/* * MrBayes 3 * * (c) 2002-2010 * * John P. Huelsenbeck * Dept. Integrative Biology * University of California, Berkeley * Berkeley, CA 94720-3140 * johnh@berkeley.edu * * Fredrik Ronquist * Swedish Museum of Natural History * Box 50007 * SE-10405 Stockholm, SWEDEN * fredrik.ronquist@nrm.se * * With important contributions by * * Paul van der Mark (paulvdm@sc.fsu.edu) * Maxim Teslenko (maxim.teslenko@nrm.se) * * and by many users (run 'acknowledgements' 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 #include #include #include #include #include #include #include "mb.h" #include "mbbeagle.h" #include "globals.h" #include "command.h" #include "bayes.h" #include "model.h" #include "mcmc.h" #include "plot.h" #include "sump.h" #include "sumt.h" #include "tree.h" #include "utils.h" #if defined (BEAGLE_ENABLED) #include "libhmsbeagle/beagle.h" #endif #if defined(__MWERKS__) #include "SIOUX.h" #endif const char* const svnRevisionCommandC="$Rev: 513 $"; /* Revision keyword which is expended/updated by svn on each commit/update*/ #define NUMCOMMANDS 61 /* Note: NUMCOMMANDS gives the total number */ /* of commands in the program */ #define NUMPARAMS 269 #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 DoShowMatrix (void); int DoShowUserTrees (void); int DoShowBeagle (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 NBits (int x); int NucID (char nuc); void PrintSettings (char *command, ModelInfo *mp); 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 (SafeLong exp, char *st); char WhichAA (int x); MrBFlt WhichCont (int x); char WhichRes (int x); char WhichStand (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 */ SafeLong **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 */ SafeLong **definedConstraint; /* bitfields representing taxa sets of defined constraints */ SafeLong **definedConstraintTwo;/* bitfields representing second taxa sets of defined constraints (used for PARTIAL constraints) */ SafeLong **definedConstraintPruned; /* bitfields representing taxa sets of defined constraints after delited taxa are removed */ SafeLong **definedConstraintTwoPruned;/* bitfields representing second taxa sets of defined constraints for PARTIAL constraints after delited*/ /* taxa are removed and for NEGATIVE constraint it contains complements of definedConstraintPruned */ int echoMB; /* flag used by Manual to prevent echoing */ SafeLong 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 */ SafeLong **taxaSet; /* holds information about defined taxasets */ char **taxaSetNames; /* holds names of taxa sets */ int *tempActiveConstraints;/* temporarily holds active constraints size allcated */ 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 *beagleResource; /* BEAGLE resource choice list */ int beagleResourceCount; /* BEAGLE resource choice list length */ int beagleInstanceCount; /* total number of BEAGLE instances */ #endif #if defined (THREADS_ENABLED) int tryToUseThreads; /* try to use pthreads with BEAGLE library */ #endif /* local (to this file) */ char *tokenP, token[CMD_STRING_LENGTH], *cmdStr=NULL; Calibration defaultCalibration = { /* name = */ "Unconstrained", /* prior = */ 0, /* = unconstrained */ /* max = */ -1.0, /* min = */ -1.0, /* offset = */ -1.0, /* lambda = */ -1.0, /* age = */ -1.0}; 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 | SEMICOLON | LEFTPAR | RIGHTPAR | LEFTCURL | RIGHTCURL = 112381728; 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, 27, {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}, 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, 16, {28,29,30,31,32,33,34,40,51,52,53,90,91,131,188,189}, 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},112381728, "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 the 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, 41, {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}, 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, 22, {13,14,94,145,170,171,179,181,182,216,229,233,234,235,236,237,238,239,240,245,268}, 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 the parameters of a stepping-stone (without starting)", IN_CMD, SHOW }, { 49, "Startvals", NO, DoStartvals, 1, {187}, 4, "Sets starting values of parameters", IN_CMD, SHOW }, { 50, "Sump", NO, DoSump, 13, {96,97,137,138,139,140,141,161,162,178,211,212,231}, 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, 23, {55,56,57,58,59,60,61,62,63,72,73,74,75,76,105,118,193,194,195,196,197,242,243}, 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 }, /* 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 } }; static int fromI, toJ, isNegative, foundDash, foundExp, foundEqual; int inDataBlock, inForeignBlock, isInterleaved, isFirstMatrixRead, isFirstInterleavedBlock, taxonCount, everyK, foundSlash, foundFirst, isMixed, whichPartition, numDivisions, charOrdering, foundColon, isFirstNode, nextAvailableNode, pairId, firstPair, inTaxaBlock, inCharactersBlock; char gapId, missingId, matchId, tempSetName[100], **tempNames; CmdType *commandPtr; /*Points to the commands array entery which corresponds to currently processed command*/ ParmInfoPtr paramPtr; /*Points to paramTable table array entery which corresponds to currently processed parameter of current command*/ TreeNode *pPtr, *qPtr; enum ConstraintType consrtainType; /* Used only in processing of constraine command to indicate what is the type of constrain */ 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 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 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 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; iindex; } 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 lenths 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 and Maxim Teslenko, both postdocs/programmers in Fredrik's \n"); MrBayesPrint (" lab. A large number of users and students, too many to list here, have also \n"); MrBayesPrint (" contributed importantly to the project (type 'Acknowledgments' for a list of \n"); MrBayesPrint (" some of them). \n"); MrBayesPrint (" \n"); MrBayesPrint (" Since 2003, MrBayes has been distributed from SourceForge. Bugs can be repor- \n"); MrBayesPrint (" ted to the MrBayes site on SourceForge or by contacting Maxim Teslenko \n"); MrBayesPrint (" (maxim.teslenko@nrm.se) directly. \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) and \n"); MrBayesPrint (" from 2010 by Maxim Teslenko (maxim.teslenko@nrm.se). \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. \n"); MrBayesPrint (" --------------------------------------------------------------------------- \n"); return (NO_ERROR); } int DoBeginParm (char *parmName, char *tkn) { if (expecting == Expecting(PARAMETER)) { /* set Data (inDataBlock) *************************************************************/ if (!strcmp(parmName, "Data")) { if (FreeModel () == ERROR) return (ERROR); if (FreeMatrix () == ERROR) return (ERROR); MrBayesPrint (" Reading data block\n"); inDataBlock = YES; expecting = Expecting(SEMICOLON); strcpy (spacer, " "); } /* set Characters (inCharactersBlock) *************************************************************/ else if (!strcmp(parmName, "Characters")) { if (FreeModel () == ERROR) return (ERROR); if (FreeCharacters () == ERROR) return (ERROR); MrBayesPrint (" Reading characters block\n"); inCharactersBlock = YES; expecting = Expecting(SEMICOLON); strcpy (spacer, " "); } /* set Taxa (inTaxaBlock) *************************************************************/ else if (!strcmp(parmName, "Taxa")) { if (FreeModel () == ERROR) return (ERROR); if (FreeMatrix () == ERROR) return (ERROR); MrBayesPrint (" Reading taxa block\n"); inTaxaBlock = YES; expecting = Expecting(SEMICOLON); strcpy (spacer, " "); } /* set Mrbayes (inMrbayesBlock) *******************************************************/ else if (!strcmp(parmName, "Mrbayes")) { MrBayesPrint (" Reading mrbayes block\n"); inMrbayesBlock = YES; expecting = Expecting(SEMICOLON); strcpy (spacer, " "); } /* set Trees (inTreesBlock) *******************************************************/ else if (!strcmp(parmName, "Trees")) { MrBayesPrint (" Reading trees block\n"); inTreesBlock = YES; expecting = Expecting(SEMICOLON); strcpy (spacer, " "); } /* set Foreign (inForeignBlock) *******************************************************/ else { MrBayesPrint (" Skipping \"%s\" block\n", tkn); inForeignBlock = YES; expecting = Expecting(SEMICOLON); strcpy (spacer, ""); } } else return (ERROR); return (NO_ERROR); } int DoBreaks (void) { int i, numBreaks; numBreaks = 0; for (i=0; i 0) { if (numBreaks == 1) MrBayesPrint ("%s One data break found after character ", spacer, numBreaks); else MrBayesPrint ("%s %d data breaks found after characters: ", spacer, numBreaks); for (i=0; i numChar) { MrBayesPrint ("%s Character number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numChar); for (i=0; i 1) { MrBayesPrint ("%s Both a taxon and a constraint named ""%s"" encountered -- please rename one\n", spacer, tkn); return (ERROR); } if (calibrationPtr->prior != unconstrained) { MrBayesPrint ("%s Resetting previous calibration for ""%s""\n", spacer, tkn); } /* reset the values of the calibration */ calibrationPtr->prior = defaultCalibration.prior; calibrationPtr->age = defaultCalibration.age; calibrationPtr->lambda = defaultCalibration.lambda; calibrationPtr->offset = defaultCalibration.offset; calibrationPtr->min = defaultCalibration.min; calibrationPtr->max = defaultCalibration.max; strcpy(calibrationPtr->name, defaultCalibration.name); /* get ready to find the equal sign */ expecting = Expecting(EQUALSIGN); } else if (expecting == Expecting(EQUALSIGN)) { /* get ready to find the calibration prior */ expecting = Expecting(ALPHA); } else if (expecting == Expecting(ALPHA)) { /* set the calibration prior type */ if (IsArgValid(tkn,tempStr) == NO_ERROR) { if (!strcmp (tempStr, "Uniform")) calibrationPtr->prior = uniform; else if (!strcmp (tempStr, "Offsetexponential")) calibrationPtr->prior = offsetExponential; else if (!strcmp (tempStr, "Fixed")) calibrationPtr->prior = fixed; else /* if (!strcmp (tempStr, "Unconstrained")) */ calibrationPtr->prior = unconstrained; strcpy (calibrationPtr->name, tempStr); if (calibrationPtr->prior == unconstrained) expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); else expecting = Expecting(LEFTPAR); } else { MrBayesPrint ("%s Invalid calibration prior argument \n", spacer); return (ERROR); } } else if (expecting == Expecting(LEFTPAR)) { strcat (calibrationPtr->name, "("); expecting = Expecting(NUMBER); } else if (expecting == Expecting(NUMBER)) { if (calibrationPtr->prior == fixed) { sscanf (tkn, "%lf", &tempD); if (tempD < 0.0) { MrBayesPrint ("%s Age must be nonnegative\n", spacer); calibrationPtr->prior = unconstrained; return (ERROR); } calibrationPtr->age = tempD; expecting = Expecting(RIGHTPAR); } else if (calibrationPtr->prior == uniform) { sscanf (tkn, "%lf", &tempD); if (tempD < 0.0) { MrBayesPrint ("%s Age must be nonnegative\n", spacer); calibrationPtr->prior = unconstrained; return (ERROR); } if (calibrationPtr->min < 0.0) { calibrationPtr->min = tempD; expecting = Expecting(COMMA); } else { if (tempD <= calibrationPtr->min) { MrBayesPrint ("%s Maximum age must be larger than minimum age\n", spacer); calibrationPtr->prior = unconstrained; return (ERROR); } calibrationPtr->max = tempD; expecting = Expecting(RIGHTPAR); } } else if (calibrationPtr->prior == offsetExponential) { sscanf (tkn, "%lf", &tempD); if (calibrationPtr->offset < 0.0) { if (tempD < 0.0) { MrBayesPrint ("%s Offset age must be nonnegative\n", spacer); calibrationPtr->prior = unconstrained; return (ERROR); } calibrationPtr->offset = tempD; expecting = Expecting(COMMA); } else { if (tempD <= OFFSETEXPLAMBDA_MIN) { MrBayesPrint ("%s Offset exponential lambda parameter must be larger than %lf\n", spacer, OFFSETEXPLAMBDA_MIN); calibrationPtr->prior = unconstrained; return (ERROR); } else if (tempD >= OFFSETEXPLAMBDA_MAX) { MrBayesPrint ("%s Offset exponential lambda parameter must be smaller than %lf\n", spacer, OFFSETEXPLAMBDA_MAX); calibrationPtr->prior = unconstrained; return (ERROR); } calibrationPtr->lambda = tempD; expecting = Expecting(RIGHTPAR); } } sprintf (s, "%1.2lf", tempD); strcat (calibrationPtr->name, s); } else if (expecting == Expecting(COMMA)) { strcat (calibrationPtr->name, ","); expecting = Expecting(NUMBER); } else if (expecting == Expecting(RIGHTPAR)) { strcat (calibrationPtr->name, ")"); if (isTaxon == YES) MrBayesPrint ("%s Setting age of taxon '%s' to %s\n", spacer, nodeName, calibrationPtr->name); else MrBayesPrint ("%s Setting age of constraint node '%s' to %s\n", spacer, nodeName, calibrationPtr->name); /* get ready to find more calibrated nodes or taxa, if present */ expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); return (NO_ERROR); } int DoCharset (void) { /* first add set to tempSet */ if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } /* add name to charSetNames */ if (AddString (&charSetNames, numCharSets, tempSetName) == ERROR) { MrBayesPrint ("%s Problem adding charset %s to list\n", spacer, tempSetName); return (ERROR); } /* store charset */ AddBitfield (&charSet, numCharSets, tempSet, numChar); /* increment number of char sets */ numCharSets++; return (NO_ERROR); } int DoCharsetParm (char *parmName, char *tkn) { int i, index, tempInt, allDigit; if (defMatrix == NO) { MrBayesPrint ("%s A matrix must be specified before charsets can be defined\n", spacer); return (ERROR); } if (expecting == Expecting(PARAMETER)) { if (!strcmp(parmName, "Xxxxxxxxxx")) { /* check that the name of the charset is not a number */ allDigit = YES; for (i=0; i<(int)strlen(tkn); i++) { if (tkn[i] == '0' || tkn[i] == '1' || tkn[i] == '2' || tkn[i] == '3' || tkn[i] == '4' || tkn[i] == '5' || tkn[i] == '6' || tkn[i] == '7' || tkn[i] == '8' || tkn[i] == '9' || tkn[i] == '.') {} else allDigit = NO; } if (allDigit == YES) { MrBayesPrint ("%s Charset name may not be a number\n", spacer); return (ERROR); } /* check size of charset name */ if (strlen(tkn) > 99) { MrBayesPrint ("%s Charset name is too long\n", spacer); return (ERROR); } /* check to see if the name has already been used as a charset */ if (numCharSets > 1) { if (CheckString (charSetNames, numCharSets, tkn, &index) == ERROR) { /* if the charset name has not been used, then we should have an ERROR returned */ /* we _want_ to be here */ } else { MrBayesPrint ("%s Charset name has been used previously\n", spacer); return (ERROR); } } /* add the name to the character set */ strcpy (tempSetName, tkn); /* clear tempSet */ for (i=0; i numChar) { MrBayesPrint ("%s Character number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numChar); return (ERROR); } tempInt--; if (foundDash == YES) { if (fromI >= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted charset\n", spacer); return (ERROR); } foundDash = NO; } else if (foundSlash == YES) { tempInt++; if (tempInt <= 1) { MrBayesPrint ("%s Improperly formatted charset\n", spacer); return (ERROR); } if (fromI >= 0 && toJ >= 0 && fromI < toJ) everyK = tempInt; else { MrBayesPrint ("%s Improperly formatted charset\n", spacer); return (ERROR); } foundSlash = NO; } else { if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; } else if (fromI < 0 && toJ < 0) { fromI = tempInt; } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted charset\n", spacer); { return (ERROR); } } } expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(SEMICOLON); expecting |= Expecting(DASH); expecting |= Expecting(BACKSLASH); } else if (expecting == Expecting(DASH)) { foundDash = YES; expecting = Expecting(NUMBER); } else if (expecting == Expecting(BACKSLASH)) { foundSlash = YES; expecting = Expecting(NUMBER); } else return (ERROR); return (NO_ERROR); } int DoCharStat (void) { int i, j, numDivs; char tempName[100]; if (defMatrix == NO) { MrBayesPrint ("%s A character matrix must be defined first\n", spacer); return (ERROR); } if (numDefinedPartitions == 1) MrBayesPrint ("%s 1 character partition defined:\n", spacer, numDefinedPartitions); else MrBayesPrint ("%s %d character partitions defined:\n", spacer, numDefinedPartitions); for (i=0; i 0) { /* find paired character */ for (j=0; j= 0 && toJ < 0) { if (AddToGivenSet (fromI, toJ, everyK, 1, tset) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToGivenSet (fromI, toJ, everyK, 1, tset) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToGivenSet (fromI, toJ, everyK, 1, tset) == ERROR) return (ERROR); } /* check that this is not a stupid constraint */ howMany = 0; for (i=0; i 99) { MrBayesPrint ("%s Constraint name is too long\n", spacer); return (ERROR); } /* check to see if the name has already been used as a constraint */ if (numDefinedConstraints > 0) { if (CheckString (constraintNames, numDefinedConstraints, tkn, &index) == ERROR) { /* if the constraint name has not been used, then we should have an ERROR returned */ /* we _want_ to be here */ } else { MrBayesPrint ("%s Constraint name '%s' has been used previously\n", spacer, tkn); return (ERROR); } } /* copy the name to the temporary constraint names string */ strcpy (tempSetName, tkn); /* clear tempSet */ for (i=0; i numTaxa) { MrBayesPrint ("%s Taxon number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numTaxa); return (ERROR); } } tempInt--; if (foundDash == YES) { if (fromI >= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted constraint\n", spacer); return (ERROR); } foundDash = NO; } else if (foundSlash == YES) { tempInt++; if (tempInt <= 1) { MrBayesPrint ("%s Improperly formatted constraint\n", spacer); return (ERROR); } if (fromI >= 0 && toJ >= 0 && fromI < toJ) everyK = tempInt; else { MrBayesPrint ("%s Improperly formatted constraint\n", spacer); return (ERROR); } foundSlash = NO; } else { if (fromI >= 0 && toJ < 0) { if (AddToGivenSet (fromI, toJ, everyK, 1, tempSetCurrent) == ERROR) return (ERROR); fromI = tempInt; } else if (fromI < 0 && toJ < 0) { fromI = tempInt; } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToGivenSet (fromI, toJ, everyK, 1, tempSetCurrent) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToGivenSet (fromI, toJ, everyK, 1, tempSetCurrent) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted constraint\n", spacer); { return (ERROR); } } } expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(DASH); expecting |= Expecting(BACKSLASH); if( consrtainType != PARTIAL || foundColon == YES ) expecting |= Expecting(SEMICOLON); else expecting |= Expecting(COLON); } } else if (expecting == Expecting(BACKSLASH)) { foundSlash = YES; expecting = Expecting(NUMBER); } else if (expecting == Expecting(COLON)) { if( foundColon == YES ) { MrBayesPrint ("%s Improperly formatted constraint: two colon charactors in constraint command.\n", spacer); return (ERROR); } /* add set to tempSet */ if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } fromI = toJ = everyK = -1; foundDash = foundSlash = NO; foundColon = YES; tempSetCurrent = tempSetNeg; expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); } else return (ERROR); return (NO_ERROR); } int DoCtype (void) { int i, foundIllegal, marks[5], numAppliedTo; /* add set to tempSet */ if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } /* merge tempSet with ctype */ numAppliedTo = 0; for (i=0; i<5; i++) marks[i] = NO; for (i=0; i 0) { MrBayesPrint ("%s Ctype was applied to %d standard characters\n", spacer, numAppliedTo); } else { MrBayesPrint ("%s No standard characters found to apply ctype to\n", spacer); } # if 0 for (i=0; i numChar) { MrBayesPrint ("%s Character number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numChar); return (ERROR); } tempInt--; if (foundDash == YES) { if (fromI >= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted ctype\n", spacer); return (ERROR); } foundDash = NO; } else if (foundSlash == YES) { tempInt++; if (tempInt <= 1) { MrBayesPrint ("%s Improperly formatted ctype\n", spacer); return (ERROR); } if (fromI >= 0 && toJ >= 0 && fromI < toJ) everyK = tempInt; else { MrBayesPrint ("%s Improperly formatted ctype\n", spacer); return (ERROR); } foundSlash = NO; } else { if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; } else if (fromI < 0 && toJ < 0) { fromI = tempInt; } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted ctype\n", spacer); { return (ERROR); } } } expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(SEMICOLON); expecting |= Expecting(DASH); expecting |= Expecting(BACKSLASH); } else if (expecting == Expecting(DASH)) { foundDash = YES; expecting = Expecting(NUMBER); } else if (expecting == Expecting(BACKSLASH)) { foundSlash = YES; expecting = Expecting(NUMBER); } else return (ERROR); return (NO_ERROR); } int DoDelete (void) { int i, alreadyDone; MrBayesPrint ("%s Excluding taxa\n", spacer); /* add set to tempSet */ if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } /* merge tempSet with taxaset */ alreadyDone = NO; for (i=0; i= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } tempSet[index] = 1; } } foundDash = NO; fromI = toJ = everyK = -1; expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(SEMICOLON); } else if (expecting == Expecting(NUMBER)) { if (strlen(tkn) == 1 && !strcmp(tkn, ".")) tempInt = numTaxa; else { sscanf (tkn, "%d", &tempInt); if (tempInt <= 0 || tempInt > numTaxa) { MrBayesPrint ("%s Taxon number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numTaxa); return (ERROR); } } tempInt--; if (foundDash == YES) { if (fromI >= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted delete set\n", spacer); return (ERROR); } foundDash = NO; } else { if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; } else if (fromI < 0 && toJ < 0) { fromI = tempInt; } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted delete set\n", spacer); { return (ERROR); } } } expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(SEMICOLON); expecting |= Expecting(DASH); } else if (expecting == Expecting(DASH)) { foundDash = YES; expecting = Expecting(NUMBER); } else return (ERROR); return (NO_ERROR); MrBayesPrint ("%s", parmName); /*just because I am tired of seeing the unused parameter error msg */ } int DoDimensions (void) { if (inDataBlock == NO && inTaxaBlock == NO && inCharactersBlock == NO) { MrBayesPrint ("%s Dimensions can only be defined in a data, characters or taxa block\n", spacer); return (ERROR); } /* other problems are detected already when reading in DoDimensionsParm */ if (inDataBlock == YES && (defTaxa == NO || defChars == NO)) { MrBayesPrint ("%s Expecting both Ntax and Nchar to be defined in a data block\n", spacer); return (ERROR); } /* allocate matrix */ if (inTaxaBlock == YES) { if (AllocTaxa () == ERROR) return ERROR; MrBayesPrint ("%s Defining new set of %d taxa\n", spacer, numTaxa); } if (inCharactersBlock == YES) { if (AllocMatrix() == ERROR) return (ERROR); MrBayesPrint ("%s Defining new character matrix with %d characters\n", spacer, numChar); } if (inDataBlock == YES) { if (AllocMatrix() == ERROR) return (ERROR); MrBayesPrint ("%s Defining new matrix with %d taxa and %d characters\n", spacer, numTaxa, numChar); } return (NO_ERROR); } int DoDimensionsParm (char *parmName, char *tkn) { if (expecting == Expecting(PARAMETER)) { expecting = Expecting(EQUALSIGN); } else { /* set Ntax (numTaxa) *****************************************************************/ if (!strcmp(parmName, "Ntax")) { if (inCharactersBlock == YES) { MrBayesPrint ("%s You cannot define ntax in a characters block\n"); return (ERROR); } if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(NUMBER); else if (expecting == Expecting(NUMBER)) { sscanf (tkn, "%d", &numTaxa); defTaxa = YES; expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Nchar (numChar) ****************************************************************/ else if (!strcmp(parmName, "Nchar")) { if (inTaxaBlock == YES) { MrBayesPrint ("%s You cannot define nchar in a taxa block\n"); return (ERROR); } if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(NUMBER); else if (expecting == Expecting(NUMBER)) { sscanf (tkn, "%d", &numChar); defChars = YES; expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } else return (ERROR); } return (NO_ERROR); } int DoDisclaimer (void) { MrBayesPrint (" --------------------------------------------------------------------------- \n"); MrBayesPrint (" Disclaimer \n"); MrBayesPrint (" \n"); MrBayesPrint (" Copyright 2003 by John P. Huelsenbeck and Fredrik Ronquist \n"); MrBayesPrint (" \n"); MrBayesPrint (" This software package is provided \"as is\" and without a warranty of any \n"); MrBayesPrint (" kind. In no event shall the authors be held responsible for any damage \n"); MrBayesPrint (" resulting from the use of this software. The program--including source code, \n"); MrBayesPrint (" example data sets, and executables--is distributed free of charge for \n"); MrBayesPrint (" academic use only. \n"); MrBayesPrint (" --------------------------------------------------------------------------- \n"); return (NO_ERROR); } int DoEndBlock (void) { if (inMrbayesBlock == YES) { MrBayesPrint (" Exiting mrbayes block\n"); inMrbayesBlock = NO; } else if (inDataBlock == YES) { MrBayesPrint (" Exiting data block\n"); inDataBlock = NO; } else if (inCharactersBlock == YES) { MrBayesPrint (" Exiting characters block\n"); inCharactersBlock = NO; } else if (inTaxaBlock == YES) { MrBayesPrint (" Exiting taxa block\n"); if (numNamedTaxa < numTaxa) { MrBayesPrint ("%s Leaving taxa block without taxon labels being defined\n", spacer); FreeTaxa(); } inTaxaBlock = NO; } else if (inTreesBlock == YES) { MrBayesPrint (" Exiting trees block\n"); inTreesBlock = NO; ResetTranslateTable(); } else if (inForeignBlock == YES) { MrBayesPrint (" Exiting foreign block\n"); inForeignBlock = NO; } else { MrBayesPrint (" Unknown \"end\" statement\n"); return (ERROR); } strcpy(spacer,""); /* reset indentation */ return (NO_ERROR); } int DoExecute (void) { int c, i, rc, cmdLine, lineTerm, longestLineLength, nErrors; char *s, exeFileName[100]; FILE *fp; CmdType *oldCommandPtr; # if defined (MPI_ENABLED) int sumErrors; # endif nErrors = 0; cmdLine = 0; numOpenExeFiles++; s = NULL; strncpy(exeFileName, inputFileName, 98); if (numOpenExeFiles > 1) MrBayesPrint ("\n%s Executing file \"%s\"...\n\n", spacer, inputFileName); else MrBayesPrint ("%s Executing file \"%s\"\n", spacer, inputFileName); /* Save old command ptr */ oldCommandPtr = commandPtr; /* open binary file */ if ((fp = OpenBinaryFileR(inputFileName)) == NULL) nErrors++; /* set indentation to 0 */ strcpy (spacer, ""); # if defined (MPI_ENABLED) MPI_Allreduce (&nErrors, &sumErrors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); if (sumErrors > 0) { MrBayesPrint ("%s There was an error on at least one processor\n", spacer); goto errorExit; } # else if (nErrors > 0) goto errorExit; # endif /* find out what type of line termination is used */ lineTerm = LineTermType (fp); if (lineTerm == LINETERM_MAC) MrBayesPrint ("%s Macintosh line termination\n", spacer); else if (lineTerm == LINETERM_DOS) MrBayesPrint ("%s DOS line termination\n", spacer); else if (lineTerm == LINETERM_UNIX) MrBayesPrint ("%s UNIX line termination\n", spacer); else { MrBayesPrint ("%s Unknown line termination\n", spacer); nErrors++; } # if defined (MPI_ENABLED) MPI_Allreduce (&nErrors, &sumErrors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); if (sumErrors > 0) { MrBayesPrint ("%s There was an error on at least one processor\n", spacer); goto errorExit; } # else if (nErrors > 0) goto errorExit; # endif /* find length of longest line */ longestLineLength = LongestLine (fp); MrBayesPrint ("%s Longest line length = %d\n", spacer, longestLineLength); longestLineLength += 50; /* check that longest line is not longer than CMD_STRING_LENGTH */ if (longestLineLength >= CMD_STRING_LENGTH - 100) { /*MrBayesPrint ("%s A maximum of %d characters is allowed on a single line\n", spacer, CMD_STRING_LENGTH - 100);*/ MrBayesPrint ("%s The longest line of the file %s\n", spacer, inputFileName); MrBayesPrint ("%s contains at least one line with %d characters.\n", spacer, longestLineLength); } /* # if defined (MPI_ENABLED) MPI_Allreduce (&nErrors, &sumErrors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); if (sumErrors > 0) { MrBayesPrint ("%s There was an error on at least one processor\n", spacer); goto errorExit; } # else if (nErrors > 0) goto errorExit; # endif */ /* allocate a string long enough to hold a line */ s = (char *)SafeMalloc((size_t) (longestLineLength * sizeof(char))); if (!s) { MrBayesPrint ("%s Problem allocating string for reading file\n", spacer); nErrors++; } # if defined (MPI_ENABLED) MPI_Allreduce (&nErrors, &sumErrors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); if (sumErrors > 0) { MrBayesPrint ("%s There was an error on at least one processor\n", spacer); goto errorExit; } # else if (nErrors > 0) goto errorExit; # endif /* close binary file */ SafeFclose (&fp); /* open text file */ if ((fp = OpenTextFileR(inputFileName)) == NULL) { nErrors++; } # if defined (MPI_ENABLED) MPI_Allreduce (&nErrors, &sumErrors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); if (sumErrors > 0) { MrBayesPrint ("%s There was an error on at least one processor\n", spacer); goto errorExit; } # else if (nErrors > 0) goto errorExit; # endif /* parse file, reading each line in turn */ MrBayesPrint ("%s Parsing file\n", spacer); inMrbayesBlock = inDataBlock = inForeignBlock = inTreesBlock = NO; foundNewLine = NO; expecting = Expecting(COMMAND); cmdLine = 0; do { /* read in a new line into s */ i = 0; do { c = fgetc(fp); if (c == '\r' || c == '\n' || c == EOF) s[i++] = '\n'; else s[i++] = c; } while (s[i-1] != '\n'); s[i] = '\0'; foundNewLine = YES; cmdLine++; /* process string if not empty */ if (strlen(s) > 1) { /* check that all characters in the string are valid */ if (CheckStringValidity (s) == ERROR) { nErrors++; } # if defined (MPI_ENABLED) MPI_Allreduce (&nErrors, &sumErrors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); if (sumErrors > 0) { MrBayesPrint ("%s There was an error on at least one processor\n", spacer); goto errorExit; } # else if (nErrors > 0) goto errorExit; # endif /* interpret commands on line */ rc = ParseCommand (s); if (rc == ERROR) nErrors++; # if defined (MPI_ENABLED) MPI_Allreduce (&nErrors, &sumErrors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); if (sumErrors > 0) { MrBayesPrint ("%s There was an error on at least one processor\n", spacer); goto errorExit; } # else if (nErrors > 0) goto errorExit; # endif if (rc == NO_ERROR_QUIT) nErrors++; # if defined (MPI_ENABLED) MPI_Allreduce (&nErrors, &sumErrors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); if (sumErrors > 0) goto quitExit; # else if (nErrors > 0) goto quitExit; # endif } } while (c != EOF); MrBayesPrint ("%s Reached end of file\n", spacer); if (inComment == YES) nErrors++; # if defined (MPI_ENABLED) MPI_Allreduce (&nErrors, &sumErrors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); if (sumErrors > 0) { MrBayesPrint ("%s There was an error on at least one processor\n", spacer); goto errorExit; } # else if (nErrors > 0) goto errorExit; # endif if (s) free (s); SafeFclose (&fp); numOpenExeFiles--; if (numOpenExeFiles > 0) { inMrbayesBlock = YES; MrBayesPrint ("\n Returning execution to calling file ...\n\n"); strcpy (spacer, " "); } else strcpy (spacer, ""); commandPtr = oldCommandPtr; return (NO_ERROR); quitExit: if (s) free (s); SafeFclose (&fp); numOpenExeFiles--; if (numOpenExeFiles > 0) { inMrbayesBlock = YES; strcpy (spacer, " "); } else strcpy (spacer, ""); commandPtr = oldCommandPtr; return (NO_ERROR_QUIT); errorExit: if (inComment == YES) { MrBayesPrint ("%s ERROR: Reached end of file while in comment.\n", spacer); inComment = NO; numComments = 0; } if (fp) { MrBayesPrint ("%s The error occurred when reading char. %d on line %d\n", spacer, tokenP-cmdStr-strlen(token)+1, cmdLine); MrBayesPrint ("%s in the file '%s'\n", spacer, exeFileName); } if (s) free (s); SafeFclose (&fp); numOpenExeFiles--; /* we increase the value above even if no file is successfully opened */ /* make sure we exit the block we were reading from correctly */ if (inMrbayesBlock == YES) inMrbayesBlock = NO; else if (inDataBlock == YES) inDataBlock = NO; else if (inTreesBlock == YES) { inTreesBlock = NO; ResetTranslateTable(); } else if (inForeignBlock == YES) inForeignBlock = NO; /* make sure correct return if we came from mrbayes block in another execute file */ if (numOpenExeFiles > 0) { inMrbayesBlock = YES; MrBayesPrint ("\n Returning execution to calling file ...\n\n"); strcpy (spacer, " "); commandPtr = oldCommandPtr; return (ERROR); } else strcpy (spacer, ""); commandPtr = oldCommandPtr; return (ERROR); } int DoExecuteParm (char *parmName, char *tkn) { if(strlen(tkn)>99) { MrBayesPrint ("%s Maximum allowed length of file name is 99 characters. The given name:\n", spacer); MrBayesPrint ("%s '%s'\n", spacer,tkn); MrBayesPrint ("%s has %d characters.\n", spacer,strlen(tkn)); return (ERROR); } strcpy (inputFileName, tkn); expecting = Expecting (SEMICOLON); return (NO_ERROR); MrBayesPrint ("%s", parmName); /* just because I am tired of seeing the unused parameter error msg */ } int DoExclude (void) { int i, alreadyDone; MrBayesPrint ("%s Excluding character(s)\n", spacer); /* add set to tempSet */ if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } /* merge tempSet with charset */ alreadyDone = NO; for (i=0; i numChar) { MrBayesPrint ("%s Character number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numChar); return (ERROR); } tempInt--; if (foundDash == YES) { if (fromI >= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted exclude set\n", spacer); return (ERROR); } foundDash = NO; } else if (foundSlash == YES) { tempInt++; if (tempInt <= 1) { MrBayesPrint ("%s Improperly formatted exclude set\n", spacer); return (ERROR); } if (fromI >= 0 && toJ >= 0 && fromI < toJ) everyK = tempInt; else { MrBayesPrint ("%s Improperly formatted exclude set\n", spacer); return (ERROR); } foundSlash = NO; } else { if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; } else if (fromI < 0 && toJ < 0) { fromI = tempInt; } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted exclude set\n", spacer); { return (ERROR); } } } expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(SEMICOLON); expecting |= Expecting(DASH); expecting |= Expecting(BACKSLASH); } else if (expecting == Expecting(DASH)) { foundDash = YES; expecting = Expecting(NUMBER); } else if (expecting == Expecting(BACKSLASH)) { foundSlash = YES; expecting = Expecting(NUMBER); } else return (ERROR); return (NO_ERROR); MrBayesPrint ("%s", parmName); /* just because I am tired of seeing the unused parameter error msg */ } int DoFormat (void) { if (inDataBlock == NO && inCharactersBlock == NO) { MrBayesPrint ("%s Formats can only be defined in a data or characters block\n", spacer); return (ERROR); } return CheckInitialPartitions(); } int DoFormatParm (char *parmName, char *tkn) { int i, tempInt; char tempStr[100]; static int foundQuote; if (inDataBlock == NO && inCharactersBlock == NO) { MrBayesPrint ("%s Formats can only be defined in a data or characters block\n", spacer); return (ERROR); } if (defTaxa == NO || defChars == NO) { MrBayesPrint ("%s The dimensions of the matrix must be defined before the format\n", spacer); return (ERROR); } if (expecting == Expecting(PARAMETER)) { expecting = Expecting(EQUALSIGN); if (!strcmp(parmName, "Interleave")) { expecting = Expecting(EQUALSIGN) | Expecting(PARAMETER) | Expecting(SEMICOLON); isInterleaved = YES; } } else { /* set Datatype (dataType) ************************************************************/ if (!strcmp(parmName, "Datatype")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (isMixed == NO) { if (!strcmp(tempStr, "Dna")) dataType = DNA; else if (!strcmp(tempStr, "Rna")) dataType = RNA; else if (!strcmp(tempStr, "Protein")) dataType = PROTEIN; else if (!strcmp(tempStr, "Restriction")) dataType = RESTRICTION; else if (!strcmp(tempStr, "Standard")) dataType = STANDARD; else if (!strcmp(tempStr, "Continuous")) dataType = CONTINUOUS; else if (!strcmp(tempStr, "Mixed")) { dataType = MIXED; isMixed = YES; for (i=0; i numChar) { MrBayesPrint ("%s Character number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numChar); return (ERROR); } tempInt--; if (foundDash == YES) { if (fromI >= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted partition\n", spacer); return (ERROR); } foundDash = NO; } else if (foundSlash == YES) { tempInt++; if (tempInt <= 1) { MrBayesPrint ("%s Improperly formatted partition\n", spacer); return (ERROR); } if (fromI >= 0 && toJ >= 0 && fromI < toJ) everyK = tempInt; else { MrBayesPrint ("%s Improperly formatted partition\n", spacer); return (ERROR); } foundSlash = NO; } else { if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, numDivisions+1) == ERROR) return (ERROR); fromI = tempInt; } else if (fromI < 0 && toJ < 0) { fromI = tempInt; } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, numDivisions+1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, numDivisions+1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted partition\n", spacer); { return (ERROR); } } } expecting = Expecting(NUMBER); expecting |= Expecting(DASH); expecting |= Expecting(BACKSLASH); expecting |= Expecting(COMMA); expecting |= Expecting(RIGHTPAR); } else if (expecting == Expecting(DASH)) { foundDash = YES; expecting = Expecting(NUMBER); } else if (expecting == Expecting(BACKSLASH)) { foundSlash = YES; expecting = Expecting(NUMBER); } else if (expecting == Expecting(COMMA)) { /* add set to tempSet */ if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, numDivisions+1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, numDivisions+1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, numDivisions+1) == ERROR) return (ERROR); } for (i=0; i= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, numDivisions+1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, numDivisions+1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, numDivisions+1) == ERROR) return (ERROR); } /* merge tempSet */ for (i=0; i 1) MrBayesPrint ("%s There are a total of %d default data divisions\n", spacer, numDivisions); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Interleave (isInterleaved) *****************************************************/ else if (!strcmp(parmName, "Interleave")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (!strcmp(tempStr, "Yes")) isInterleaved = YES; else isInterleaved = NO; } else { MrBayesPrint ("%s Invalid argument for interleaved data\n", spacer); return (ERROR); } if (isInterleaved == YES) MrBayesPrint ("%s Data matrix is interleaved\n", spacer); else MrBayesPrint ("%s Data matrix is not interleaved\n", spacer); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Gap (gapId) ********************************************************************/ else if (!strcmp(parmName, "Gap")) { if (expecting == Expecting(EQUALSIGN)) { expecting = Expecting(ALPHA); expecting |= Expecting(QUESTIONMARK); expecting |= Expecting(DASH); expecting |= Expecting(NUMBER); expecting |= Expecting(ASTERISK); expecting |= Expecting(EXCLAMATIONMARK); expecting |= Expecting(PERCENT); expecting |= Expecting(WEIRD); } else if (((expecting & Expecting(ALPHA)) == Expecting(ALPHA)) || ((expecting & Expecting(QUESTIONMARK)) == Expecting(QUESTIONMARK)) || ((expecting & Expecting(DASH)) == Expecting(DASH)) || ((expecting & Expecting(NUMBER)) == Expecting(NUMBER)) || ((expecting & Expecting(ASTERISK)) == Expecting(ASTERISK)) || ((expecting & Expecting(EXCLAMATIONMARK)) == Expecting(EXCLAMATIONMARK)) || ((expecting & Expecting(PERCENT)) == Expecting(PERCENT)) || ((expecting & Expecting(WEIRD)) == Expecting(WEIRD))) { if (strlen(tkn) == 1) { if (tkn[0] == matchId || tkn[0] == missingId) { MrBayesPrint ("%s Gap character matches matching or missing characters\n", spacer); return (ERROR); } gapId = tkn[0]; } else { MrBayesPrint ("%s Invalid gap argument %s\n", spacer, tkn); return (ERROR); } MrBayesPrint ("%s Gaps coded as %s\n", spacer, tkn); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Missing (missingId) ************************************************************/ else if (!strcmp(parmName, "Missing")) { if (expecting == Expecting(EQUALSIGN)) { expecting = Expecting(ALPHA); expecting |= Expecting(QUESTIONMARK); expecting |= Expecting(DASH); expecting |= Expecting(NUMBER); expecting |= Expecting(ASTERISK); expecting |= Expecting(EXCLAMATIONMARK); expecting |= Expecting(PERCENT); expecting |= Expecting(WEIRD); } else if (((expecting & Expecting(ALPHA)) == Expecting(ALPHA)) || ((expecting & Expecting(QUESTIONMARK)) == Expecting(QUESTIONMARK)) || ((expecting & Expecting(DASH)) == Expecting(DASH)) || ((expecting & Expecting(NUMBER)) == Expecting(NUMBER)) || ((expecting & Expecting(ASTERISK)) == Expecting(ASTERISK)) || ((expecting & Expecting(EXCLAMATIONMARK)) == Expecting(EXCLAMATIONMARK)) || ((expecting & Expecting(PERCENT)) == Expecting(PERCENT)) || ((expecting & Expecting(WEIRD)) == Expecting(WEIRD))) { if (strlen(tkn) == 1) { if (tkn[0] == gapId || tkn[0] == matchId) { MrBayesPrint ("%s Missing character matches matching or gap characters\n", spacer); return (ERROR); } missingId = tkn[0]; } else { MrBayesPrint ("%s Invalid missing argument %s\n", spacer, tkn); return (ERROR); } MrBayesPrint ("%s Missing data coded as %s\n", spacer, tkn); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Matchchar (matchId) ************************************************************/ else if (!strcmp(parmName, "Matchchar")) { if (expecting == Expecting(EQUALSIGN)) { expecting = Expecting(ALPHA); expecting |= Expecting(QUESTIONMARK); expecting |= Expecting(DASH); expecting |= Expecting(NUMBER); expecting |= Expecting(ASTERISK); expecting |= Expecting(EXCLAMATIONMARK); expecting |= Expecting(PERCENT); expecting |= Expecting(WEIRD); } else if (((expecting & Expecting(ALPHA)) == Expecting(ALPHA)) || ((expecting & Expecting(QUESTIONMARK)) == Expecting(QUESTIONMARK)) || ((expecting & Expecting(DASH)) == Expecting(DASH)) || ((expecting & Expecting(NUMBER)) == Expecting(NUMBER)) || ((expecting & Expecting(ASTERISK)) == Expecting(ASTERISK)) || ((expecting & Expecting(EXCLAMATIONMARK)) == Expecting(EXCLAMATIONMARK)) || ((expecting & Expecting(PERCENT)) == Expecting(PERCENT)) || ((expecting & Expecting(WEIRD)) == Expecting(WEIRD))) { if (strlen(tkn) == 1) { if (tkn[0] == gapId || tkn[0] == missingId) { MrBayesPrint ("%s Matching character matches gap or missing characters\n", spacer); return (ERROR); } matchId = tkn[0]; } else { MrBayesPrint ("%s Invalid matchchar argument %s\n", spacer, tkn); return (ERROR); } MrBayesPrint ("%s Matching characters coded as %s\n", spacer, tkn); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* skip Symbols ***************************************************************/ else if (!strcmp(parmName, "Symbols")) { if (expecting == Expecting(EQUALSIGN)) { MrBayesPrint ("%s Warning: MrBayes does not support 'symbols' specifications; default symbols assumed\n", spacer); expecting = Expecting(QUOTATIONMARK); foundQuote = NO; } else if (expecting == Expecting(QUOTATIONMARK)) { if (foundQuote == NO) { foundQuote = YES; expecting = Expecting(ALPHA); } else /* if (foundQuote == YES) */ { foundQuote = NO; expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } } else if (expecting == Expecting(ALPHA)) { expecting = Expecting(ALPHA) | Expecting(COMMA); } else return (ERROR); } /* on Equate return ERROR ***************************************************************/ else if (!strcmp(parmName, "Equate")) { MrBayesPrint ("%s Error: MrBayes does not support 'Equate' macros; please remove or comment out\n", spacer); return (ERROR); } else return (ERROR); } return (NO_ERROR); } int DoHelp (void) { int i, j, longestDescription; CmdType *p; if (foundFirst == NO) { longestDescription = 0; for (i=1; istring) > longestDescription) longestDescription = (int) strlen(p->string); } MrBayesPrint (" --------------------------------------------------------------------------- \n"); MrBayesPrint (" Commands that are available from the command \n"); MrBayesPrint (" line or from a MrBayes block include: \n"); MrBayesPrint (" \n"); for (i=1; icmdUse == IN_CMD && p->hiding == SHOW) { MrBayesPrint (" %s", p->string); for (j=0; jstring); j++) MrBayesPrint (" "); MrBayesPrint (" -- %s\n", p->cmdDescription); } } MrBayesPrint (" \n"); MrBayesPrint (" Commands that should be in a NEXUS file (data \n"); MrBayesPrint (" block, trees block or taxa block) include: \n"); MrBayesPrint (" \n"); for (i=1; icmdUse == IN_FILE && p->hiding == SHOW) { MrBayesPrint (" %s", p->string); for (j=0; jstring); j++) MrBayesPrint (" "); MrBayesPrint (" -- %s\n", p->cmdDescription); } } MrBayesPrint (" \n"); MrBayesPrint (" Note that this program supports the use of the shortest unambiguous \n"); MrBayesPrint (" spelling of the above commands (e.g., \"exe\" instead of \"execute\"). \n"); MrBayesPrint (" --------------------------------------------------------------------------- \n"); } foundFirst = NO; return (NO_ERROR); } int DoHelpParm (char *parmName, char *tkn) { int i, j, tkLen, targetLen, numDiff, numMatches; CmdType *p, *q=NULL; if (expecting == Expecting(ALPHA)) { p = commands + 0; tkLen = (int) strlen(tkn); numMatches = 0; for (i=0; istring); if (tkLen <= targetLen) { for (j=0, numDiff=0; jstring[j])) numDiff++; } if (numDiff == 0) { numMatches++; q = p; if (tkLen == targetLen) break; } } p++; } if (numMatches == 0) { MrBayesPrint ("%s Could not find command \"%s\"\n", spacer, tkn); return (ERROR); } else if (numMatches == 1) { if (GetUserHelp (q->string) == ERROR) { MrBayesPrint ("%s Problem getting help for command \"%s\"\n", spacer, q->string); } } else { MrBayesPrint ("%s Ambiguous command \"%s\"\n", spacer, tkn); return (ERROR); } expecting = Expecting(SEMICOLON); foundFirst = YES; } else return (ERROR); return (NO_ERROR); MrBayesPrint ("%s", parmName); /* just because I am tired of seeing the unused parameter error msg */ } int DoInclude (void) { int i, alreadyDone; MrBayesPrint ("%s Including character(s)\n", spacer); /* add set to tempSet */ if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } /* merge tempSet with excludedChars */ alreadyDone = NO; for (i=0; i numChar) { MrBayesPrint ("%s Character number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numChar); return (ERROR); } tempInt--; if (foundDash == YES) { if (fromI >= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted include set\n", spacer); return (ERROR); } foundDash = NO; } else if (foundSlash == YES) { tempInt++; if (tempInt <= 1) { MrBayesPrint ("%s Improperly formatted include set\n", spacer); return (ERROR); } if (fromI >= 0 && toJ >= 0 && fromI < toJ) everyK = tempInt; else { MrBayesPrint ("%s Improperly formatted include set\n", spacer); return (ERROR); } foundSlash = NO; } else { if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; } else if (fromI < 0 && toJ < 0) { fromI = tempInt; } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted include set\n", spacer); { return (ERROR); } } } expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(SEMICOLON); expecting |= Expecting(DASH); expecting |= Expecting(BACKSLASH); } else if (expecting == Expecting(DASH)) { foundDash = YES; expecting = Expecting(NUMBER); } else if (expecting == Expecting(BACKSLASH)) { foundSlash = YES; expecting = Expecting(NUMBER); } else return (ERROR); return (NO_ERROR); MrBayesPrint ("%s", parmName); /* just because I am tired of seeing the unused parameter error msg */ } int DoLog (void) { if (logToFile == YES) { SafeFclose (&logFileFp); if (replaceLogFile == YES) { if ((logFileFp = OpenTextFileW (logFileName)) == NULL) { logToFile = NO; return (ERROR); } } else { if ((logFileFp = OpenTextFileA (logFileName)) == NULL) { logToFile = NO; return (ERROR); } } MrBayesPrint ("%s Logging screen output to file \"%s\"\n", spacer, logFileName); } else { SafeFclose (&logFileFp); MrBayesPrint ("%s Terminating log output\n", spacer); } return (NO_ERROR); } int DoLogParm (char *parmName, char *tkn) { if (expecting == Expecting(PARAMETER)) { if (!strcmp(parmName, "Start")) { if (logToFile == YES) MrBayesPrint ("%s Logging to file is already on\n", spacer, logFileName); else logToFile = YES; expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else if (!strcmp(parmName, "Stop")) { if (logToFile == NO) MrBayesPrint ("%s Logging to file is already off\n", spacer, logFileName); else logToFile = NO; expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else if (!strcmp(parmName, "Replace")) { replaceLogFile = YES; expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else if (!strcmp(parmName, "Append")) { replaceLogFile = NO; expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else expecting = Expecting(EQUALSIGN); } else { if (!strcmp(parmName, "Filename")) { if (expecting == Expecting(EQUALSIGN)) { expecting = Expecting(ALPHA); readWord = YES; } else if (expecting == Expecting(ALPHA)) { strcpy (logFileName, tkn); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } else { MrBayesPrint ("%s Unknown parameter in Log\n", spacer); return (ERROR); } } return (NO_ERROR); } int DoManual (void) { int i, j, logSetting; char title[100]; FILE *fp, *logfp; CmdType *p; /* try to open file, return error if present */ if ((fp = OpenTextFileRQuait(manFileName)) != NULL) { MrBayesPrint ("%s File \"%s\" already exists \n", spacer, manFileName); SafeFclose(&fp); return (ERROR); } /* try to open file for writing, return error if not possible */ if ((fp = OpenTextFileW(manFileName)) == NULL) return (ERROR); /* print message */ MrBayesPrint ("%s Producing command reference file \"%s\"\n", spacer, manFileName); /* temporarily disable normal logging and switch echoing off */ logSetting = logToFile; logfp = logFileFp; echoMB = NO; logToFile = YES; logFileFp = fp; /* produce command reference file */ /* header */ strcpy (title, "Command Reference for MrBayes ver. "); strcat (title, VERSION_NUMBER); i = (70 - (int) strlen (title)) / 2; j = 70 - i - (int) strlen(title); MrBayesPrint (" \n"); MrBayesPrint (" \n"); MrBayesPrint (" \n"); MrBayesPrint (" \n"); MrBayesPrint (" %*c%s%*c \n", i, ' ', title, j, ' '); MrBayesPrint (" \n"); MrBayesPrint (" (c) John P. Huelsenbeck, Fredrik Ronquist \n"); MrBayesPrint (" and Maxim Teslenko \n"); MrBayesPrint (" \n"); /* summary */ MrBayesPrint (" \n"); MrBayesPrint (" *************************************************************************** \n"); MrBayesPrint (" * * \n"); MrBayesPrint (" * 1. Command summary * \n"); MrBayesPrint (" * * \n"); MrBayesPrint (" *************************************************************************** \n"); MrBayesPrint (" \n"); foundFirst = NO; if (DoHelp() == ERROR) { MrBayesPrint ("%s Could not produce command reference summary\n", spacer); goto errorExit; } /* list of MrBayes commands */ MrBayesPrint (" \n"); MrBayesPrint (" *************************************************************************** \n"); MrBayesPrint (" * * \n"); MrBayesPrint (" * 2. MrBayes commands * \n"); MrBayesPrint (" * * \n"); MrBayesPrint (" *************************************************************************** \n"); MrBayesPrint (" \n"); for (i=1; icmdUse == IN_CMD && p->hiding == SHOW) { if (GetUserHelp(p->string)==ERROR) goto errorExit; } } /* list of data or tree block commands */ MrBayesPrint (" \n"); MrBayesPrint (" *************************************************************************** \n"); MrBayesPrint (" * * \n"); MrBayesPrint (" * 3. 'Data' or 'tree' block commands (in #NEXUS file) * \n"); MrBayesPrint (" * * \n"); MrBayesPrint (" *************************************************************************** \n"); MrBayesPrint (" \n"); for (i=1; icmdUse == IN_FILE && p->hiding == SHOW) { if (GetUserHelp(p->string) == ERROR) goto errorExit; } } /* return logging to previous setings and switch echoing on */ SafeFclose (&fp); logToFile = logSetting; logFileFp = logfp; echoMB = YES; MrBayesPrint ("%s Successfully produced command reference file \"%s\"\n", spacer, manFileName); return (NO_ERROR); errorExit: SafeFclose (&fp); logToFile = logSetting; logFileFp = logfp; echoMB = YES; return (ERROR); } int DoManualParm (char *parmName, char *tkn) { if (expecting == Expecting(PARAMETER)) { expecting = Expecting(EQUALSIGN); } else { if (!strcmp(parmName, "Filename")) { if (expecting == Expecting(EQUALSIGN)) { expecting = Expecting(ALPHA); readWord = YES; } else if (expecting == Expecting(ALPHA)) { strcpy (manFileName, tkn); expecting = Expecting(SEMICOLON); } else return (ERROR); } else { MrBayesPrint ("%s Unknown parameter in Manual\n", spacer); return (ERROR); } } return (NO_ERROR); } int DoMatrix (void) { int i, j, hasMissingAmbig; if (taxonCount != numTaxa) { MrBayesPrint ("%s Problem with number of taxa read in (%d taxa read in, while expecting %d)\n", spacer, taxonCount, numTaxa); FreeMatrix(); return (ERROR); } for (i=0; i 1) */ { sprintf (comptreeParams.comptFileName1, "%s.run1.t", inputFileName); sprintf (comptreeParams.comptFileName2, "%s.run2.t", inputFileName); } if (chainParams.numRuns == 1) sprintf (plotParams.plotFileName, "%s.p", inputFileName); else /* if (chainParams.numRuns > 1) */ sprintf (plotParams.plotFileName, "%s.run1.p", inputFileName); strcpy (chainParams.chainFileName, inputFileName); if (chainParams.numRuns > 1) MrBayesPrint ("%s Setting output file names to \"%s.run.\"\n", spacer, chainParams.chainFileName); else MrBayesPrint ("%s Setting output file names to \"%s.\"\n", spacer, chainParams.chainFileName); # if 0 for (i=0; i 0) { if (taxaInfo[taxonCount-1].charCount < numChar) foundNewLine = NO; } } if (taxonCount >= numTaxa && foundNewLine == YES) { if (isInterleaved == YES) { taxonCount = 0; isFirstInterleavedBlock = NO; } else { MrBayesPrint ("%s Too many taxa in matrix\n", spacer); goto errorExit; } } if (taxaInfo[0].charCount > 4010) i = 1; if (foundNewLine == YES) { /* Should be a taxon. */ if (isFirstInterleavedBlock == YES) { /* If this is the first interleaved block, then we need to add the taxon to the set of taxon names unless there is already a defined taxon set. */ if ( strlen(tkn)>99 ) { MrBayesPrint ("%s Taxon name %s is too long. Maximun 99 characters is allowed.\n", spacer, tkn); goto errorExit; } if (isTaxsetDef == NO && AddString (&taxaNames, taxonCount, tkn) == ERROR) { MrBayesPrint ("%s Problem adding taxon %s to taxon set\n", spacer, tkn); goto errorExit; } if (numTaxa < 10) MrBayesPrint ("%s Taxon %d -> %s\n", spacer, taxonCount+1, tkn); else if (numTaxa < 100 && numTaxa >= 10) MrBayesPrint ("%s Taxon %2d -> %s\n", spacer, taxonCount+1, tkn); else if (numTaxa < 1000 && numTaxa >= 100) MrBayesPrint ("%s Taxon %3d -> %s\n", spacer, taxonCount+1, tkn); else MrBayesPrint ("%s Taxon %4d -> %s\n", spacer, taxonCount+1, tkn); } else { /* If this is not the first interleaved block, then we need to check to see if taxon name is present and in correct place. */ if (CheckString (taxaNames, numTaxa, tkn, &index) == ERROR) { MrBayesPrint ("%s Could not find taxon %s in list of taxa\n", spacer, tkn); goto errorExit; } if (index != taxonCount) { MrBayesPrint ("%s Could not find taxon %s in correct position in list of taxa\n", spacer, tkn); goto errorExit; } } foundNewLine = NO; isNegative = NO; taxonCount++; } else { /* Should be a character (either continuous or otherwise). */ if (charInfo[taxaInfo[taxonCount-1].charCount].charType == CONTINUOUS) { /* If we have a CONTINUOUS character, then the entire token should either be a number or a dash (for a negative sign). */ if (!strcmp(tkn, "-")) { /* Dealing with a negative number. We will multiply the next tkn, which had better be a number, by -1. */ isNegative = YES; } else { /* We have a number, we hope. */ if (tkn[0] == matchId) { /* If the token is a matchchar, then things are simple. */ if (taxonCount == 1) { MrBayesPrint ("%s Matching characters cannot be in first taxon\n", spacer); goto errorExit; } charCode = matrix[pos(0,taxaInfo[taxonCount-1].charCount,numChar)]; matrix[pos(taxonCount-1,taxaInfo[taxonCount-1].charCount,numChar)] = charCode; } else { /* Otherwise, we have a number. Check that it is a valid number first... */ if (!IsIn(tkn[0],"0123456789.")) { MrBayesPrint ("%s Expecting a number for the continuous character\n", spacer); goto errorExit; } /* ... and then put the character into the matrix. Note that matrix is defined as an integer, but we may have floating precision continuous characters. To get around this, we multiply the value of the character by 1000 before putting it into matrix. We will divide by 1000 later on when/if we use the characters. */ sscanf (tkn, "%lf", &charValue); charValue *= 1000.0; if (isNegative == YES) { charValue *= -1.0; isNegative = NO; } /*MrBayesPrint ("%d \n", (int)charValue);*/ matrix[pos(taxonCount-1,taxaInfo[taxonCount-1].charCount++,numChar)] = (int)charValue; } } } else { /* Otherwise, we are dealing with a run-of-the-mill character, and we cannot expect the entire token to contain only a single character. We must, therefore, go through the token character-by-character. */ i = 0; while (tkn[i] != '\0') { /*MrBayesPrint ("%c", tkn[i]);*/ if (tkn[i] == matchId) { if (taxonCount == 1) { MrBayesPrint ("%s Matching characters cannot be in first taxon\n", spacer); goto errorExit; } charCode = matrix[pos(0,taxaInfo[taxonCount-1].charCount,numChar)]; matrix[pos(taxonCount-1,taxaInfo[taxonCount-1].charCount++,numChar)] = charCode; } else { if ((tkn[i] == ')' && isInAmbig == YES) || (tkn[i] == '}' && isInPoly == YES)) { isInAmbig = isInPoly = NO; charCode = theAmbigChar; j = CharacterNumber (charCode, charInfo[taxaInfo[taxonCount-1].charCount].charType); if (j > charInfo[taxaInfo[taxonCount-1].charCount].numStates) charInfo[taxaInfo[taxonCount-1].charCount].numStates = j; matrix[pos(taxonCount-1,taxaInfo[taxonCount-1].charCount++,numChar)] = charCode; theAmbigChar = 0; } else if ((tkn[i] == '(' && isInAmbig == YES) || (tkn[i] == '{' && isInPoly == YES)) { if (isInAmbig == YES) MrBayesPrint ("%s Found an inappropriate \"(\"\n", spacer); else MrBayesPrint ("%s Found an inappropriate \"{\"\n", spacer); goto errorExit; } else if (isInAmbig == YES || isInPoly == YES) { if (tkn[i] == ',') expecting |= Expecting (COMMA); else { if (CharacterCode(tkn[i], &charCode, charInfo[taxaInfo[taxonCount-1].charCount].charType) == ERROR) goto errorExit; if (charCode == MISSING || charCode == GAP) goto errorExit; theAmbigChar |= charCode; expecting ^= Expecting (COMMA); } } else if (tkn[i] == '{' && isInPoly == NO && isInAmbig == NO) { isInPoly = YES; matrixHasPoly = YES; theAmbigChar = 0; } else if (tkn[i] == '(' && isInPoly == NO && isInAmbig == NO) { isInAmbig = YES; theAmbigChar = 0; } else if (tkn[i] == '(' && isInPoly == NO && isInAmbig == NO) { isInAmbig = YES; theAmbigChar = 0; } else { if (CharacterCode(tkn[i], &charCode, charInfo[taxaInfo[taxonCount-1].charCount].charType) == ERROR) { MrBayesPrint ("%s Error while reading character position %d (charCode %d)\n", spacer, taxaInfo[taxonCount-1].charCount+1, charCode); goto errorExit; } if (charCode != MISSING && charCode != GAP) { j = CharacterNumber (charCode, charInfo[taxaInfo[taxonCount-1].charCount].charType); if (j > charInfo[taxaInfo[taxonCount-1].charCount].numStates) charInfo[taxaInfo[taxonCount-1].charCount].numStates = j; } matrix[pos(taxonCount-1,taxaInfo[taxonCount-1].charCount++,numChar)] = charCode; } } i++; } } } return (NO_ERROR); MrBayesPrint ("%s", parmName); /* just because I am tired of seeing the unused parameter error msg */ errorExit: numTaxa=taxonCount; FreeMatrix(); return (ERROR); } int DoNexusParm (char *parmName, char *tkn) { if (!strcmp(parmName, "NEXUS")) { MrBayesPrint ("%s Expecting NEXUS formatted file\n", spacer); expecting = Expecting(COMMAND); } else { MrBayesPrint ("%s Found %s\n", spacer, tkn); return (ERROR); } return (NO_ERROR); } int DoOutgroup (void) { MrBayesPrint ("%s Setting outgroup to taxon \"%s\"\n", spacer, taxaNames[outGroupNum]); return (NO_ERROR); } int DoOutgroupParm (char *parmName, char *tkn) { int index, tempInt; if (expecting == Expecting(ALPHA)) { if (CheckString (taxaNames, numTaxa, tkn, &index) == ERROR) { MrBayesPrint ("%s Could not find taxon %s in list of taxa\n", spacer, tkn); return (ERROR); } outGroupNum = index; expecting = Expecting(SEMICOLON); } else if (expecting == Expecting(NUMBER)) { if (CheckString (taxaNames, numTaxa, tkn, &index) == ERROR) { /* OK, as we expect, the taxon is not a digit. So, now we assume that the user is assigning the outgroup by its number */ sscanf (tkn, "%d", &tempInt); if (tempInt < 1 || tempInt > numTaxa) { MrBayesPrint ("%s Taxon number %d is out of range\n", spacer, tempInt); return (ERROR); } outGroupNum = tempInt - 1; } else { outGroupNum = index; } expecting = Expecting(SEMICOLON); } else return (ERROR); return (NO_ERROR); MrBayesPrint ("%s", parmName); /* just because I am tired of seeing the unused parameter error msg */ } int DoPairs (void) { MrBayesPrint ("\n"); MrBayesPrint ("%s Successfully defined character pairings\n", spacer); defPairs = YES; foundFirst = NO; return (NO_ERROR); } int DoPairsParm (char *parmName, char *tkn) { int i, tempInt; if (defMatrix == NO) { MrBayesPrint ("%s A matrix must be specified before you can define pairs of characters\n", spacer); return (ERROR); } if (defPairs == YES) { MrBayesPrint ("%s Character pairs have been previously defined \n", spacer); MrBayesPrint ("%s Now overwriting old pairings\n", spacer); for (i=0; i numChar) { MrBayesPrint ("\n"); MrBayesPrint ("%s Character number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numChar); for (i=0; i= 0) if (AddToSet (fromI, toJ, everyK, whichPartition+1) == ERROR) return (ERROR); /* check that all characters are included */ for (i=0; i 99) { MrBayesPrint ("%s Partition name is too long. Max 100 characters\n", spacer); return (ERROR); } /* check to see if the name has already been used as a partition */ if (numDefinedPartitions > 1) { if (CheckString (partitionNames, numDefinedPartitions, tkn, &index) == ERROR) { /* if the partition name has not been used, then we should have an ERROR returned */ /* we _want_ to be here */ } else { MrBayesPrint ("%s Partition name '%s' has been used previously\n", spacer, tkn); return (ERROR); } } /* add the name temporarily to tempSetName */ strcpy (tempSetName, tkn); /* clear tempSet */ for (i=0; i numChar) { MrBayesPrint ("%s Character number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numChar); return (ERROR); } tempInt--; if (foundDash == YES) { if (fromI >= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted partition\n", spacer); return (ERROR); } foundDash = NO; } else if (foundSlash == YES) { tempInt++; if (tempInt <= 1) { MrBayesPrint ("%s Improperly formatted charset\n", spacer); return (ERROR); } if (fromI >= 0 && toJ >= 0 && fromI < toJ) everyK = tempInt; else { MrBayesPrint ("%s Improperly formatted charset\n", spacer); return (ERROR); } foundSlash = NO; } else { if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, whichPartition+1) == ERROR) return (ERROR); fromI = tempInt; } else if (fromI < 0 && toJ < 0) { fromI = tempInt; } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, whichPartition+1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, whichPartition+1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted charset\n", spacer); { return (ERROR); } } } expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(SEMICOLON); expecting |= Expecting(DASH); expecting |= Expecting(BACKSLASH); expecting |= Expecting(COMMA); } } else if (expecting == Expecting(COMMA)) { /* add set to tempSet */ if (fromI >= 0) if (AddToSet (fromI, toJ, everyK, whichPartition+1) == ERROR) return (ERROR); fromI = toJ = everyK = -1; foundDash = foundSlash = NO; whichPartition++; if (whichPartition > numDivisions) { MrBayesPrint ("%s Too many partitions of the data (expecting %d)\n", spacer, numDivisions); return (ERROR); } expecting = Expecting(NUMBER); expecting |= Expecting(ALPHA); } else if (expecting == Expecting(COLON)) { expecting = Expecting(NUMBER); expecting |= Expecting(ALPHA); } else if (expecting == Expecting(DASH)) { foundDash = YES; expecting = Expecting(NUMBER); } else if (expecting == Expecting(BACKSLASH)) { foundSlash = YES; expecting = Expecting(NUMBER); } else return (ERROR); return (NO_ERROR); } int DoRestore (void) { int i, alreadyDone; MrBayesPrint ("%s Restore taxa\n", spacer); /* add set to tempSet */ if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } /* merge tempSet with excludedTaxa */ alreadyDone = NO; for (i=0; i= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } tempSet[index] = 1; } fromI = toJ = everyK = -1; } expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(SEMICOLON); } else if (expecting == Expecting(NUMBER)) { if (strlen(tkn) == 1 && !strcmp(tkn, ".")) { tempInt = numTaxa; } else { sscanf (tkn, "%d", &tempInt); if (tempInt <= 0 || tempInt > numTaxa) { MrBayesPrint ("%s Taxon number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numTaxa); return (ERROR); } } tempInt--; if (foundDash == YES) { if (fromI >= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted restore set\n", spacer); return (ERROR); } foundDash = NO; } else { if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; } else if (fromI < 0 && toJ < 0) { fromI = tempInt; } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted restore set\n", spacer); { return (ERROR); } } } expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(SEMICOLON); expecting |= Expecting(DASH); } else if (expecting == Expecting(DASH)) { foundDash = YES; expecting = Expecting(NUMBER); } else return (ERROR); return (NO_ERROR); MrBayesPrint ("%s", parmName); /* just because I am tired of seeing the unused parameter error msg */ } int DoSet (void) { return (NO_ERROR); } int DoSetParm (char *parmName, char *tkn) { int index; char tempStr[100]; int tempI; if (expecting == Expecting(PARAMETER)) { expecting = Expecting(EQUALSIGN); } else { /* set Autoclose (autoClose) **********************************************************/ if (!strcmp(parmName, "Autoclose")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (!strcmp(tempStr, "Yes")) autoClose = YES; else autoClose = NO; } else { MrBayesPrint ("%s Invalid argument for autoclose\n", spacer); return (ERROR); } if (autoClose == YES) MrBayesPrint ("%s Setting autoclose to yes\n", spacer); else MrBayesPrint ("%s Setting autoclose to no\n", spacer); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Nowarnings (noWarn) **********************************************************/ else if (!strcmp(parmName, "Nowarnings")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (!strcmp(tempStr, "Yes")) noWarn = YES; else noWarn = NO; } else { MrBayesPrint ("%s Invalid argument for nowarnings\n", spacer); return (ERROR); } if (noWarn == YES) MrBayesPrint ("%s Setting nowarnings to yes\n", spacer); else MrBayesPrint ("%s Setting nowarnings to no\n", spacer); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Quitonerror (quitOnError) **************************************************/ else if (!strcmp(parmName, "Quitonerror")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (!strcmp(tempStr, "Yes")) quitOnError = YES; else quitOnError = NO; } else { MrBayesPrint ("%s Invalid argument for quitonerror\n", spacer); return (ERROR); } if (quitOnError == YES) MrBayesPrint ("%s Setting quitonerror to yes\n", spacer); else MrBayesPrint ("%s Setting quitonerror to no\n", spacer); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Autoreplace (autoOverwrite) **************************************************/ else if (!strcmp(parmName, "Autoreplace")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (!strcmp(tempStr, "Yes")) { autoOverwrite = YES; MrBayesPrint ("%s Setting autoreplace to yes\n", spacer); } else { autoOverwrite = NO; MrBayesPrint ("%s Setting autoreplace to no\n", spacer); } } else { MrBayesPrint ("%s Invalid argument for autoreplace\n", spacer); return (ERROR); } expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Scientific (scientific) *********************************************/ else if (!strcmp(parmName, "Scientific")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (!strcmp(tempStr, "Yes")) scientific = YES; else scientific = NO; } else { MrBayesPrint ("%s Invalid argument for Scientific\n", spacer); return (ERROR); } if ( scientific == YES) MrBayesPrint ("%s Setting Scientific to Yes\n", spacer); else MrBayesPrint ("%s Setting Scientific to No\n", spacer); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Userlevel (userLevel) **********************************************************/ else if (!strcmp(parmName, "Userlevel")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (!strcmp(tempStr, "Standard")) userLevel = STANDARD_USER; else if (!strcmp (tempStr,"Developer")) userLevel = DEVELOPER; } else { MrBayesPrint ("%s Invalid argument for userlevel\n", spacer); return (ERROR); } MrBayesPrint ("%s Setting userlevel to %s\n", spacer, tempStr); if (SetMoves() == ERROR) { MrBayesPrint ("%s Problem seting up the moves for this user level\n", spacer); return (ERROR); } expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Npthreads (number of pthreads) ****************************************************/ else if (!strcmp(parmName, "Npthreads")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(NUMBER); else if (expecting == Expecting(NUMBER)) { sscanf (tkn, "%d", &tempI); nPThreads = tempI; MrBayesPrint ("%s Setting Npthreads to %ld\n", spacer, nPThreads); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Precision (number of decimals) ****************************************************/ else if (!strcmp(parmName, "Precision")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(NUMBER); else if (expecting == Expecting(NUMBER)) { sscanf (tkn, "%d", &tempI); if (tempI < 3 || tempI > 15) { MrBayesPrint ("%s Precision must be in the range 3 to 15\n", spacer); return ERROR; } precision = tempI; MrBayesPrint ("%s Setting Precision to %d\n", spacer, precision); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Partition (partitionNum) *******************************************************/ else if (!strcmp(parmName, "Partition")) { if (defMatrix == NO) { MrBayesPrint ("%s A character matrix must be defined first\n", spacer); return (ERROR); } if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA) | Expecting(NUMBER); else if (expecting == Expecting(ALPHA)) { /* first check to see if name is there */ if (CheckString (partitionNames, numDefinedPartitions, tkn, &index) == ERROR) { MrBayesPrint ("%s Could not find \"%s\" as a defined partition\n", spacer, tkn); return (ERROR); } if (SetPartition (index) == ERROR) return ERROR; if (numCurrentDivisions == 1) MrBayesPrint ("%s Setting %s as the partition (does not divide up characters).\n", spacer, tkn); else MrBayesPrint ("%s Setting %s as the partition, dividing characters into %d parts.\n", spacer, tkn, numCurrentDivisions); if (SetModelDefaults () == ERROR) return (ERROR); if (SetUpAnalysis (&globalSeed) == ERROR) return (ERROR); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else if (expecting == Expecting(NUMBER)) { sscanf (tkn, "%d", &index); if (index > numDefinedPartitions) { MrBayesPrint ("%s Partition number %d is not a valid partition. Only %d partitions\n", spacer, index, numDefinedPartitions); MrBayesPrint ("%s have been defined.\n", spacer); return (ERROR); } if (index < 1) { MrBayesPrint ("%s Partition number %d is not a valid partition. Must be between 1 and %d.\n", spacer, index+1, numDefinedPartitions); return (ERROR); } if (SetPartition (index) == ERROR) return ERROR; if (numCurrentDivisions == 1) MrBayesPrint ("%s Setting %s as the partition (does not divide up characters).\n", spacer, partitionNames[index]); else MrBayesPrint ("%s Setting %s as the partition, dividing characters into %d parts.\n", spacer, partitionNames[index], numCurrentDivisions); if (SetModelDefaults () == ERROR) return (ERROR); if (SetUpAnalysis (&globalSeed) == ERROR) return (ERROR); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Speciespartition (speciespartitionNum) *******************************************************/ else if (!strcmp(parmName, "Speciespartition")) { if (defTaxa == NO) { MrBayesPrint ("%s A taxaset must be defined first\n", spacer); return (ERROR); } if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA) | Expecting(NUMBER); else if (expecting == Expecting(ALPHA)) { /* first check to see if name is there */ if (CheckString (speciespartitionNames, numDefinedSpeciespartitions, tkn, &index) == ERROR) { MrBayesPrint ("%s Could not find \"%s\" as a defined speciespartition\n", spacer, tkn); return (ERROR); } if (SetSpeciespartition (index) == ERROR) return ERROR; MrBayesPrint ("%s Setting %s as the speciespartition, dividing taxa into %d species.\n", spacer, tkn, numSpecies); if (SetModelDefaults () == ERROR) return (ERROR); if (SetUpAnalysis (&globalSeed) == ERROR) return (ERROR); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else if (expecting == Expecting(NUMBER)) { sscanf (tkn, "%d", &index); if (index > numDefinedSpeciespartitions) { MrBayesPrint ("%s Speciespartition number %d is not valid. Only %d speciespartitions\n", spacer, index, numDefinedSpeciespartitions); MrBayesPrint ("%s have been defined.\n", spacer); return (ERROR); } if (index < 1) { MrBayesPrint ("%s Speciespartition number %d is not valid. Must be between 1 and %d.\n", spacer, index, numDefinedSpeciespartitions); return (ERROR); } if (SetSpeciespartition (index-1) == ERROR) return ERROR; MrBayesPrint ("%s Setting %s as the speciespartition, dividing taxa into %d species.\n", spacer, speciespartitionNames[index-1], numSpecies); if (SetModelDefaults () == ERROR) return (ERROR); if (SetUpAnalysis (&globalSeed) == ERROR) return (ERROR); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Seed (global variable globalSeed) ****************************************************/ else if (!strcmp(parmName, "Seed")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(NUMBER); else if (expecting == Expecting(NUMBER)) { sscanf (tkn, "%d", &tempI); if( tempI == 0 || tempI == 2147483647 ) { MrBayesPrint ("%s Error: Seed can be any natural number except 0 and 2147483647\n", spacer); return (ERROR); } globalSeed = tempI; MrBayesPrint ("%s Setting seed to %ld\n", spacer, globalSeed); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Swapseed (global variable swapSeed) ***************************************************************/ else if (!strcmp(parmName, "Swapseed")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(NUMBER); else if (expecting == Expecting(NUMBER)) { sscanf (tkn, "%d", &tempI); if( tempI == 0 || tempI == 2147483647 ) { MrBayesPrint ("%s Error: Swapseed can be any natural number except 0 and 2147483647\n", spacer); return (ERROR); } swapSeed = tempI; MrBayesPrint ("%s Setting swapseed to %ld\n", spacer, swapSeed); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Dir (global variable workingDir) ***************************************************************/ else if (!strcmp(parmName, "Dir")) { if (expecting == Expecting(EQUALSIGN)) { expecting = Expecting(ALPHA); readWord = YES; } else if (expecting == Expecting(ALPHA)) { if(strlen(tkn)>99) { MrBayesPrint ("%s Maximum allowed length of working directory name is 99 characters. The given name:\n", spacer); MrBayesPrint ("%s '%s'\n", spacer,tkn); MrBayesPrint ("%s has %d characters.\n", spacer,strlen(tkn)); return (ERROR); } strcpy (workingDir, tkn); #if defined (WIN_VERSION) /* Reformat to Windows with trailing '\' */ for (index=0; index<(int)strlen(workingDir); index++) { if (workingDir[index] == ':' || workingDir[index] == '/') workingDir[index] = '\\'; } if (strlen(workingDir) > 0 && workingDir[strlen(workingDir)-1] != '\\') strcat(workingDir,"\\"); #else /* Reformat to Unix with trailing '/' */ for (index=0; index<(int)strlen(workingDir); index++) { if (workingDir[index] == ':' || workingDir[index] == '\\') workingDir[index] = '/'; } if (strlen(workingDir) > 0 && workingDir[strlen(workingDir)-1] != '/') strcat(workingDir,"/"); #endif MrBayesPrint ("%s Setting working directory to \"%s\"\n", spacer, workingDir); expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Usebeagle (global variable BEAGLE usage) ***************************************************************/ else if (!strcmp(parmName, "Usebeagle")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { #if defined (BEAGLE_ENABLED) if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (!strcmp(tempStr, "Yes")) tryToUseBEAGLE = YES; else tryToUseBEAGLE = NO; } else { MrBayesPrint ("%s Invalid argument for usebeagle\n", spacer); return (ERROR); } if (tryToUseBEAGLE == YES) MrBayesPrint ("%s Setting usebeagle to yes\n", spacer); else MrBayesPrint ("%s Setting usebeagle to no\n", spacer); #else BeagleNotLinked(); #endif expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } /* set Beagle resources requirements (global variable BEAGLE flag) ****************************************/ else if (!strcmp(parmName, "Beagledevice")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { #if defined (BEAGLE_ENABLED) if (IsArgValid(tkn, tempStr) == NO_ERROR) { long oldFlags = beagleFlags; if (!strcmp(tempStr, "Gpu")) { beagleFlags &= ~BEAGLE_FLAG_PROCESSOR_CPU; beagleFlags |= BEAGLE_FLAG_PROCESSOR_GPU; BeagleAddGPUDevicesToList(&beagleResource, &beagleResourceCount); } else { beagleFlags &= ~BEAGLE_FLAG_PROCESSOR_GPU; beagleFlags |= BEAGLE_FLAG_PROCESSOR_CPU; BeagleRemoveGPUDevicesFromList(&beagleResource, &beagleResourceCount); } if (BeagleCheckFlagCompatability(beagleFlags) == NO) { beagleFlags = oldFlags; } else { if (beagleFlags & BEAGLE_FLAG_PROCESSOR_GPU) MrBayesPrint ("%s Setting beagledevice to GPU\n", spacer); else MrBayesPrint ("%s Setting beagledevice to CPU\n", spacer); } } else { MrBayesPrint ("%s Invalid argument for beagledevice\n", spacer); return (ERROR); } #else BeagleNotLinked(); #endif expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } else if (!strcmp(parmName, "Beagleprecision")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { #if defined (BEAGLE_ENABLED) if (IsArgValid(tkn, tempStr) == NO_ERROR) { long oldFlags = beagleFlags; if (!strcmp(tempStr, "Single")) { beagleFlags &= ~BEAGLE_FLAG_PRECISION_DOUBLE; beagleFlags |= BEAGLE_FLAG_PRECISION_SINGLE; } else { beagleFlags &= ~BEAGLE_FLAG_PRECISION_SINGLE; beagleFlags |= BEAGLE_FLAG_PRECISION_DOUBLE; } if (BeagleCheckFlagCompatability(beagleFlags) == NO) { beagleFlags = oldFlags; } else { if (beagleFlags & BEAGLE_FLAG_PRECISION_DOUBLE) MrBayesPrint ("%s Setting beagleprecision to double\n", spacer); else MrBayesPrint ("%s Setting beagleprecision to single\n", spacer); } } else { MrBayesPrint ("%s Invalid argument for beagleprecision\n", spacer); return (ERROR); } #else BeagleNotLinked(); #endif expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } else if (!strcmp(parmName, "Beagleopenmp")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { #if defined (BEAGLE_ENABLED) if (IsArgValid(tkn, tempStr) == NO_ERROR) { long oldFlags = beagleFlags; if (!strcmp(tempStr, "Yes")) { beagleFlags |= BEAGLE_FLAG_THREADING_OPENMP; } else { beagleFlags &= ~BEAGLE_FLAG_THREADING_OPENMP; } if (BeagleCheckFlagCompatability(beagleFlags) == NO) { beagleFlags = oldFlags; } else { if (beagleFlags & BEAGLE_FLAG_THREADING_OPENMP) MrBayesPrint ("%s Setting beagleopenmp to Yes\n", spacer); else MrBayesPrint ("%s Setting beagleopenmp to No\n", spacer); } } else { MrBayesPrint ("%s Invalid argument for beagleopenmp\n", spacer); return (ERROR); } #else BeagleNotLinked(); #endif expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } else if (!strcmp(parmName, "Beaglefreq")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(NUMBER); else if (expecting == Expecting(NUMBER)) { #if defined (BEAGLE_ENABLED) sscanf (tkn, "%d", &tempI); if (tempI < 0) { MrBayesPrint ("%s Beaglefreq must be greater than 0\n", spacer); return ERROR; } beagleScalingFrequency= tempI; MrBayesPrint ("%s Setting Beaglefreq to %d\n", spacer, beagleScalingFrequency); #else BeagleNotLinked(); #endif expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } else if (!strcmp(parmName, "Beaglesse")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { #if defined (BEAGLE_ENABLED) if (IsArgValid(tkn, tempStr) == NO_ERROR) { long oldFlags = beagleFlags; if (!strcmp(tempStr, "Yes")) { beagleFlags |= BEAGLE_FLAG_VECTOR_SSE; } else { beagleFlags &= ~BEAGLE_FLAG_VECTOR_SSE; } if (BeagleCheckFlagCompatability(beagleFlags) == NO) { beagleFlags = oldFlags; } else { if (beagleFlags & BEAGLE_FLAG_VECTOR_SSE) MrBayesPrint ("%s Setting beaglesse to Yes\n", spacer); else MrBayesPrint ("%s Setting beaglesse to No\n", spacer); } } else { MrBayesPrint ("%s Invalid argument for beagleopenmp\n", spacer); return (ERROR); } #else BeagleNotLinked(); #endif expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } else if (!strcmp(parmName, "Beaglethreads")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { #if defined (BEAGLE_ENABLED) && defined (THREADS_ENABLED) if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (!strcmp(tempStr, "Yes")) { tryToUseThreads = YES; } else { tryToUseThreads = NO; } if (tryToUseThreads == YES) MrBayesPrint ("%s Setting beaglethreads to Yes\n", spacer); else MrBayesPrint ("%s Setting beaglethreads to No\n", spacer); } else { MrBayesPrint ("%s Invalid argument for beaglethreads\n", spacer); return (ERROR); } #else BeagleThreadsNotLinked(); #endif expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } } else if (!strcmp(parmName, "Beaglescaling")) { if (expecting == Expecting(EQUALSIGN)) expecting = Expecting(ALPHA); else if (expecting == Expecting(ALPHA)) { #if defined (BEAGLE_ENABLED) if (IsArgValid(tkn, tempStr) == NO_ERROR) { if (!strcmp(tempStr, "Always")) { beagleScalingScheme = MB_BEAGLE_SCALE_ALWAYS; } else { beagleScalingScheme = MB_BEAGLE_SCALE_DYNAMIC; } if (beagleScalingScheme == MB_BEAGLE_SCALE_ALWAYS) MrBayesPrint ("%s Setting beaglescaling to Always\n", spacer); else MrBayesPrint ("%s Setting beaglescaling to Dynamic\n", spacer); } else { MrBayesPrint ("%s Invalid argument for beaglescaling\n", spacer); return (ERROR); } #else BeagleThreadsNotLinked(); #endif expecting = Expecting(PARAMETER) | Expecting(SEMICOLON); } else return (ERROR); } else return (ERROR); } return (NO_ERROR); } int DoShowMatrix (void) { int i, j, nameLen, start, finish, ct, longestName; char tempStr[100], stride; if (defMatrix == NO) { MrBayesPrint ("%s A character matrix must be defined first\n", spacer); return (ERROR); } longestName = 0; for (i=0; i longestName) longestName = nameLen; } stride = 50; start = finish = 0; do { finish += stride; if (finish > numChar) finish = numChar; MrBayesPrint ("%s ", spacer); for (j=0; j= longestName) { for (j=0; jname); ShowConTree (stdout, userTree[i], 70, NO); MrBayesPrint ("\n"); } } return (NO_ERROR); } int DoShowBeagle (void) { #if defined (BEAGLE_ENABLED) BeaglePrintResources(); #else BeagleNotLinked(); #endif return (NO_ERROR); } int DoTaxlabels (void) { isTaxsetDef = YES; /* add default speciespartition name to list of valid speciespartitions */ if (AddString (&speciespartitionNames, 0, "Default") == ERROR) { MrBayesPrint ("%s Problem adding Default speciespartition to list\n", spacer); return (ERROR); } /* add default species name set */ AddNameSet(&speciesNameSets, 0, taxaNames, numTaxa); /* set number of defined speciespartitions to 1 */ numDefinedSpeciespartitions = 1; return (NO_ERROR); } int DoTaxlabelsParm (char *parmName, char *tkn) { int index; if (inTaxaBlock == NO) { MrBayesPrint ("%s You must be in a taxa block to read a taxlabels command\n", spacer); return (ERROR); } if (defTaxa == NO) { MrBayesPrint ("%s The number of taxa must be given before a set of taxon labels can be read\n", spacer); return ERROR; } if (isTaxsetDef == YES) { MrBayesPrint ("%s A set of taxon labels has already been defined\n", spacer); if (defMatrix == NO) if (WantTo ("Do you want to delete the current set of taxon labels") == NO) return (SKIP_COMMAND); else FreeTaxa(); else if (WantTo ("Do you want to delete the current character matrix") == NO) return (SKIP_COMMAND); else FreeMatrix(); } if (expecting == Expecting(ALPHA) || expecting == Expecting(NUMBER)) { if (CheckString (taxaNames, numNamedTaxa, tkn, &index) == ERROR) { if ( strlen(tkn)>99 ) { MrBayesPrint ("%s Taxon name %s is too long. Maximun 99 characters is allowed.\n", spacer, tkn); return (ERROR); } if (AddString (&taxaNames, numNamedTaxa, tkn) == ERROR) { MrBayesPrint ("%s Problem adding label %s to list of taxon labels\n", spacer, tkn); return (ERROR); } numNamedTaxa++; } else { MrBayesPrint ("%s Taxon label '%s' is included twice in list of taxon labels\n", spacer, tkn); return (ERROR); } if (numNamedTaxa < numTaxa) { expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); } else expecting |= Expecting(SEMICOLON); } return (NO_ERROR); MrBayesPrint ("%s", parmName); /* just because I am tired of seeing the unused parameter error msg */ MrBayesPrint ("%s", tkn); } int DoSpeciespartition (void) { int i, *partCount; /* add set to tempSet */ if (fromI >= 0) if (AddToSet (fromI, toJ, everyK, whichPartition+1) == ERROR) { for (i=0; i numTaxa) { MrBayesPrint ("%s Speciespartition index for tip %d out of bound (%d)\n", spacer, i+1, tempSet[i]); free (partCount); for (i=0; i 99) { MrBayesPrint ("%s Partition name is too long. Max 100 characters\n", spacer); return (ERROR); } /* check to see if the name has already been used as a partition */ if (numDefinedSpeciespartitions > 0) { if (CheckString (speciespartitionNames, numDefinedSpeciespartitions, tkn, &index) == ERROR) { /* if the partition name has not been used, then we should have an ERROR returned */ /* we _want_ to be here */ } else { MrBayesPrint ("%s Speciespartition name '%s' has been used previously\n", spacer, tkn); return (ERROR); } } /* add the name temporarily to tempSetName */ strcpy (tempSetName, tkn); /* clear tempSet */ for (i=0; i numTaxa) { MrBayesPrint ("%s Tip number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numTaxa); for (i=0; i= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted speciespartition\n", spacer); for (i=0; i= 0 && toJ >= 0 && fromI < toJ) everyK = tempInt; else { MrBayesPrint ("%s Improperly formatted speciespartition\n", spacer); for (i=0; i= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, whichPartition+1) == ERROR) { for (i=0; i= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, whichPartition+1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, whichPartition+1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted speciespartition\n", spacer); { for (i=0; i= 0) if (AddToSet (fromI, toJ, everyK, whichPartition+1) == ERROR) { for (i=0; i numTaxa) { MrBayesPrint ("%s Too many speciespartitions (expecting maximum %d speciespartitions)\n", spacer, numTaxa); for (i=0; i= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); } /* add name to taxaSetNames */ if (AddString (&taxaSetNames, numTaxaSets, tempSetName) == ERROR) { MrBayesPrint ("%s Problem adding taxset %s to list\n", spacer, tempSetName); return (ERROR); } /* merge tempSet with taxaSet */ AddBitfield (&taxaSet, numTaxaSets, tempSet, numTaxa); /* increment number of char sets */ numTaxaSets++; /* show taxset (for debugging) */ # if 0 for (i=0; i 99) { MrBayesPrint ("%s Taxset name is too long\n", spacer); return (ERROR); } /* check to see if the name has already been used as a taxset */ if (numTaxaSets > 0) { if (CheckString (taxaSetNames, numTaxaSets, tkn, &index) == ERROR) { /* if the taxset name has not been used, then we should have an ERROR returned */ /* we _want_ to be here */ } else { MrBayesPrint ("%s Taxset name has been used previously\n", spacer); return (ERROR); } } else if (numTaxaSets > 30) { MrBayesPrint ("%s You cannot define more than 30 taxsets\n", spacer); return (ERROR); } /* add the name to the taxa set */ strcpy (tempSetName, tkn); /* clear tempSet */ for (i=0; i numTaxa) { MrBayesPrint ("%s Taxon number %d is out of range (should be between %d and %d)\n", spacer, tempInt, 1, numTaxa); return (ERROR); } } tempInt--; if (foundDash == YES) { if (fromI >= 0) toJ = tempInt; else { MrBayesPrint ("%s Improperly formatted taxset\n", spacer); return (ERROR); } foundDash = NO; } else if (foundSlash == YES) { tempInt++; if (tempInt <= 1) { MrBayesPrint ("%s Improperly formatted taxset\n", spacer); return (ERROR); } if (fromI >= 0 && toJ >= 0 && fromI < toJ) everyK = tempInt; else { MrBayesPrint ("%s Improperly formatted taxset\n", spacer); return (ERROR); } foundSlash = NO; } else { if (fromI >= 0 && toJ < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; } else if (fromI < 0 && toJ < 0) { fromI = tempInt; } else if (fromI >= 0 && toJ >= 0 && everyK < 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else if (fromI >= 0 && toJ >= 0 && everyK >= 0) { if (AddToSet (fromI, toJ, everyK, 1) == ERROR) return (ERROR); fromI = tempInt; toJ = everyK = -1; } else { MrBayesPrint ("%s Improperly formatted taxset\n", spacer); { return (ERROR); } } } expecting = Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(SEMICOLON); expecting |= Expecting(DASH); expecting |= Expecting(BACKSLASH); } else if (expecting == Expecting(DASH)) { foundDash = YES; expecting = Expecting(NUMBER); } else if (expecting == Expecting(BACKSLASH)) { foundSlash = YES; expecting = Expecting(NUMBER); } else return (ERROR); return (NO_ERROR); } int DoTaxaStat (void) { int i, j, maxLen, nameLen, nIncludedTaxa; char tempName[100]; if (defMatrix == NO) { MrBayesPrint ("%s A character matrix must be defined first\n", spacer); return (ERROR); } /* find maximum length of taxon name */ maxLen = nIncludedTaxa = 0; for (i=0; i maxLen) maxLen = (int) strlen(tempName); if (taxaInfo[i].isDeleted == NO) nIncludedTaxa++; } MrBayesPrint ("%s Showing taxon status:\n\n", spacer); if (nIncludedTaxa == numTaxa) MrBayesPrint ("%s Number of taxa = %d (all of which are included)\n", spacer, numTaxa); else MrBayesPrint ("%s Number of taxa = %d (of which %d are included)\n", spacer, numTaxa, nIncludedTaxa); MrBayesPrint ("%s Number of constraints = %d\n\n", spacer, numDefinedConstraints); if (numDefinedConstraints > 0) { for (j=0; j 0) { MrBayesPrint ("----"); for (j=0; j%4d (%s) ", spacer, i+1, tempName); else MrBayesPrint ("%s %4d (%s) ", spacer, i+1, tempName); for (j=0; j<(maxLen-nameLen); j++) MrBayesPrint (" "); MrBayesPrint (" -- "); if (taxaInfo[i].isDeleted == YES) MrBayesPrint ("Deleted "); else MrBayesPrint ("Included"); MrBayesPrint (" "); for (j=0; j = [&R] ; tree = [&U] ; tree [&E CppEvents{1,2,5}] = [&R] [&clockrate = 1.23] ((1:0.021[&E CppEvents{1,2,5} 2:(0.10 1.11,0.83 3.17)],2:0.021):0.038,3:0.059); tree [&B TK02BranchRates{1,2,5}] = [&R] [&clockrate = 1.23] ((1:0.021[&B TK02BranchRates{1,2,5} 1.12],2:0.021[&B TK02BranchRates{1,2,5}... Values will be stored in event sets that go with the tree and that are used to initialize the relaxed clock parameters before a run is started. Note that several sets of events can be stored with each tree. */ if (isTaxsetDef == NO) { MrBayesPrint ("%s Taxon labels must be specified before a tree could be red in\n", spacer); return (ERROR); } if (inTreesBlock == NO) { MrBayesPrint ("%s You must be in a trees block to read a tree\n", spacer); return (ERROR); } if (expecting == Expecting(PARAMETER)) { /* this is the name of the tree */ if (inSumtCommand==YES || inComparetreeCommand == YES) { /* we are reading in a tree to sumt or comparetree counters */ t = sumtParams.tree; ResetPolyTree (t); } else { /* we are reading in a user tree */ /* check if the tree exists */ treeIndex = 0; for (i=0; iname) == 0) break; treeIndex = i; if (treeIndex < numUserTrees) { MrBayesPrint ("%s Overwriting tree '%s'.\n", spacer, userTree[treeIndex]); FreePolyTree (userTree[treeIndex]); } if ((userTree[treeIndex] = AllocatePolyTree (numTaxa)) == NULL) return (ERROR); t = userTree[treeIndex]; } strncpy (t->name, tkn, 99); foundColon = foundAmpersand = foundEqual = foundComment = NO; foundE = foundB = foundN = foundFirst = foundClockrate = foundName = NO; eSetIndex = bSetIndex = eventIndex = 0; nextAvailableNode = 0; if (isTranslateDef == YES && isTranslateDiff == YES) nextIntNodeIndex = numTranslates; else nextIntNodeIndex = numTaxa; pp = &t->nodes[nextAvailableNode++]; t->root = pp; t->isRooted = NO; /* expect unrooted tree */ t->isClock = NO; /* expect nonclock tree */ t->isCalibrated = NO; /* expect uncalibrated tree */ t->isRelaxed = NO; /* expect strict clock if clock tree */ t->clockRate = 0.0; /* expect no clock rate */ t->popSizeSet = NO; readComment = YES; expecting = Expecting(EQUALSIGN) | Expecting(LEFTCOMMENT); lastExpecting = expecting; } else if (expecting == Expecting(EQUALSIGN)) { if (foundClockrate == YES) expecting = Expecting(NUMBER); else { for (i=0; i= 2*numTaxa) { MrBayesPrint ("%s Too many nodes on tree '%s'\n", spacer, t->name); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } qq = &t->nodes[nextAvailableNode++]; qq->anc = pp; pp->left = qq; pp->index = nextIntNodeIndex++; pp = qq; expecting = Expecting(LEFTPAR); expecting |= Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(LEFTCOMMENT); lastExpecting = expecting; } } else if (expecting == Expecting(ALPHA)) { if (foundAmpersand == YES) { if (strcmp(tkn,"E") == 0) { foundE = YES; expecting = Expecting(ALPHA); } else if (strcmp(tkn,"B") == 0) { foundB = YES; expecting = Expecting(ALPHA); } else if (strcmp(tkn,"N") == 0) { foundN = YES; expecting = Expecting(ALPHA); } else if (strcmp(tkn, "R") == 0) { t->isRooted = YES; t->isClock = YES; /* assume clock if rooted */ expecting = Expecting(RIGHTCOMMENT); } else if (strcmp(tkn, "U") == 0) { t->isRooted = NO; expecting = Expecting(RIGHTCOMMENT); } else if (strcmp(tkn, "clockrate") == 0) { t->isCalibrated = YES; foundClockrate = YES; expecting = Expecting(EQUALSIGN); } else { inComment = YES; numComments++; expecting = lastExpecting; } foundAmpersand = NO; } else if (foundName == YES && foundCurly == YES) { if( strcmp("all",tkn) == 0 ) { SafeStrcat (&tempNameString,tkn); expecting = Expecting(RIGHTCURL); } else { MrBayesPrint ("%s Urecognized argument '%s'\n", spacer, tkn); return (ERROR); } } else if (foundE == YES) /* We have seen &E */ { if (foundEqual == NO) /* We have not seen name before and we are in header */ { t->nESets++; t->isRelaxed = YES; t->nEvents = (int **) SafeRealloc ((void *)t->nEvents, t->nESets*sizeof(int *)); t->position = (MrBFlt ***) SafeRealloc ((void *)t->position, t->nESets*sizeof(MrBFlt **)); t->rateMult = (MrBFlt ***) SafeRealloc ((void *)t->rateMult, t->nESets*sizeof(MrBFlt **)); t->nEvents[t->nESets-1] = (int *) SafeCalloc ((size_t)(2*numTaxa), sizeof(int)); t->position[t->nESets-1] = (MrBFlt **) SafeCalloc ((size_t)(2*numTaxa), sizeof(MrBFlt *)); t->rateMult[t->nESets-1] = (MrBFlt **) SafeCalloc ((size_t)(2*numTaxa), sizeof(MrBFlt *)); t->eSetName = (char **) SafeRealloc ((void *)t->eSetName, t->nESets*sizeof(char **)); } SafeStrcpy (&tempNameString,tkn); foundName = YES; expecting = Expecting(LEFTCURL); if (foundEqual == YES) expecting |= Expecting(NUMBER); else expecting |= Expecting(RIGHTCOMMENT); } else if (foundB == YES) { if (foundEqual == NO) { t->nBSets++; t->isRelaxed = YES; t->effectiveBrLen = (MrBFlt **) SafeRealloc ((void *)t->effectiveBrLen, (size_t)(t->nBSets*sizeof(MrBFlt *))); t->effectiveBrLen[t->nBSets-1] = (MrBFlt *) SafeCalloc ((size_t)(2*numTaxa),sizeof(MrBFlt)); for (i=0; i<2*numTaxa; i++) t->effectiveBrLen[t->nBSets-1][i] = 1.0; t->bSetName = (char **) SafeRealloc ((void *)t->bSetName, t->nBSets*sizeof(char **)); t->bSetName[t->nBSets-1] = (char *) SafeCalloc (strlen(tkn)+1,sizeof(char)); } SafeStrcpy (&tempNameString,tkn); foundName = YES; expecting = Expecting(LEFTCURL); if (foundEqual == YES) expecting |= Expecting(NUMBER); else expecting |= Expecting(RIGHTCOMMENT); } else if (foundN == YES) { if (foundEqual == NO) { if (t->popSizeSet == YES) { MrBayesPrint ("%s Cannot hold more than one population size set\n", spacer); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } t->popSizeSet = YES; if (isTranslateDef == YES && isTranslateDiff == YES) t->popSize = (MrBFlt *) SafeCalloc (2*numTranslates-1, sizeof(MrBFlt)); else t->popSize = (MrBFlt *) SafeCalloc (2*numLocalTaxa-1, sizeof(MrBFlt)); } SafeStrcpy (&tempNameString,tkn); foundName = YES; expecting = Expecting(LEFTCURL); if (foundEqual == YES) expecting |= Expecting(NUMBER); else expecting |= Expecting(RIGHTCOMMENT); } else /* taxon name */ { if (isTranslateDef == YES) { /* we are using the translation table */ if (CheckString (transTo, numTranslates, tkn, &index) == ERROR) { MrBayesPrint ("%s Could not find token '%s' in taxon translation table\n", spacer, tkn); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } strcpy (tempName, transFrom[index]); if (isTranslateDiff == NO && CheckString (taxaNames, numTaxa, tempName, &index) == ERROR) { MrBayesPrint ("%s Could not find taxon '%s' in list of taxa\n", spacer, tkn); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } if (tempSet[index] == YES) { MrBayesPrint ("%s Taxon name '%s' already used in tree\n", spacer, tkn); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } tempSet[index] = YES; strcpy (pp->label, tempName); pp->index = index; } else { /* Check to see if the name is in the list of taxon names. */ if (CheckString (taxaNames, numTaxa, tkn, &index) == ERROR) { MrBayesPrint ("%s Could not find taxon '%s' in list of taxa\n", spacer, tkn); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } if (tempSet[index] == YES) { MrBayesPrint ("%s Taxon name '%s' already used in tree\n", spacer, tkn); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } tempSet[index] = YES; strcpy (pp->label, tkn); pp->index = index; } expecting = Expecting(COMMA); expecting |= Expecting(COLON); expecting |= Expecting(RIGHTPAR); } } else if (expecting == Expecting(RIGHTPAR)) { if (foundE == YES) expecting = Expecting(RIGHTCOMMENT); else { if (pp->anc == NULL) { MrBayesPrint ("%s Incorrect tree format: cannot go down\n", spacer);//, tkn if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } if( pp->anc->left == pp ) { MrBayesPrint ("%s Incorrect tree format: all nodes except tips should have more then one child. Either a single\n", spacer); MrBayesPrint ("%s taxon is surrounded with brackets or there is a clade surrounded by double brackets.\n", spacer); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } pp = pp->anc; if (pp->anc == NULL) { /* finish up tree */ t->nNodes = nextAvailableNode; t->nIntNodes = t->nNodes; for (i=0; inNodes; i++) { if (t->nodes[i].left == NULL) t->nIntNodes--; } GetPolyDownPass(t); /* check that number of taxa is correct */ if (t->isRooted == NO && t->nNodes-t->nIntNodes == t->nIntNodes + 1) t->isRooted = YES; if ((t->isRooted == YES && t->nNodes-t->nIntNodes != t->nIntNodes + 1) || (t->isRooted == NO && t->nNodes-t->nIntNodes != t->nIntNodes + 2)) { /* we are protected from adding too many taxa by taxon-matching code above */ if (t->isRooted == YES && t->nNodes-t->nIntNodes == t->nIntNodes + 2) { MrBayesPrint ("%s The tree is declared as rooted (by comment [&R]) but\n", spacer); MrBayesPrint ("%s the given tree has unrooted structure.\n", spacer); } else MrBayesPrint ("%s Taxa missing in tree\n", spacer); return (ERROR); } /* check other properties */ if (t->isClock == YES && t->isRooted == NO) { MrBayesPrint ("%s Tree has clock rate but is not rooted\n", spacer); return (ERROR); /* Note: any deviation from an ultrametric tree must be assumed to be due to dated tips at this point */ } if (t->isRelaxed == YES && t->isClock == NO) { MrBayesPrint ("%s Tree has relaxed clock rates but is not a clock tree\n", spacer); return (ERROR); } if (inSumtCommand == NO && inComparetreeCommand == NO) { if (treeIndex == numUserTrees) numUserTrees++; MrBayesPrint ("%s Successfully read tree '%s'\n", spacer, userTree[treeIndex]->name); } if (t->popSize == NULL) { readComment = NO; expecting = Expecting(SEMICOLON); } else { readComment = YES; expecting = Expecting(LEFTCOMMENT); lastExpecting = expecting; } } else { expecting = Expecting(COMMA); expecting |= Expecting(COLON); expecting |= Expecting(RIGHTPAR); } } } else if (expecting == Expecting(COLON)) { foundColon = YES; if (foundE == YES) expecting = Expecting(LEFTPAR); else expecting = Expecting(NUMBER); expecting |= Expecting(LEFTCOMMENT); lastExpecting = expecting; } else if (expecting == Expecting(COMMA)) { if (foundName == YES) { SafeStrcat (&tempNameString,","); expecting = Expecting(NUMBER); } else if (foundE == YES) { expecting = Expecting(NUMBER); } else { if (nextAvailableNode >= 2*numTaxa) { MrBayesPrint ("%s Too many nodes on tree '%s'\n", spacer, t->name); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } qq = &t->nodes[nextAvailableNode++]; pp->sib = qq; qq->anc = pp->anc; pp = qq; expecting = Expecting(LEFTPAR); expecting |= Expecting(ALPHA); expecting |= Expecting(NUMBER); expecting |= Expecting(LEFTCOMMENT); lastExpecting = expecting; } } else if (expecting == Expecting(NUMBER)) { if (foundClockrate == YES) { sscanf (tkn, "%lf", &tempD); t->clockRate = tempD; foundClockrate = NO; expecting = Expecting(RIGHTCOMMENT); } else if (foundName == YES && foundCurly == YES) { /* still assembling name of a param set */ SafeStrcat (&tempNameString,tkn); expecting = Expecting(RIGHTCURL) | Expecting(COMMA); } else if (foundN == YES) { /* we only know now that name is complete if it does not have curlies in it */ foundName = NO; if (strcmp(tempNameString,t->popSizeSetName) != 0) { MrBayesPrint ("%s Could not find population size set '%s'\n", spacer, tempNameString); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } sscanf (tkn, "%lf", &tempD); t->popSize[pp->index] = tempD; foundN = NO; expecting = Expecting(RIGHTCOMMENT); } else if (foundB == YES) { /* we only know now that name is complete if it does not have curlies in it */ foundName = NO; /* find the right effective branch length set */ for (i=0; inBSets; i++) if (strcmp(t->bSetName[i],tempNameString) == 0) break; if (i == t->nBSets) { MrBayesPrint ("%s Could not find effective branch length set '%s'\n", spacer, tempNameString); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } bSetIndex = i; sscanf (tkn, "%lf", &tempD); t->effectiveBrLen[bSetIndex][pp->index] = tempD; foundB = NO; expecting = Expecting(RIGHTCOMMENT); } else if (foundE == YES) { if (foundColon == NO) { /* we only know now that name is complete if it does not have curlies in it */ foundName = NO; /* find the right event set */ for (i=0; inESets; i++) if (strcmp(t->eSetName[i],tempNameString) == 0) break; if (i == t->nESets) { MrBayesPrint ("%s Could not find event set '%s'\n", spacer, tempNameString); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } eSetIndex = i; sscanf (tkn, "%d", &tempInt); if (tempInt < 0) { MrBayesPrint ("%s Wrong number of events (%d) for event set '%s'\n", spacer, tempInt, t->eSetName[eSetIndex]); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } t->nEvents[eSetIndex][pp->index] = tempInt; if (tempInt > 0) { t->position[eSetIndex][pp->index] = (MrBFlt *) SafeCalloc (tempInt, sizeof(MrBFlt)); t->rateMult[eSetIndex][pp->index] = (MrBFlt *) SafeCalloc (tempInt, sizeof(MrBFlt)); expecting = Expecting (COLON); if (inSumtCommand == YES || inComparetreeCommand == YES) expecting |= Expecting (RIGHTCOMMENT); /* we allow empty event specifications in sumt and comparetree */ } else expecting = Expecting (RIGHTCOMMENT); eventIndex = 0; } else if (foundFirst == NO) { /* processing the first number in the cpp event pair */ sscanf (tkn, "%lf", &tempD); t->position[eSetIndex][pp->index][eventIndex] = tempD; expecting = Expecting(NUMBER); foundFirst = YES; } else { /* processing the second number in the cpp event pair */ foundFirst = NO; sscanf (tkn, "%lf", &tempD); t->rateMult[eSetIndex][pp->index][eventIndex] = tempD; #if defined (PRINT_RATEMULTIPLIERS_CPP) //if(rateMultfp!=NULL) // fprintf(rateMultfp,"%s\n",tkn); #endif eventIndex++; if (eventIndex == t->nEvents[eSetIndex][pp->index]) { expecting = Expecting(RIGHTPAR); foundColon = NO; } else expecting = Expecting(COMMA); } } else if (foundColon == YES) { /* branch length */ sscanf (tkn, "%lf", &tempD); pp->length = tempD; foundColon = NO; t->brlensDef = YES; expecting = Expecting(COMMA); expecting |= Expecting(RIGHTPAR); expecting |= Expecting(LEFTCOMMENT); lastExpecting = expecting; } else /* taxon identifier */ { if (isTranslateDef == YES) { /* we are using the translation table */ if (CheckString (transTo, numTranslates, tkn, &index) == ERROR) { MrBayesPrint ("%s Could not find token '%s' in taxon translation table\n", spacer, tkn); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } strcpy (tempName, transFrom[index]); if (isTranslateDiff == NO && CheckString (taxaNames, numTaxa, tempName, &index) == ERROR) { MrBayesPrint ("%s Could not find taxon '%s' in list of taxa\n", spacer, tkn); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } if (tempSet[index] == YES) { MrBayesPrint ("%s Taxon name '%s' already used in tree\n", spacer, tkn); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } tempSet[index] = YES; strcpy (pp->label, tempName); pp->index = index; } else { /* Simply use taxon number; first check to see if the name is in the list of taxon names. */ if (CheckString (taxaNames, numTaxa, tkn, &index) == ERROR) { /* The number could not be found as a taxon name in the list of taxon names. We will assume that the user has then input taxa as numbers and not the names. */ sscanf (tkn, "%d", &index); if (index < 1 || index > numTaxa) { MrBayesPrint ("%s Taxon number %d is out of range\n", spacer, index); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } index--; if (tempSet[index] == YES) { MrBayesPrint ("%s Taxon name %d has already been used in tree '%s'\n", spacer, index+1, t->name); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } } else { /* The number is in the list of taxon names */ if (index < 0 || index >= numTaxa) { MrBayesPrint ("%s Taxon name %s could not be found\n", spacer, tkn); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } if (tempSet[index] == YES) { MrBayesPrint ("%s Taxon %d has already been used in tree '%s'\n", spacer, index+1, t->name); if (inSumtCommand == NO && inComparetreeCommand == NO) FreePolyTree (userTree[treeIndex]); return (ERROR); } } tempSet[index] = YES; strcpy (pp->label, taxaNames[index]); pp->index = index; } expecting = Expecting(COMMA); expecting |= Expecting(COLON); expecting |= Expecting(RIGHTPAR); expecting |= Expecting(LEFTCOMMENT); lastExpecting = expecting; } } else if (expecting == Expecting(LEFTCOMMENT)) { expecting = Expecting(AMPERSAND); foundComment = YES; } else if (expecting == Expecting(RIGHTCOMMENT)) { if (foundEqual == NO) { /* We may have a complete name of a set of branch parameters, which needs to be recorded */ if (foundName == YES) { if (foundE == YES) { t->eSetName[t->nESets-1] = (char *) SafeCalloc (strlen(tempNameString)+1,sizeof(char)); strcat(t->eSetName[t->nESets-1],tempNameString); } else if (foundB == YES) { t->bSetName[t->nBSets-1] = (char *) SafeCalloc (strlen(tempNameString)+1,sizeof(char)); strcat(t->bSetName[t->nBSets-1],tempNameString); } else if (foundN == YES) { t->popSizeSetName = (char *) SafeCalloc (strlen(tempNameString)+1,sizeof(char)); strcpy(t->popSizeSetName,tempNameString); } foundName = NO; } expecting = Expecting(EQUALSIGN); } else { if (pp->anc == NULL) { if (pp->left == NULL) expecting = Expecting(LEFTPAR); else expecting = Expecting(SEMICOLON); } else if (pp == pp->anc->left) expecting = Expecting(COMMA); else expecting = Expecting(RIGHTPAR); } foundE = foundB = foundN = NO; expecting |= Expecting(LEFTCOMMENT); } else if (expecting == Expecting(AMPERSAND)) { foundAmpersand = YES; foundComment = NO; expecting = Expecting (ALPHA); } else if (foundComment == YES) { numComments++; foundComment = NO; } else if (expecting == Expecting(LEFTCURL)) { if( foundName == YES) { foundCurly=YES; SafeStrcat (&tempNameString,"{"); expecting = Expecting(NUMBER) | Expecting(ALPHA); } else return(ERROR); } else if (expecting == Expecting(RIGHTCURL)) { if( foundName == YES) { SafeStrcat (&tempNameString,"}"); foundCurly=NO; if (foundEqual == NO) { /* We are processing a name of a set of branch params in the header of a tree. */ expecting = Expecting(RIGHTCOMMENT); } else { /* We are processing a param value of a branch param set */ expecting = Expecting(NUMBER); } } else return(ERROR); } return (NO_ERROR); MrBayesPrint ("%s", parmName); /* just because I am tired of seeing the unused parameter error msg */ } int DoUserTree (void) { MrBayesPrint ("%s Usertree command deprecated. Define the tree in a treeblock and use 'Startvals' instead.\n", spacer); return (ERROR); } int DoUserTreeParm (char *parmName, char *tkn) { if (expecting == Expecting(EQUALSIGN)) { expecting = Expecting(LEFTPAR); expecting |= Expecting(RIGHTPAR); expecting |= Expecting(COLON); expecting |= Expecting(NUMBER); expecting |= Expecting(ALPHA); expecting |= Expecting(SEMICOLON); } else if (expecting == Expecting(LEFTPAR)) { expecting = Expecting(LEFTPAR); expecting |= Expecting(ALPHA); expecting |= Expecting(NUMBER); } else if (expecting == Expecting(ALPHA)) { expecting = Expecting(COLON); expecting |= Expecting(COMMA); expecting |= Expecting(RIGHTPAR); } else if (expecting == Expecting(NUMBER)) { expecting = Expecting(COLON); expecting |= Expecting(COMMA); expecting |= Expecting(RIGHTPAR); } else if (expecting == Expecting(COLON)) { expecting = Expecting(NUMBER); } else if (expecting == Expecting(COMMA)) { expecting = Expecting(LEFTPAR); expecting |= Expecting(ALPHA); expecting |= Expecting(NUMBER); } else if (expecting == Expecting(RIGHTPAR)) { expecting = Expecting(RIGHTPAR); expecting |= Expecting(COMMA); expecting |= Expecting(COLON); expecting |= Expecting(SEMICOLON); } else return (ERROR); return (NO_ERROR); } int DoVersion (void) { MrBayesPrint (" --------------------------------------------------------------------------- \n"); MrBayesPrint (" Version \n"); MrBayesPrint (" \n"); MrBayesPrint (" MrBayes v%s \n", VERSION_NUMBER); MrBayesPrint (" --------------------------------------------------------------------------- \n"); return (NO_ERROR); } SafeLong Expecting (int y) { SafeLong x; x = (SafeLong)pow(2.0, (MrBFlt)y); return (x); } #ifdef HAVE_LIBREADLINE /* This function is for commandline substitution: first word is always a command */ char *command_generator(const char *text, int state) { static int list_index, len; char *command; if(state==0) { list_index=0; len= (int) strlen(text); } while ((command=commands[list_index].string)!=NULL) { list_index++; if (strncasecmp(command,text,len)==0) /* memory is freed by the readline library so we need a strdup here */ return strdup(command); } return (char *)NULL; } #endif int FindValidCommand (char *tk, int *numMatches) { int i, j, tkLen, targetLen, numDiff; CmdType *p; p = commands + 0; tkLen = (int) strlen(tk); (*numMatches) = 0; for (i=0; istring); if (tkLen <= targetLen) { for (j=0, numDiff=0; jstring[j])) numDiff++; } if (numDiff == 0) { (*numMatches)++; commandPtr = p; if (tkLen == targetLen) break; } } p++; } inValidCommand = NO; if (*numMatches == 1) { inValidCommand = YES; return (NO_ERROR); } else return (ERROR); } int FindValidParam (char *tk, int *numMatches) { int i, j, tkLen, targetLen, numDiff; CmdType *p; ParmInfoPtr q; if (commandPtr) p = commandPtr; else { MrBayesPrint ("%s Command pointer is NULL\n", spacer); return (ERROR); } tkLen = (int) strlen(tk); *numMatches = 0; for (i=0; inumParms; i++) { q = paramTable + (p->parmList[i]); targetLen = (int) strlen(q->string); /*printf ("%s %d (%s %d)\n", q->string, targetLen, tk, p->numParms);*/ if (!strcmp(q->string, "Xxxxxxxxxx")) { (*numMatches)++; paramPtr = q; } else if (tkLen <= targetLen) { for (j=0, numDiff=0; jstring[j])) numDiff++; } if (numDiff == 0) { (*numMatches)++; paramPtr = q; if (tkLen == targetLen) break; } } } if (*numMatches == 1) return (NO_ERROR); else return (ERROR); } int FreeCharacters (void) { int i, memoryLetFree; memoryLetFree = NO; if (memAllocs[ALLOC_TMPSET] == YES) { if (numChar > numTaxa) tempSet = (int *) SafeRealloc ((void *) tempSet, (size_t)(numTaxa*sizeof(int))); tempSetNeg = (int *) SafeRealloc ((void *) tempSetNeg, (size_t)(numTaxa*sizeof(int))); } if (memAllocs[ALLOC_MATRIX] == YES) { free (matrix); matrix = NULL; defMatrix = NO; memAllocs[ALLOC_MATRIX] = NO; memoryLetFree = YES; } if (memAllocs[ALLOC_CHARINFO] == YES) { free (charInfo); charInfo = NULL; memAllocs[ALLOC_CHARINFO] = NO; memoryLetFree = YES; } if (memAllocs[ALLOC_CHARSETS] == YES) { for (i=0; i 0) { MrBayesPrint ("%s Deleting user trees\n", spacer); for (i=0; i maxDiv) maxDiv = partitionId[i][n]; divFound = (int *) SafeCalloc (maxDiv, sizeof(int)); for (i=0; i tempMax ) { *tokenType = NOTHING; token[20]='\0'; MrBayesPrint ("%s Error while parsing a string. Token \"%s...[followed by at least %d more charectors]\" is too long.\n", spacer,token,tempMax-token-20 ); MrBayesPrint ("%s Maximum allowed lenght of a token is %d\n", spacer,tempMax-token ); return (ERROR); } *temp++ = *(*sourceH)++; } *tokenType = ALPHA; } *temp = '\0'; readWord = NO; return (NO_ERROR);; } *tokenType = UNKNOWN_TOKEN_TYPE; if (IsIn(**sourceH,"=")) { *temp++ = *(*sourceH)++; *tokenType = EQUALSIGN; } else if (IsIn(**sourceH,";")) { *temp++ = *(*sourceH)++; *tokenType = SEMICOLON; } else if (IsIn(**sourceH,":")) { *temp++ = *(*sourceH)++; *tokenType = COLON; } else if (IsIn(**sourceH,",")) { *temp++ = *(*sourceH)++; *tokenType = COMMA; } else if (IsIn(**sourceH,"#")) { *temp++ = *(*sourceH)++; *tokenType = POUNDSIGN; } else if (IsIn(**sourceH,"(")) { *temp++ = *(*sourceH)++; *tokenType = LEFTPAR; } else if (IsIn(**sourceH,")")) { *temp++ = *(*sourceH)++; *tokenType = RIGHTPAR; } else if (IsIn(**sourceH,"{")) { *temp++ = *(*sourceH)++; *tokenType = LEFTCURL; } else if (IsIn(**sourceH,"}")) { *temp++ = *(*sourceH)++; *tokenType = RIGHTCURL; } else if (IsIn(**sourceH,"[")) { *temp++ = *(*sourceH)++; *tokenType = LEFTCOMMENT; } else if (IsIn(**sourceH,"]")) { *temp++ = *(*sourceH)++; *tokenType = RIGHTCOMMENT; } else if (IsIn(**sourceH,"?")) { *temp++ = *(*sourceH)++; *tokenType = QUESTIONMARK; } else if (IsIn(**sourceH,"-")) { *temp++ = *(*sourceH)++; *tokenType = DASH; } else if (IsIn(**sourceH,"$")) { *temp++ = *(*sourceH)++; *tokenType = DOLLAR; } else if (IsIn(**sourceH,"\"") && readWord == YES) { (*sourceH)++; while(**sourceH != '"' && **sourceH != '\0') { if( temp > tempMax ) { *tokenType = NOTHING; token[20]='\0'; MrBayesPrint ("%s Error while parsing a string. Token \"%s...[followed by at least %d more charectors]\" is too long.\n", spacer,token,tempMax-token-20 ); MrBayesPrint ("%s Maximum allowed lenght of a token is %d\n", spacer,tempMax-token ); return (ERROR); } *temp++ = *((*sourceH)++); } *temp='\0'; *tokenType = ALPHA; (*sourceH)++; readWord = NO; } else if (IsIn(**sourceH,"abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ_0123456789.")) { if (IsIn(**sourceH,"0123456789.")) allNumbers = TRUE; else allNumbers = FALSE; foundExp = foundExpSign = FALSE; *temp++ = *(*sourceH)++; while(IsIn(**sourceH,"abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ_0123456789.-+")) { if( temp > tempMax ) { *tokenType = NOTHING; token[20]='\0'; MrBayesPrint ("%s Error while parsing a string. Token \"%s...[followed by at least %d more charectors]\" is too long.\n", spacer,token,tempMax-token-20 ); MrBayesPrint ("%s Maximum allowed lenght of a token is %d\n", spacer,tempMax-token ); return (ERROR); } if(allNumbers == TRUE && !IsIn((*sourceH)[-1],"Ee") && **sourceH=='-') break; else if (allNumbers == TRUE && IsIn(**sourceH,"Ee") && foundExp == NO) foundExp = TRUE; else if (allNumbers == TRUE && IsIn(**sourceH,"+-") && IsIn((*sourceH)[-1],"Ee")) foundExpSign = TRUE; else if (!IsIn(**sourceH,"0123456789.")) allNumbers = FALSE; *temp++ = *(*sourceH)++; } if (allNumbers == TRUE) *tokenType = NUMBER; else *tokenType = ALPHA; } else if (IsIn(**sourceH,"*")) { *temp++ = *(*sourceH)++; *tokenType = ASTERISK; } else if (IsIn(**sourceH,"/")) { *temp++ = *(*sourceH)++; *tokenType = FORWARDSLASH; } else if (IsIn(**sourceH,"'\\'")) { *temp++ = *(*sourceH)++; *tokenType = BACKSLASH; } else if (IsIn(**sourceH,"!")) { *temp++ = *(*sourceH)++; *tokenType = EXCLAMATIONMARK; } else if (IsIn(**sourceH,"%")) { *temp++ = *(*sourceH)++; *tokenType = PERCENT; } else if (IsIn(**sourceH,"\"")) { *temp++ = *(*sourceH)++; *tokenType = QUOTATIONMARK; } else if (IsIn(**sourceH,"&")) { *temp++ = *(*sourceH)++; *tokenType = AMPERSAND; } else if (IsIn(**sourceH,"~+^@|{}`><")) { *temp++ = *(*sourceH)++; *tokenType = WEIRD; } *temp = '\0'; return (NO_ERROR); } int GetUserHelp (char *helpTkn) { int i, j, k, tempInt; char yesNoStr[4], tempString[100]; Model *mp; if (!strcmp(helpTkn, "Begin")) { MrBayesPrint (" --------------------------------------------------------------------------- \n"); MrBayesPrint (" Begin \n"); MrBayesPrint (" \n"); MrBayesPrint (" This command is used to format data or commands in the program. The correct \n"); MrBayesPrint (" usage is \n"); MrBayesPrint (" \n"); MrBayesPrint (" begin ; \n"); MrBayesPrint (" \n"); MrBayesPrint (" The two valid uses of the \"begin\" command, then, are \n"); MrBayesPrint (" \n"); MrBayesPrint (" begin data; \n"); MrBayesPrint (" begin mrbayes; \n"); MrBayesPrint (" \n"); MrBayesPrint (" The \"data\" specifier is used to specify the beginning of a data block; your \n"); MrBayesPrint (" character data should follow. For example, the following is an example of \n"); MrBayesPrint (" a data block for four taxa and ten DNA sites: \n"); MrBayesPrint (" \n"); MrBayesPrint (" begin data; \n"); MrBayesPrint (" dimensions ntax=4 nchar=10; \n"); MrBayesPrint (" format datatype=dna; \n"); MrBayesPrint (" matrix \n"); MrBayesPrint (" taxon_1 AACGATTCGT \n"); MrBayesPrint (" taxon_2 AAGGATTCCA \n"); MrBayesPrint (" taxon_3 AACGACTCCT \n"); MrBayesPrint (" taxon_4 AAGGATTCCT \n"); MrBayesPrint (" ; \n"); MrBayesPrint (" end; \n"); MrBayesPrint (" \n"); MrBayesPrint (" The other commands -- dimensions, format, and matrix -- are discussed \n"); MrBayesPrint (" in the appropriate help menu. The only thing to note here is that the \n"); MrBayesPrint (" block begins with a \"begin data\" command. The \"mrbayes\" command is \n"); MrBayesPrint (" used to enter commands specific to the MrBayes program into the file. \n"); MrBayesPrint (" This allows you to automatically process commands on execution of the \n"); MrBayesPrint (" program. The following is a simple mrbayes block: \n"); MrBayesPrint (" \n"); MrBayesPrint (" begin mrbayes; \n"); MrBayesPrint (" charset first = 1-10\\3; \n"); MrBayesPrint (" charset second = 2-10\\3; \n"); MrBayesPrint (" charset third = 3-10\\3; \n"); MrBayesPrint (" end; \n"); MrBayesPrint (" \n"); MrBayesPrint (" This mrbayes block sets off the three \"charset\" commands, used to \n"); MrBayesPrint (" predefine some blocks of characters. The mrbayes block can be very useful. \n"); MrBayesPrint (" For example, in this case, it would save you the time of typing the char- \n"); MrBayesPrint (" acter sets each time you executed the file. Also, note that every \n"); MrBayesPrint (" \"begin \" command ends with an \"end\". Finally, you can \n"); MrBayesPrint (" have so-called foreign blocks in the file. An example of a foreign block \n"); MrBayesPrint (" would be \"begin paup\". The program will simply skip this block. This is \n"); MrBayesPrint (" useful because it means that you can use the same file for MrBayes, PAUP* \n"); MrBayesPrint (" or MacClade (although it isn't clear why you would want to use those other \n"); MrBayesPrint (" programs). \n"); MrBayesPrint (" --------------------------------------------------------------------------- \n"); } else if (!strcmp(helpTkn, "End")) { MrBayesPrint (" --------------------------------------------------------------------------- \n"); MrBayesPrint (" End \n"); MrBayesPrint (" \n"); MrBayesPrint (" This command is used to terminate a data or mrbayes block. The correct \n"); MrBayesPrint (" usage is \n"); MrBayesPrint (" \n"); MrBayesPrint (" end; \n"); MrBayesPrint (" \n"); MrBayesPrint (" For more information on this, check the help for the \"begin\" command. \n"); MrBayesPrint (" --------------------------------------------------------------------------- \n"); } else if (!strcmp(helpTkn, "Endblock")) { MrBayesPrint (" --------------------------------------------------------------------------- \n"); MrBayesPrint (" Endblock \n"); MrBayesPrint (" \n"); MrBayesPrint (" This is an older, deprecated version of \"End\", see that command. \n"); MrBayesPrint (" --------------------------------------------------------------------------- \n"); } else if (!strcmp(helpTkn, "Plot")) { MrBayesPrint (" --------------------------------------------------------------------------- \n"); MrBayesPrint (" Plot \n"); MrBayesPrint (" \n"); MrBayesPrint (" This command plots specified parameters in the .p file or one of the .p files \n"); MrBayesPrint (" created during an MCMC analysis. An x-y graph of the parameter over the course\n"); MrBayesPrint (" of the chain is created. The command can be useful for visually diagnosing \n"); MrBayesPrint (" convergence for many of the parameters of the phylogenetic model. The para- \n"); MrBayesPrint (" meter to be plotted is specified by the \"parameter\" option. Several para- \n"); MrBayesPrint (" meters can be plotted at once by using the \"match\" option, which has a \n"); MrBayesPrint (" default value of \"perfect\". For example, if you were to set \"parameter = pi\"\n"); MrBayesPrint (" and \"match = consistentwith\", then all of the state frequency parameters \n"); MrBayesPrint (" would be plotted. You can also set \"match=all\", in which case all of the \n"); MrBayesPrint (" parameters are plotted. \n"); MrBayesPrint (" \n"); MrBayesPrint (" Note that the \"Sump\" command provides a different set of convergence diag- \n"); MrBayesPrint (" nostics tools that you may also want to explore. Unlike \"Plot\", \"Sump\" can\n"); MrBayesPrint (" compare two or more parameter samples and will calculate convergence diagnos- \n"); MrBayesPrint (" tics as wel as parameter summaries for the pooled sample. \n"); MrBayesPrint (" \n"); MrBayesPrint (" Options: \n"); MrBayesPrint (" \n"); MrBayesPrint (" Relburnin -- If this option is set to 'Yes', then a proportion of the \n"); MrBayesPrint (" samples will be discarded as burnin when creating the plot. \n"); MrBayesPrint (" The proportion to be discarded is set with Burninfrac (see \n"); MrBayesPrint (" Burninfrac below). When the Relburnin option is set to 'No', \n"); MrBayesPrint (" then a specific number of samples is discarded instead. This \n"); MrBayesPrint (" number is set by Burnin (see below). Note that the burnin \n"); MrBayesPrint (" setting is shared across the 'comparetree', 'sump' and 'sumt'\n"); MrBayesPrint (" commands. \n"); MrBayesPrint (" Burnin -- Determines the number of samples (not generations) that will \n"); MrBayesPrint (" be discarded when summary statistics are calculated. The \n"); MrBayesPrint (" value of this option is only relevant when Relburnin is set \n"); MrBayesPrint (" to 'No'. \n"); MrBayesPrint (" Burninfrac -- Determines the fraction of samples that will be discarded \n"); MrBayesPrint (" when creating a plot. The value of this parameter is only \n"); MrBayesPrint (" relevant when Relburnin is set to 'Yes'. Example: A value of \n"); MrBayesPrint (" this option of 0.25 means that 25%% of the samples will be \n"); MrBayesPrint (" discarded. \n"); MrBayesPrint (" Filename -- The name of the file to plot. \n"); MrBayesPrint (" Parameter -- Specification of parameters to be plotted. See above for \n"); MrBayesPrint (" details. \n"); MrBayesPrint (" Match -- Specifies how to match parameter names to the Parameter \n"); MrBayesPrint (" specification. See above for details. \n"); MrBayesPrint (" \n"); MrBayesPrint (" Current settings: \n"); MrBayesPrint (" \n"); MrBayesPrint (" Parameter Options Current Setting \n"); MrBayesPrint (" ------------------------------------------------------------ \n"); MrBayesPrint (" Relburnin Yes/No %s \n", chainParams.relativeBurnin == YES ? "Yes" : "No"); MrBayesPrint (" Burnin %d \n", chainParams.chainBurnIn); MrBayesPrint (" Burninfrac %1.2lf \n", chainParams.burninFraction); MrBayesPrint (" Filename %s \n", plotParams.plotFileName); MrBayesPrint (" Parameter %s \n", plotParams.parameter); MrBayesPrint (" Match Perfect/Consistentwith/All %s \n", plotParams.match); MrBayesPrint (" \n"); MrBayesPrint (" --------------------------------------------------------------------------- \n"); } else if (!strcmp(helpTkn, "Dimensions")) { MrBayesPrint (" --------------------------------------------------------------------------- \n"); MrBayesPrint (" Dimensions \n"); MrBayesPrint (" \n"); MrBayesPrint (" This command is used in a data block to define the number of taxa and \n"); MrBayesPrint (" characters. The correct usage is \n"); MrBayesPrint (" \n"); MrBayesPrint (" dimensions ntax= nchar= \n"); MrBayesPrint (" \n"); MrBayesPrint (" The dimensions must be the first command in a data block. The following \n"); MrBayesPrint (" provides an example of the proper use of this command: \n"); MrBayesPrint (" \n"); MrBayesPrint (" begin data; \n"); MrBayesPrint (" dimensions ntax=4 nchar=10; \n"); MrBayesPrint (" format datatype=dna; \n"); MrBayesPrint (" matrix \n"); MrBayesPrint (" taxon_1 AACGATTCGT \n"); MrBayesPrint (" taxon_2 AAGGATTCCA \n"); MrBayesPrint (" taxon_3 AACGACTCCT \n"); MrBayesPrint (" taxon_4 AAGGATTCCT \n"); MrBayesPrint (" ; \n"); MrBayesPrint (" end; \n"); MrBayesPrint (" \n"); MrBayesPrint (" Here, the dimensions command tells MrBayes to expect a matrix with four \n"); MrBayesPrint (" taxa and 10 characters. \n"); MrBayesPrint (" --------------------------------------------------------------------------- \n"); } else if (!strcmp(helpTkn, "Format")) { MrBayesPrint (" --------------------------------------------------------------------------- \n"); MrBayesPrint (" Format \n"); MrBayesPrint (" \n"); MrBayesPrint (" This command is used in a data block to define the format of the char- \n"); MrBayesPrint (" acter matrix. The correct usage is \n"); MrBayesPrint (" \n"); MrBayesPrint (" format datatype= ... =