/* * puzzle.h * * * Part of TREE-PUZZLE 5.0 (June 2000) * * (c) 1999-2000 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. */ #ifndef _PUZZLE_ #define _PUZZLE_ #ifndef PACKAGE # define PACKAGE "tree-puzzle" #endif #ifndef VERSION # define VERSION "5.0" #endif #define DATE "October 2000" /* prototypes */ #include #include #include #include #include #include #include #include #include "util.h" #include "ml.h" #ifdef PARALLEL # include "ppuzzle.h" #endif #define STDOUT stdout #ifndef PARALLEL /* because printf() runs significantly faster */ /* than fprintf(stdout) on an Apple McIntosh */ /* (HS) */ # define FPRINTF printf # define STDOUTFILE #else # define FPRINTF fprintf # define STDOUTFILE STDOUT, #endif /* filenames */ # define FILENAMELENTH 2048 # define INFILEDEFAULT "infile" # define OUTFILEDEFAULT "outfile" # define TREEFILEDEFAULT "outtree" # define INTREEDEFAULT "intree" # define DISTANCESDEFAULT "outdist" # define TRIANGLEDEFAULT "outlm.eps" # define UNRESOLVEDDEFAULT "outqlist" # define ALLQUARTDEFAULT "outallquart" # define ALLQUARTLHDEFAULT "outallquartlh" # define OUTPTLISTDEFAULT "outpstep" # define OUTPTORDERDEFAULT "outptorder" # define INFILE infilename # define OUTFILE outfilename # define TREEFILE outtreename # define INTREE intreename # define DISTANCES outdistname # define TRIANGLE outlmname # define UNRESOLVED outqlistname # define ALLQUART outallquartname # define ALLQUARTLH outallquartlhname # define OUTPTLIST outpstepname # define OUTPTORDER outptordername EXTERN char infilename [FILENAMELENTH]; EXTERN char outfilename [FILENAMELENTH]; EXTERN char outtreename [FILENAMELENTH]; EXTERN char intreename [FILENAMELENTH]; EXTERN char outdistname [FILENAMELENTH]; EXTERN char outlmname [FILENAMELENTH]; EXTERN char outqlistname [FILENAMELENTH]; EXTERN char outallquartname [FILENAMELENTH]; EXTERN char outallquartlhname [FILENAMELENTH]; EXTERN char outpstepname [FILENAMELENTH]; EXTERN char outptordername [FILENAMELENTH]; #define OUTFILEEXT "puzzle" #define TREEFILEEXT "tree" #define DISTANCESEXT "dist" #define TRIANGLEEXT "eps" #define UNRESOLVEDEXT "qlist" #define ALLQUARTEXT "allquart" #define ALLQUARTLHEXT "allquartlh" #define OUTPTLISTEXT "pstep" #define OUTPTORDEREXT "ptorder" #ifndef PARALLEL /* because printf() runs significantly faster */ /* than fprintf(stdout) on an Apple McIntosh */ /* (HS) */ # define FPRINTF printf # define STDOUTFILE #else # define FPRINTF fprintf # define STDOUT stdout # define STDOUTFILE STDOUT, #endif /* auto_aamodel/auto_datatype values (xxx) */ #define AUTO_OFF 0 #define AUTO_GUESS 1 #define AUTO_DEFAULT 2 /* qptlist values (xxx) */ #define PSTOUT_NONE 0 #define PSTOUT_ORDER 1 #define PSTOUT_LISTORDER 2 #define PSTOUT_LIST 3 /* dtat_optn values (xxx) */ #define NUCLEOTIDE 0 #define AMINOACID 1 #define BINARY 2 /* typ_optn values (xxx) */ #define LIKMAPING_OPTN 1 #define TREERECON_OPTN 0 /* puzzlemodes (xxx) */ #define QUARTPUZ 0 #define USERTREE 1 #define PAIRDIST 2 /* rhetmodes (xxx) Modes of rate heterogeneity */ #define UNIFORMRATE 0 #define GAMMARATE 1 #define TWORATE 2 #define MIXEDRATE 3 /* defines for types of quartet likelihood computation (xxx) */ #define EXACT 0 #define APPROX 1 /* tree structure */ typedef struct oneedge { /* pointer to other three edges */ struct oneedge *up; struct oneedge *downleft; struct oneedge *downright; int numedge; /* number of edge */ uli edgeinfo; /* value of this edge */ int *edgemap; /* pointer to the local edgemap */ } ONEEDGE; /* variables */ EXTERN cmatrix biparts; /* bipartitions of tree of current puzzling step */ EXTERN cmatrix consbiparts; /* bipartitions of majority rule consensus tree */ EXTERN cmatrix seqchars; /* characters contained in data set */ EXTERN cmatrix treepict; /* picture of consensus tree */ EXTERN double minscore; /* value of edgescore on minedge */ EXTERN double tstvf84; /* F84 transition/transversion ratio */ EXTERN double tstvratio; /* expected transition/transversion ratio */ EXTERN double yrtsratio; /* expected pyrimidine/purine transition ratio */ EXTERN dvector ulkl; /* log L of user trees */ EXTERN dmatrix allsites; /* log L per sites of user trees */ EXTERN dvector ulklc; /* log L of user trees (clock) */ EXTERN dmatrix allsitesc; /* log L per sites of user trees (clock) */ EXTERN FILE *utfp; /* pointer to user tree file */ EXTERN FILE *seqfp; /* pointer to sequence input file */ EXTERN FILE *tfp; /* pointer to tree file */ EXTERN FILE *dfp; /* pointer to distance file */ EXTERN FILE *trifp; /* pointer to triangle file */ EXTERN FILE *unresfp; /* pointer to file with unresolved quartets */ EXTERN FILE *tmpfp; /* pointer to temporary file */ EXTERN FILE *qptlist; /* pointer to file with puzzling step trees */ EXTERN FILE *qptorder; /* pointer to file with unique puzzling step trees */ EXTERN int SHcodon; /* whether SH should be applied to 1st, 2nd codon positions */ EXTERN int utree_optn; /* use first user tree for estimation */ EXTERN int listqptrees; /* list puzzling step trees */ EXTERN int approxqp; /* approximate QP quartets */ EXTERN int *edgeofleaf; /* vector with edge number of all leaves */ EXTERN int codon_optn; /* declares what positions in a codon should be used */ EXTERN int compclock; /* computation of clocklike branch lengths */ EXTERN int chooseA; /* leaf variable */ EXTERN int chooseB; /* leaf variable */ EXTERN int clustA, clustB, clustC, clustD; /* number of members of LM clusters */ EXTERN int column; /* used for breaking lines (writing tree to treefile) */ EXTERN int Frequ_optn; /* use empirical base frequencies */ EXTERN int Maxbrnch; /* 2*Maxspc - 3 */ EXTERN int Maxseqc; /* number of sequence characters per taxum */ EXTERN int mflag; /* flag used for correct printing of runtime messages */ EXTERN int minedge; /* edge with minimum edgeinfo */ EXTERN int nextedge; /* number of edges in the current tree */ EXTERN int nextleaf; /* next leaf to add to tree */ EXTERN int numclust; /* number of clusters in LM analysis */ EXTERN int outgroup; /* outgroup */ EXTERN int puzzlemode; /* computation of QP tree and/or ML distances */ EXTERN int rootsearch; /* how location of root is found */ EXTERN int rhetmode; /* model of rate heterogeneity */ EXTERN int splitlength; /* length of one entry in splitpatterns */ EXTERN int *splitsizes; /* size of all different splits of all trees */ EXTERN int usebestq_optn; /* use only best quartet topology, no bayesian weights */ EXTERN int show_optn; /* show unresolved quartets */ EXTERN int savequart_optn; /* save memory block which quartets to file */ EXTERN int savequartlh_optn; /* save quartet likelihoods to file */ EXTERN int saveqlhbin_optn; /* save quartet likelihoods binary */ EXTERN int readquart_optn; /* read memory block which quartets from file */ EXTERN int sym_optn; /* symmetrize doublet frequencies */ EXTERN int xsize; /* depth of consensus tree picture */ EXTERN int ytaxcounter; /* counter for establishing y-coordinates of all taxa */ EXTERN int numutrees; /* number of users trees in input tree file */ EXTERN ivector clusterA, clusterB, clusterC, clusterD; /* clusters for LM analysis */ EXTERN ivector consconfid; /* confidence values of majority rule consensus tree */ EXTERN ivector conssizes; /* partition sizes of majority rule consensus tree */ EXTERN ivector trueID; /* leaf -> taxon on this leaf */ EXTERN ivector xcor; /* x-coordinates of consensus tree nodes */ EXTERN ivector ycor; /* y-coordinates of consensus tree nodes */ EXTERN ivector ycormax; /* maximal y-coordinates of consensus tree nodes */ EXTERN ivector ycormin; /* minimal y-coordinates of consensus tree nodes */ EXTERN ivector ycortax; /* y-coordinates of all taxa */ EXTERN ONEEDGE *edge; /* vector with all the edges of the tree */ EXTERN uli *splitcomp; /* bipartition storage */ EXTERN uli *splitfreqs; /* frequencies of all different splits of all trees */ EXTERN uli *splitpatterns; /* all different splits of all trees */ EXTERN uli badqs; /* number of bad quartets */ EXTERN uli consincluded; /* number of included biparts in the consensus tree */ EXTERN uli Currtrial; /* counter for puzzling steps */ EXTERN uli maxbiparts; /* space is reserved for that many bipartitions */ EXTERN uli mininfo; /* value of edgeinfo on minedge */ EXTERN uli numbiparts; /* number of different bipartitions */ EXTERN uli Numquartets; /* number of quartets */ EXTERN uli Numtrial; /* number of puzzling steps */ EXTERN uli lmqts; /* quartets investigated in LM analysis (0 = ALL) */ EXTERN int auto_datatype; /* guess datatype ? */ EXTERN int guessdata_optn; /* guessed datatype */ EXTERN int auto_aamodel; /* guess amino acid modell ? */ EXTERN int guessauto_aamodel; /* guessed amino acid modell ? */ EXTERN int guessDayhf_optn; /* guessed Dayhoff model option */ EXTERN int guessJtt_optn; /* guessed JTT model option */ EXTERN int guessblosum62_optn; /* guessed BLOSUM 62 model option */ EXTERN int guessmtrev_optn; /* guessed mtREV model option */ EXTERN int guesscprev_optn; /* guessed cpREV model option */ EXTERN int guessvtmv_optn; /* guessed VT model option */ EXTERN int guesswag_optn; /* guessed WAG model option */ /* counter variables needed in likelihood mapping analysis */ EXTERN uli ar1, ar2, ar3; EXTERN uli reg1, reg2, reg3, reg4, reg5, reg6, reg7; EXTERN uli reg1l, reg1r, reg2u, reg2d, reg3u, reg3d, reg4u, reg4d, reg5l, reg5r, reg6u, reg6d; EXTERN unsigned char *quartetinfo; /* place where quartets are stored */ EXTERN dvector qweight; /* for use in QP and LM analysis */ EXTERN dvector sqdiff; EXTERN ivector qworder; EXTERN ivector sqorder; EXTERN int randseed; EXTERN int psteptreestrlen; typedef struct treelistitemtypedummy { struct treelistitemtypedummy *pred; struct treelistitemtypedummy *succ; struct treelistitemtypedummy *sortnext; struct treelistitemtypedummy *sortlast; char *tree; int count; int id; int idx; } treelistitemtype; EXTERN treelistitemtype *psteptreelist; EXTERN treelistitemtype *psteptreesortlist; EXTERN int psteptreenum; EXTERN int psteptreesum; /* prototypes */ void makeF84model(void); void compnumqts(void); void setoptions(void); void openfiletoread(FILE **, const char[], const char[]); void openfiletowrite(FILE **, const char[], const char[]); void openfiletoappend(FILE **, const char[], const char[]); void closefile(FILE *); void symdoublets(void); void computeexpectations(void); void putdistance(FILE *); void findidenticals(FILE *); double averagedist(void); void initps(FILE *); void plotlmpoint(FILE *, double, double); void finishps(FILE *); void makelmpoint(FILE *, double, double, double); void printtreestats(FILE *); void timestamp(FILE *); void writeoutputfile(FILE *, int); /* definitions for writing output */ #define WRITEALL 0 #define WRITEPARAMS 1 #define WRITEREST 2 void writetimesstat(FILE *ofp); void writecutree(FILE *, int); void starttimer(void); void checktimer(uli); void estimateparametersnotree(void); void estimateparameterstree(void); int main(int, char *[]); int ulicmp(const void *, const void *); int intcmp(const void *, const void *); void readid(FILE *, int); char readnextcharacter(FILE *, int, int); void skiprestofline(FILE *, int, int); void skipcntrl(FILE *, int, int); void getseqs(FILE *); void initid(int); void fputid10(FILE *, int); int fputid(FILE *, int); void getsizesites(FILE *); void getdataset(FILE *); int guessdatatype(void); void translatedataset(void); void estimatebasefreqs(void); void guessmodel(void); void inittree(void); void addnextleaf(int); void freetree(void); void writeOTU(FILE *, int); void writetree(FILE *); int *initctree(); void copytree(int *ctree); void freectree(int **snodes); void printctree(int *ctree); char *sprintfctree(int *ctree, int strlen); void fprintffullpstree(FILE *outf, char *treestr); int printfsortctree(int *ctree); int sortctree(int *ctree); int ct_1stedge(int node); int ct_2ndedge(int node); int ct_3rdedge(int node); void printfpstrees(treelistitemtype *list); void printfsortedpstrees(treelistitemtype *list); void fprintfsortedpstrees(FILE *output, treelistitemtype *list, int itemnum, int itemsum, int comment, float cutoff); void sortbynum(treelistitemtype *list, treelistitemtype **sortlist); treelistitemtype *addtree2list(char **tree, int numtrees, treelistitemtype **list, int *numitems, int *numsum); void freetreelist(treelistitemtype **list, int *numitems, int *numsum); void resetedgeinfo(void); void incrementedgeinfo(int, int); void minimumedgeinfo(void); void initconsensus(void); void makepart(int, int); void computebiparts(void); void printsplit(FILE *, uli); void makenewsplitentries(void); void copysplit(uli, int); void makeconsensus(void); void writenode(FILE *, int); void writeconsensustree(FILE *); void nodecoordinates(int); void drawnode(int, int); void plotconsensustree(FILE *); unsigned char *mallocquartets(int); void freequartets(void); unsigned char readquartet(int, int, int, int); void writequartet(int, int, int, int, unsigned char); void sort3doubles(dvector, ivector); void computeallquartets(void); void checkquartet(int, int, int, int); void num2quart(uli qnum, int *a, int *b, int *c, int *d); uli numquarts(int maxspc); uli quart2num (int a, int b, int c, int d); void writetpqfheader(int nspec, FILE *ofp, int flag); /* extracted from main (xxx) */ void compute_quartlklhds(int a, int b, int c, int d, double *d1, double *d2, double *d3, int approx); /* definitions for timing */ #define OVERALL 0 #define GENERAL 1 #define OPTIONS 2 #define PARAMEST 3 #define QUARTETS 4 #define PUZZLING 5 #define TREEEVAL 6 typedef struct { int currentjob; clock_t tempcpu; clock_t tempfullcpu; clock_t tempcpustart; time_t temptime; time_t tempfulltime; time_t temptimestart; clock_t maxcpu; clock_t mincpu; time_t maxtime; time_t mintime; double maxcpublock; double mincpublock; double mincputick; double mincputicktime; double maxtimeblock; double mintimeblock; double generalcpu; double optionscpu; double paramestcpu; double quartcpu; double quartblockcpu; double quartmaxcpu; double quartmincpu; double puzzcpu; double puzzblockcpu; double puzzmaxcpu; double puzzmincpu; double treecpu; double treeblockcpu; double treemaxcpu; double treemincpu; double cpu; double fullcpu; double generaltime; double optionstime; double paramesttime; double quarttime; double quartblocktime; double quartmaxtime; double quartmintime; double puzztime; double puzzblocktime; double puzzmaxtime; double puzzmintime; double treetime; double treeblocktime; double treemaxtime; double treemintime; double time; double fulltime; } timearray_t; EXTERN double cputime, walltime; EXTERN double fullcpu, fulltime; EXTERN double fullcputime, fullwalltime; EXTERN double altcputime, altwalltime; EXTERN clock_t cputimestart, cputimestop, cputimedummy; EXTERN time_t walltimestart, walltimestop, walltimedummy; EXTERN clock_t Startcpu; /* start cpu time */ EXTERN clock_t Stopcpu; /* stop cpu time */ EXTERN time_t Starttime; /* start time */ EXTERN time_t Stoptime; /* stop time */ EXTERN time_t time0; /* timer variable */ EXTERN time_t time1; /* yet another timer */ EXTERN time_t time2; /* yet another timer */ EXTERN timearray_t tarr; void resetqblocktime(timearray_t *ta); void resetpblocktime(timearray_t *ta); void inittimearr(timearray_t *ta); void addtimes(int jobtype, timearray_t *ta); #ifdef TIMEDEBUG void printtimearr(timearray_t *ta); #endif /* TIMEDEBUG */ #endif /* _PUZZLE_ */