link", NO, DoLink, 30, {55,56,57,58,59,60,61,62,63,72,73,74,75,76,105,118,193,194,195,196,197,242,243,252,253,255,256,
270,273,274}, 4, "Links parameters across character partitions", IN_CMD, SHOW },
{ 23, "Log", NO, DoLog, 5, {85,86,87,88,89}, 4, "Logs screen output to a file", IN_CMD, SHOW },
{ 24, "Lset", NO, DoLset, 20, {28,29,30,31,32,33,34,40,51,52,53,90,91,131,188,189,276,277,280,282},4, "Sets the parameters of the likelihood model", IN_CMD, SHOW },
{ 25, "Manual", NO, DoManual, 1, {126}, 36, "Prints a command reference to a text file", IN_CMD, SHOW },
{ 26, "Matrix", YES, DoMatrix, 1, {11},649252640, "Defines matrix of characters in data block", IN_FILE, SHOW },
{ 27, "Mcmc", NO, DoMcmc, 46, {17,18,19,20,21,22,23,24,25,26,27,84,98,112,113,114,115,116,132,142,143,144,148,149,150,151,152,
153,154,155,156,157,158,159,160,166,169,190,191,198,199,200,202,213,214,215}, 36, "Starts Markov chain Monte Carlo analysis", IN_CMD, SHOW },
{ 28, "Mcmcp", NO, DoMcmcp, 46, {17,18,19,20,21,22,23,24,25,26,27,84,98,112,113,114,115,116,132,142,143,144,148,149,150,151,152,
153,154,155,156,157,158,159,160,166,169,190,191,198,199,200,202,213,214,215}, 4, "Sets parameters of a chain (without starting analysis)", IN_CMD, SHOW },
{ 29, "Outgroup", YES, DoOutgroup, 1, {78}, 49152, "Changes outgroup taxon", IN_CMD, SHOW },
{ 30, "Pairs", YES, DoPairs, 1, {92}, 32768, "Defines nucleotide pairs (doublets) for stem models", IN_CMD, SHOW },
{ 31, "Partition", NO, DoPartition, 1, {16}, 4, "Assigns a character partition", IN_CMD, SHOW },
{ 32, "Plot", NO, DoPlot, 6, {106,107,108,109,224,225}, 36, "Plots parameters from MCMC analysis", IN_CMD, SHOW },
{ 33, "Prset", NO, DoPrset, 44, {35,36,37,38,39,41,42,43,44,54,64,67,68,69,70,71,77,100,101,102,103,104,110,111,117,120,121,133,
168,172,173,174,183,184,185,218,241,246,247,251,254,269,271,272}, 4, "Sets the priors for the parameters", IN_CMD, SHOW },
{ 34, "Propset", NO, DoPropset, 1, {186}, 4, "Sets proposal probabilities and tuning parameters", IN_CMD, SHOW },
{ 35, "Quit", NO, DoQuit, 0, {-1}, 32, "Quits the program", IN_CMD, SHOW },
{ 36, "Report", NO, DoReport, 9, {122,123,124,125,134,135,136,192,217}, 4, "Controls how model parameters are reported", IN_CMD, SHOW },
{ 37, "Restore", YES, DoRestore, 1, {48}, 49152, "Restores taxa", IN_CMD, SHOW },
{ 38, "Set", NO, DoSet, 23, {13,14,94,145,170,171,179,181,182,216,229,233,234,235,236,238,239,240,245,268,275,278,279}, 4, "Sets run conditions and defines active data partition", IN_CMD, SHOW },
{ 39, "Showbeagle", NO, DoShowBeagle, 0, {-1}, 32, "Show available BEAGLE resources", IN_CMD, SHOW },
{ 40, "Showmatrix", NO, DoShowMatrix, 0, {-1}, 32, "Shows current character matrix", IN_CMD, SHOW },
{ 41, "Showmcmctrees", NO, DoShowMcmcTrees, 0, {-1}, 32, "Shows trees used in MCMC analysis", IN_CMD, SHOW },
{ 42, "Showmodel", NO, DoShowModel, 0, {-1}, 32, "Shows model settings", IN_CMD, SHOW },
{ 43, "Showmoves", NO, DoShowMoves, 1, {180}, 36, "Shows moves for current model", IN_CMD, SHOW },
{ 44, "Showparams", NO, DoShowParams, 0, {-1}, 32, "Shows parameters in current model", IN_CMD, SHOW },
{ 45, "Showusertrees", NO, DoShowUserTrees, 0, {-1}, 32, "Shows user-defined trees", IN_CMD, SHOW },
{ 46,"Speciespartition", NO,DoSpeciespartition, 1, {244}, 4, "Defines a partition of tips into species", IN_CMD, SHOW },
{ 47, "Ss", NO, DoSs, 50, {17,18,19,20,21,22,23,24,25,26,27,84,98,112,113,114,115,116,132,142,143,144,148,149,150,151,152,
153,154,155,156,157,158,159,160,166,169,190,191,198,199,200,202,213,214,215,248,249,250,257}, 36, "Starts stepping-stone sampling", IN_CMD, SHOW },
{ 48, "Ssp", NO, DoSsp, 50, {17,18,19,20,21,22,23,24,25,26,27,84,98,112,113,114,115,116,132,142,143,144,148,149,150,151,152,
153,154,155,156,157,158,159,160,166,169,190,191,198,199,200,202,213,214,215,248,249,250,257}, 36,"Sets parameters of stepping-stone analysis (without starting)",IN_CMD, SHOW },
{ 49, "Startvals", NO, DoStartvals, 1, {187}, 4, "Sets starting values of parameters", IN_CMD, SHOW },
{ 50, "Sump", NO, DoSump, 14, {96,97,137,138,139,140,141,161,162,176,178,211,212,231}, 36, "Summarizes parameters from MCMC analysis", IN_CMD, SHOW },
{ 51, "Sumss", NO, DoSumSs, 10, {258,259,260,261,262,263,264,265,266,267}, 36, "Summarizes parameters from stepping-stone analysis", IN_CMD, SHOW },
{ 52, "Sumt", NO, DoSumt, 21, {80,81,82,95,146,147,163,164,165,167,175,177,204,205,206,207,208,209,210,230,232}, 36, "Summarizes trees from MCMC analysis", IN_CMD, SHOW },
{ 53, "Taxastat", NO, DoTaxaStat, 0, {-1}, 32, "Shows status of taxa", IN_CMD, SHOW },
{ 54, "Taxset", NO, DoTaxaset, 1, {49}, 4, "Assigns a group of taxa to a set", IN_CMD, SHOW },
{ 55, "Taxlabels", YES, DoTaxlabels, 1, {228}, 49152, "Defines taxon labels", IN_FILE, SHOW },
{ 56, "Translate", YES, DoTranslate, 1, {83}, 49152, "Defines alternative names for taxa", IN_FILE, SHOW },
{ 57, "Tree", NO, DoTree, 1, {79}, 4, "Defines a tree", IN_FILE, SHOW },
{ 58, "Unlink", NO, DoUnlink, 30, {55,56,57,58,59,60,61,62,63,72,73,74,75,76,105,118,193,194,195,196,197,242,243,252,253,255,256,
270,273,274}, 4, "Unlinks parameters across character partitions", IN_CMD, SHOW },
{ 59, "Usertree", YES, DoUserTree, 1, {203}, 8, "Defines a single user tree", IN_CMD, HIDE },
{ 60, "Version", NO, DoVersion, 0, {-1}, 32, "Shows program version", IN_CMD, SHOW },
{ 61, "Compareref", NO, DoCompRefTree, 7, {127,128,129,130,221,222,223}, 36, "Compares the tree to the reference trees", IN_CMD, HIDE },
/* NOTE: If you add a command here, make certain to change NUMCOMMANDS (above, in this file) appropriately! */
{ 999, NULL, NO, NULL, 0, {-1}, 32, "", IN_CMD, HIDE }
};
int inDataBlock, inForeignBlock, isInterleaved, isFirstMatrixRead, isFirstInterleavedBlock,
taxonCount, fromI, toJ, everyK, foundDash, foundSlash, foundFirst, isMixed, whichPartition,
isNegative, numDivisions, charOrdering, foundExp, foundColon, isFirstNode, nextAvailableNode,
pairId, firstPair, inTaxaBlock, inCharactersBlock, foundEqual;
char gapId, missingId, matchId, tempSetName[100], **tempNames;
CmdType *commandPtr; /* Points to the commands array entry which corresponds to currently processed command */
ParmInfoPtr paramPtr; /* Points to paramTable table array entry which corresponds to currently processed parameter of current command */
TreeNode *pPtr, *qPtr;
enum ConstraintType constraintType; /* Used only in processing of constraint command to indicate the type of constraint */
int AddToGivenSet (int i, int j, int k, int id, int *Set)
{
int m, n;
if (id <= 0)
{
MrBayesPrint ("%s The id for a temporary set should be greater than 0\n", spacer);
return (ERROR);
}
if (i < 0 && j < 0)
return (ERROR);
else if (i < 0 && j >= 0)
return (ERROR);
else if (i >= 0 && j < 0)
{
if (k >= 0)
return (ERROR);
else
{
if (Set[i] != 0)
{
MrBayesPrint ("%s Character %d defined more than once\n", spacer, i+1);
return (ERROR);
}
Set[i] = id;
}
}
else if (i >= 0 && j >= 0)
{
if (k < 0)
{
for (m=i; m<=j; m++)
{
if (Set[m] != 0)
{
MrBayesPrint ("%s Character %d defined more than once\n", spacer, m+1);
return (ERROR);
}
Set[m] = id;
}
}
else
{
n = k;
for (m=i; m<=j; m++)
{
if (n % k == 0)
{
if (Set[m] != 0)
{
MrBayesPrint ("%s Character %d defined more than once\n", spacer, m+1);
return (ERROR);
}
Set[m] = id;
}
n++;
}
}
}
return (NO_ERROR);
}
int AddToSet (int i, int j, int k, int id)
{
return AddToGivenSet (i, j, k,id, tempSet);
}
/* AddNameSet: Push a name set onto the end of a list of name sets, with reallocation
of list to hold the extra element. The calling function needs to keep track of
the counter holding the length of the list. */
int AddNameSet (NameSet **nameSetList, int numNameSets, char **nameSet, int numNames)
{
int i;
(*nameSetList) = (NameSet*) SafeRealloc ((void*)(*nameSetList), ((size_t)numNameSets+1)*sizeof(NameSet));
(*nameSetList)[numNameSets].names = NULL;
(*nameSetList)[numNameSets].numNames = numNames;
for (i=0; i<numNames; i++)
AddString(&((*nameSetList)[numNameSets].names), i, nameSet[i]);
return NO_ERROR;
}
/* AddString: Push a string onto the end of a list, with reallocation of list
to hold the extra element. The calling function needs to keep track of
the counter holding the length of the list. */
int AddString (char ***list, int len, char *token)
{
(*list) = (char **) SafeRealloc ((void *)(*list), ((size_t)len+1)*sizeof(char*));
if (!(*list))
return ERROR;
(*list)[len] = (char *) SafeCalloc ((strlen(token)+1), sizeof(char));
if (!(*list)[len])
return ERROR;
strcpy ((*list)[len], token);
return NO_ERROR;
}
int AllocCharacters (void)
{
int i, tempSetSize;
if (memAllocs[ALLOC_MATRIX] == YES)
goto errorExit;
matrix = (int *) SafeMalloc((size_t)numTaxa * (size_t)numChar * sizeof(int));
if (!matrix)
{
MrBayesPrint ("%s Problem allocating matrix (%d)\n", spacer, numTaxa * numChar * sizeof(int));
goto errorExit;
}
for (i=0; i<numTaxa * numChar; i++)
matrix[i] = 0;
memAllocs[ALLOC_MATRIX] = YES;
if (memAllocs[ALLOC_CHARINFO] == YES)
goto errorExit;
charInfo = (CharInformation *) SafeMalloc ((size_t)numChar * sizeof(CharInformation));
if (!charInfo)
{
MrBayesPrint ("%s Problem allocating charInfo (%d)\n", spacer, numChar * sizeof(CharInformation));
goto errorExit;
}
for (i=0; i<numChar; i++)
{
charInfo[i].isExcluded = NO;
charInfo[i].numStates = 0;
charInfo[i].charType = 0;
charInfo[i].isMissAmbig = NO;
charInfo[i].ctype = UNORD;
charInfo[i].charId = 0;
charInfo[i].pairsId = 0;
charInfo[i].bigBreakAfter = NO;
}
memAllocs[ALLOC_CHARINFO] = YES;
if (memAllocs[ALLOC_CHARSETS] == YES)
goto errorExit;
charSetNames = NULL;
charSet = NULL;
numCharSets = 0;
memAllocs[ALLOC_CHARSETS] = YES; /* safe to do free */
if (memAllocs[ALLOC_PARTITIONS] == YES)
goto errorExit;
partitionNames = NULL;
partitionId = (int**) SafeMalloc ((size_t)numChar * sizeof(int*));
for (i=0; i<numChar; i++)
partitionId[i] = (int *) SafeMalloc (sizeof(int));
numDefinedPartitions = 0; /* number of defined partitions */
memAllocs[ALLOC_PARTITIONS] = YES; /* safe to do free */
if (memAllocs[ALLOC_PARTITIONVARS] == YES)
goto errorExit;
numVars = NULL;
tempLinkUnlinkVec = NULL;
activeParts = NULL;
tempLinkUnlinkVec = NULL;
tempNum = NULL;
linkTable[0] = NULL;
tempLinkUnlink[0] = NULL;
for (i=0; i<NUM_LINKED; i++)
{
linkTable[i] = NULL;
tempLinkUnlink[i] = NULL;
activeParams[i] = NULL;
}
memAllocs[ALLOC_PARTITIONVARS] = YES;
if (memAllocs[ALLOC_TMPSET] == NO)
goto errorExit;
if (numChar > numTaxa)
tempSetSize = numChar;
else
tempSetSize = numTaxa;
tempSet = (int *) SafeRealloc ((void *)tempSet, (size_t)tempSetSize * sizeof(int));
tempSetNeg = (int *) SafeRealloc ((void *)tempSetNeg, (size_t)tempSetSize * sizeof(int));
if (!tempSet || !tempSetNeg)
{
MrBayesPrint ("%s Problem reallocating tempSet (%d)\n", spacer, tempSetSize * sizeof(int));
goto errorExit;
}
MrBayesPrint ("%s Allocated matrix\n", spacer);
return (NO_ERROR);
errorExit:
MrBayesPrint ("%s Problem allocating matrix\n", spacer);
FreeMatrix();
return (ERROR);
}
int AllocMatrix (void)
{
if (memAllocs[ALLOC_TAXA] == NO && AllocTaxa() == ERROR)
return ERROR;
else
return (AllocCharacters());
}
int AllocTaxa (void)
{
int i;
if (defTaxa == NO)
{
MrBayesPrint ("%s Number of taxa not defined\n", spacer);
return (ERROR);
}
if (numTaxa == 0)
{
MrBayesPrint ("%s Number of taxa is 0\n", spacer);
return (ERROR);
}
/* allocate space for taxa */
if (memAllocs[ALLOC_TAXA] == YES)
goto errorExit;
taxaNames = NULL; /* This variable is allocated in AddString */
taxaInfo =
(TaxaInformation *) SafeMalloc ((size_t) numTaxa *
sizeof (TaxaInformation));
if (!taxaInfo)
goto errorExit;
tipCalibration =
(Calibration *) SafeMalloc ((size_t) numTaxa * sizeof (Calibration));
if (!tipCalibration)
{
free (taxaInfo);
taxaInfo = NULL;
goto errorExit;
}
for (i = 0; i < numTaxa; i++)
{
taxaInfo[i].isDeleted = NO;
taxaInfo[i].charCount = 0;
}
memAllocs[ALLOC_TAXA] = YES;
/* taxa sets */
if (memAllocs[ALLOC_TAXASETS] == YES)
goto errorExit;
taxaSetNames = NULL;
taxaSet = NULL;
numTaxaSets = 0;
memAllocs[ALLOC_TAXASETS] = YES; /* safe to free */
/* species partitions; allocate space and set default species partition */
if (memAllocs[ALLOC_SPECIESPARTITIONS] == YES)
goto errorExit;
speciespartitionNames = NULL;
speciesNameSets = NULL;
speciespartitionId =
(int **) SafeMalloc ((size_t) numTaxa * sizeof (int *));
for (i = 0; i < numTaxa; i++)
{
speciespartitionId[i] = (int *) SafeMalloc (sizeof (int));
speciespartitionId[i][0] = i + 1; /* 1-based taxon index, do not ask me why */
}
numDefinedSpeciespartitions = 0; /* number of defined species partitions */
memAllocs[ALLOC_SPECIESPARTITIONS] = YES; /* safe to do free */
/* constraints */
if (memAllocs[ALLOC_CONSTRAINTS] == YES)
goto errorExit;
constraintNames = NULL;
definedConstraintsType = NULL;
definedConstraint = NULL;
definedConstraintTwo = NULL;
definedConstraintPruned = NULL;
definedConstraintTwoPruned = NULL;
numDefinedConstraints = 0;
tempActiveConstraints = NULL;
memAllocs[ALLOC_CONSTRAINTS] = YES; /* safe to free */
/* translate table */
transFrom = NULL;
transTo = NULL;
numTranslates = 0;
/* tempSet */
if (memAllocs[ALLOC_TMPSET] == YES)
goto errorExit;
tempSet = (int *) SafeMalloc ((size_t) numTaxa * sizeof (int));
tempSetNeg = (int *) SafeMalloc ((size_t) numTaxa * sizeof (int));
if (!tempSet || !tempSetNeg)
goto errorExit;
memAllocs[ALLOC_TMPSET] = YES;
/* make sure previous user trees are freed */
if (numUserTrees > 0)
{
MrBayesPrint ("%s Previous user trees not freed\n", spacer);
goto errorExit;
}
MrBayesPrint ("%s Allocated taxon set\n", spacer);
return NO_ERROR;
errorExit:
MrBayesPrint ("%s Problem allocating taxon set\n", spacer);
FreeTaxa();
return ERROR;
}
char ChangeCase (char c)
{
int x;
x = tolower(c);
return (x);
}
int CharacterCode (char ch, int *charCode, int chType)
{
if (chType == DNA || chType == RNA)
{
if ((*charCode = NucID (ch)) == -1)
{
MrBayesPrint ("%s Unrecognized DNA/RNA character '%c'\n", spacer, ch);
return (ERROR);
}
}
else if (chType == PROTEIN)
{
if ((*charCode = ProtID (ch)) == -1)
{
MrBayesPrint ("%s Unrecognized Protein character '%c'\n", spacer, ch);
return (ERROR);
}
}
else if (chType == RESTRICTION)
{
if ((*charCode = MBResID (ch)) == -1)
{
MrBayesPrint ("%s Unrecognized Restriction character '%c'\n", spacer, ch);
return (ERROR);
}
}
else if (chType == STANDARD)
{
if ((*charCode = StandID (ch)) == -1)
{
MrBayesPrint ("%s Unrecognized Standard character '%c'\n", spacer, ch);
return (ERROR);
}
}
else if (chType == CONTINUOUS)
{
MrBayesPrint ("%s CharacterCode function cannot check continuous characters\n", spacer);
}
else
{
MrBayesPrint ("%s Unrecognized character type (%d)\n", spacer, chType);
return (ERROR);
}
return (NO_ERROR);
}
int CharacterNumber (int charCode, int chType)
{
int i, x = charCode;
if (chType == CONTINUOUS)
return 0;
for (i=0; x!=0; i++)
x >>= 1;
return (i);
}
int CheckInitialPartitions (void)
{
int i;
for (i=0; i<numChar; i++)
{
if (partitionId[i][0] <= 0 || partitionId[i][0] > numDivisions)
{
MrBayesPrint ("%s The partition for site %d is incorrect\n", spacer, i+1);
return (ERROR);
}
}
return (NO_ERROR);
}
int CheckStringValidity (char *s)
{
int i, numUnknownChars, tempNumComments, tempInComment;
char temp[100];
i = 0;
numUnknownChars = 0;
tempNumComments = numComments;
tempInComment = inComment;
while (s[i] != '\0')
{
if (tempInComment == NO)
{
if (!IsIn(s[i],"=abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ_0123456789.;:,#()[]?-*/'\\'!%\"&~+^$@|{}`>< "))
{
if (IsWhite(s[i]) == 1 || IsWhite(s[i]) == 2)
{
}
else
{
if (commandPtr == NULL)
return (ERROR);
MrBayesPrint ("%s Unknown character \"%c\" (ASCII code %d)\n", spacer, s[i], s[i]);
if (!strcmp(commandPtr->string,"Matrix"))
{
if (foundNewLine == NO)
{
MrBayesPrint ("%s The error is in character %d for taxon %s\n", spacer, taxaInfo[taxonCount-1].charCount+i+1, "???"); /* bug? */
}
else
{
if (taxonCount == 0)
MrBayesPrint ("%s The error is in the first taxon name\n", spacer);
else
{
strcpy(temp, taxaNames[taxonCount]);
if (isInterleaved == NO)
MrBayesPrint ("%s The error is in the name of the taxon following taxon %s\n", spacer, temp);
else
{
MrBayesPrint ("%s The error is in the name of the taxon following taxon %s\n", spacer, temp);
MrBayesPrint ("%s in one of the interleaved data blocks\n", spacer);
}
}
}
}
else if (!strcmp(commandPtr->string,"Execute"))
{
MrBayesPrint ("%s Assuming irrelevant characters at beginning of file; processing continues\n", spacer);
return (NO_ERROR);
}
return (ERROR);
}
}
if (s[i]=='[')
{
tempInComment = YES;
tempNumComments++;
}
}
else if (tempInComment == YES)
{
if (s[i]==']')
{
tempNumComments--;
if (tempNumComments == 0)
tempInComment = NO;
}
}
i++;
}
if (numUnknownChars > 0)
return (ERROR);
else
return (NO_ERROR);
}
/* CheckString: This function simply checks a vector of strings for a match against token.
Upon return, matchIndex contains the index of the matched string. An
ERROR is returned if there are no matches. */
int CheckString (char **list, int len, char *token, int *matchIndex)
{
int i;
*matchIndex = -1;
for (i=0; i<len; i++)
{
if (StrCmpCaseInsensitive(token,list[i]) == 0)
{
*matchIndex = i;
return (NO_ERROR);
}
}
return (ERROR);
}
int Dex (TreeNode *p)
{
return (p == NULL) ? -1 : p->index;
}
int DoAbout (void)
{
MrBayesPrint (" --------------------------------------------------------------------------- \n");
MrBayesPrint (" About the program \n");
MrBayesPrint (" \n");
MrBayesPrint (" MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian \n");
MrBayesPrint (" inference of phylogeny is based upon the posterior probability distribution \n");
MrBayesPrint (" of trees. Trees are labelled T1, T2, ..., Tn, where n is the number of \n");
MrBayesPrint (" possible trees. The posterior probability of the i-th tree is calculated \n");
MrBayesPrint (" using Bayes\'s formula as \n");
MrBayesPrint (" \n");
MrBayesPrint (" Pr[Ti | X] = Pr[X | Ti] X Pr[Ti] / Pr[X] \n");
MrBayesPrint (" \n");
MrBayesPrint (" where X is a character matrix. Here, \"Pr[Ti | X]\" is the posterior \n");
MrBayesPrint (" probability of the i-th tree, \"Pr[X | Ti]\" is the likelihood of the \n");
MrBayesPrint (" i-th tree, and \"Pr[Ti]\" is the prior probability of the i-th tree. The \n");
MrBayesPrint (" denominator of Bayes\'s formula (\"Pr[X]\") is a normalizing constant that \n");
MrBayesPrint (" involves a summation over all possible trees. The likelihood, as described \n");
MrBayesPrint (" above, cannot be calculated with knowledge of only the tree\'s topology. You \n");
MrBayesPrint (" also need to have information on the lengths of the branches and on the \n");
MrBayesPrint (" mechanism of character change. Hence, the likelihood (\"Pr[X | Ti]\") \n");
MrBayesPrint (" involves a multidimensional integral over all possible combinations of \n");
MrBayesPrint (" branch lengths and substitution model parameters. \n");
MrBayesPrint (" \n");
MrBayesPrint (" In practice, it is impossible to calculate the posterior probability dist- \n");
MrBayesPrint (" ribution of trees analytically. Instead, the posterior probability \n");
MrBayesPrint (" of trees must be approximated. MrBayes uses a method called Markov chain \n");
MrBayesPrint (" Monte Carlo (MCMC) to approximate the posterior probability of trees. \n");
MrBayesPrint (" The object of MCMC is to construct a Markov chain that has as its state \n");
MrBayesPrint (" space the parameters of the phylogenetic model and a stationary distribution \n");
MrBayesPrint (" that is the posterior probability distribution of trees. MCMC takes valid, \n");
MrBayesPrint (" albeit dependent, samples from the posterior probability distribution of \n");
MrBayesPrint (" trees. The fraction of the time any tree appears in this sample is a \n");
MrBayesPrint (" valid approximation of the posterior probability of the tree. MrBayes keeps \n");
MrBayesPrint (" track of all the parameters of the phylogenetic model. The trees (with branch \n");
MrBayesPrint (" lengths) that were sampled by the MCMC procedure are saved in one file \n");
MrBayesPrint (" (a file with a \".t\" extension) whereas the parameters of the model of \n");
MrBayesPrint (" character change are saved in another file (a file with a \".p\" ext- \n");
MrBayesPrint (" ension). You can summarize the results in the \".t\" and \".p\" files \n");
MrBayesPrint (" using the \"sumt\" and \"sump\" commands, respectively. \n");
MrBayesPrint (" \n");
MrBayesPrint (" MrBayes was originally written by John Huelsenbeck in August of 2000 and was \n");
MrBayesPrint (" intended to be distributed to a small number of people. In March of 2001, \n");
MrBayesPrint (" Fredrik Ronquist started making contributions to the program. The contribu- \n");
MrBayesPrint (" tions were of such a significant nature that he was made a coauthor of the \n");
MrBayesPrint (" program. Version 3 of MrBayes was a fully joint effort, started in the summer \n");
MrBayesPrint (" of 2002 when JPH visited Sweden on a grant from the Wenner-Gren Foundations. \n");
MrBayesPrint (" Several others have contributed to the MrBayes code since then, most notably \n");
MrBayesPrint (" Paul van der Mark, Maxim Teslenko and Chi Zhang, all postdocs/programmers in \n");
MrBayesPrint (" Fredrik's lab. A large number of users and students, too many to list here, \n");
MrBayesPrint (" have also contributed importantly to the project (type 'Acknowledgments' for \n");
MrBayesPrint (" a list of some of them). \n");
MrBayesPrint (" \n");
MrBayesPrint (" From 2003, MrBayes was distributed from SourceForge; the repository was moved \n");
MrBayesPrint (" to GitHub in 2018, when the project entered maintenance phase and the res- \n");
MrBayesPrint (" ponsibility was transferred to National Bioinformatics Infrastructure Sweden \n");
MrBayesPrint (" (https://nbis.se), where Andreas Kahari and Johan Nylander jointly take care \n");
MrBayesPrint (" of bug fixes, documentation updates, and other maintenance tasks. \n");
MrBayesPrint (" --------------------------------------------------------------------------- \n");
return (NO_ERROR);
}
int DoAcknowledgments (void)
{
MrBayesPrint (" --------------------------------------------------------------------------- \n");
MrBayesPrint (" Acknowledgments \n");
MrBayesPrint (" \n");
MrBayesPrint (" JPH and FR would like to thank Gautam Altekar, Andrea Betancourt, Jon \n");
MrBayesPrint (" Bollback, Barry Hall, Jimmy McGuire, Rasmus Nielsen, David Swofford, \n");
MrBayesPrint (" Johan Nylander, Mikael Thollesson, and Derrick Zwickl for help during the \n");
MrBayesPrint (" initial development of this program. Gautam Altekar, especially, was instru- \n");
MrBayesPrint (" mental in getting the parallel version of the program working. Important bug- \n");
MrBayesPrint (" fixes and additional functionality was contributed by Clemens Lakner, Sebas- \n");
MrBayesPrint (" tian Hoehna, Paul Lewis, Mark Holder, Julian Catchen and Bret Larget. Marc \n");
MrBayesPrint (" Suchard, Daniel Ayres and Aaron Darling got MrBayes working with beagle and \n");
MrBayesPrint (" contributed a lot of related functionality and bug fixes. Aaron Darling was \n");
MrBayesPrint (" instrumental in getting the Windows installer set up. Liu Liang and Dennis \n");
MrBayesPrint (" Pearl helped integrate MrBayes with BEST. \n");
MrBayesPrint (" \n");
MrBayesPrint (" Bug fixes and user support was provided by Paul van der Mark (2005-2007), \n");
MrBayesPrint (" Maxim Teslenko (2010-2012) and Chi Zhang (2012-2015). From 2015, Andreas \n");
MrBayesPrint (" Kahari and Johan Nylander at the National Bioinformatics Infrastructure \n");
MrBayesPrint (" Sweden (NBIS; https://nbis.se) have been responsible for bug fixes and \n");
MrBayesPrint (" maintenance of the code base. \n");
MrBayesPrint (" \n");
MrBayesPrint (" Our wives -- Edna Huelsenbeck and Eva Ronquist -- showed extraordinary \n");
MrBayesPrint (" patience with us while we spent many late nights programming. \n");
MrBayesPrint (" \n");
MrBayesPrint (" JPH was supported by NSF grants DEB-007540 and MCB-0075404 and a Wenner- \n");
MrBayesPrint (" Gren scholarship while writing this program. FR was supported by grants \n");
MrBayesPrint (" from the Swedish Natural Science Research Council and the Swedish Research \n");
MrBayesPrint (" Council, which also supports NBIS work on MrBayes. \n");
MrBayesPrint (" --------------------------------------------------------------------------- \n");