#ifndef _PHYLIP_H_ #define _PHYLIP_H_ /* version 3.6. (c) Copyright 1993-2004 by the University of Washington. Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, Andrew Keeffe, Mike Palczewski, Doug Buxton and Dan Fineman. Permission is granted to copy and use this program provided no fee is charged for it and provided that this copyright notice is not removed. */ #define VERSION "3.67" /* Debugging options */ /* Define this to disable assertions */ #define NDEBUG /* Define this to enable debugging code */ /* #define DEBUG */ /* machine-specific stuff: based on a number of factors in the library stdlib.h, we will try to determine what kind of machine/compiler this program is being built on. However, it doesn't always succeed. However, if you have ANSI conforming C, it will probably work. We will try to figure out machine type based on defines in stdio, and compiler-defined things as well.: */ #include #include #ifdef WIN32 #include void phyClearScreen(void); void phySaveConsoleAttributes(void); void phySetConsoleAttributes(void); void phyRestoreConsoleAttributes(void); void phyFillScreenColor(void); #endif #ifdef GNUDOS #define DJGPP #define DOS #endif #ifdef THINK_C #define MAC #endif #ifdef __MWERKS__ #ifndef WIN32 #define MAC #endif #endif #ifdef __CMS_OPEN #define CMS #define EBCDIC true #define INFILE "infile data" #define OUTFILE "outfile data" #define FONTFILE "fontfile data" #define PLOTFILE "plotfile data" #define INTREE "intree data" #define INTREE2 "intree data 2" #define OUTTREE "outtree data" #define CATFILE "categories data" #define WEIGHTFILE "weights data" #define ANCFILE "ancestors data" #define MIXFILE "mixture data" #define FACTFILE "factors data" #else #define EBCDIC false #define INFILE "infile" #define OUTFILE "outfile" #define FONTFILE "fontfile" /* on unix this might be /usr/local/lib/fontfile */ #define PLOTFILE "plotfile" #define INTREE "intree" #define INTREE2 "intree2" #define OUTTREE "outtree" #define CATFILE "categories" #define WEIGHTFILE "weights" #define ANCFILE "ancestors" #define MIXFILE "mixture" #define FACTFILE "factors" #endif #ifdef L_ctermid /* try and detect for sysV or V7. */ #define SYSTEM_FIVE #endif #ifdef sequent #define SYSTEM_FIVE #endif #ifndef SYSTEM_FIVE #include # if defined(_STDLIB_H_) || defined(_H_STDLIB) || defined(H_SCCSID) || defined(unix) # define UNIX # define MACHINE_TYPE "BSD Unix C" # endif #endif #ifdef __STDIO_LOADED #define VMS #define MACHINE_TYPE "VAX/VMS C" #endif #ifdef __WATCOMC__ #define QUICKC #define WATCOM #define DOS #include "graph.h" #endif /* watcom-c has graphics library calls that are almost identical to * * quick-c, so the "QUICKC" symbol name stays. */ #ifdef _QC #define MACHINE_TYPE "MS-DOS / Quick C" #define QUICKC #include "graph.h" #define DOS #endif #ifdef _DOS_MODE #define MACHINE_TYPE "MS-DOS /Microsoft C " #define DOS /* DOS is always defined if on a DOS machine */ #define MSC /* MSC is defined for microsoft C */ #endif #ifdef __MSDOS__ /* TURBO c compiler, ONLY (no other DOS C compilers) */ #define DOS #define TURBOC #include #include #endif #ifdef DJGPP /* DJ Delorie's original gnu C/C++ port */ #include #endif #ifndef MACHINE_TYPE #define MACHINE_TYPE "ANSI C" #endif #ifdef DOS #define MALLOCRETURN void #else #define MALLOCRETURN void #endif #ifdef VMS #define signed /* signed doesn't exist in VMS */ #endif /* default screen types */ /* if on a DOS but not a Windows system can use IBM PC screen controls */ #ifdef DOS #ifndef WIN32 #define IBMCRT true #define ANSICRT false #endif #endif /* if on a Mac cannot use screen controls */ #ifdef MAC #define IBMCRT false #define ANSICRT false #endif /* if on a Windows system can use IBM PC screen controls */ #ifdef WIN32 #define IBMCRT true #define ANSICRT false #endif /* otherwise, let's assume we are on a Linux or Unix system with ANSI terminal controls */ #ifndef MAC #ifndef DOS #ifndef WIN32 #define IBMCRT false #define ANSICRT true #endif #endif #endif #ifdef DJGPP #undef MALLOCRETURN #define MALLOCRETURN void #endif /* includes: */ #ifdef UNIX #include #else #include #endif #include #include #include #ifdef MAC #ifdef DRAW #include "interface.h" #else #include "macface.h" #endif #define getch gettch #endif /* directory delimiters */ #ifdef MAC #define DELIMITER ':' #else #ifdef WIN32 #define DELIMITER '\\' #else #define DELIMITER '/' #endif #endif #define FClose(file) if (file) fclose(file) ; file=NULL #define Malloc(x) mymalloc((long)x) typedef void *Anyptr; #define Signed signed #define Const const #define Volatile volatile #define Char char /* Characters (not bytes) */ #define Static static /* Private global funcs and vars */ #define Local static /* Nested functions */ typedef unsigned char boolean; #define true 1 #define false 0 /* Number of items per machine word in set. * Used in consensus programs and clique */ #define SETBITS 31 MALLOCRETURN *mymalloc(long); /*** UI behavior ***/ /* Set to 1 to not ask before overwriting files */ #define OVERWRITE_FILES 0 /*** Static memory parameters ***/ #define FNMLNGTH 200 /* length of array to store a file name */ #define nmlngth 10 /* number of characters in species name */ #define MAXNCH 20 /* must be greater than or equal to nmlngth */ #define maxcategs 9 /* maximum number of site types */ #define maxcategs2 11 /* maximum number of site types + 2 */ #define point "." #define pointe '.' #define down 2 #define MAXSHIMOTREES 100 /*** Maximum likelihood parameters ***/ /* Used in proml, promlk, dnaml, dnamlk, etc. */ #define UNDEFINED 1.0 /* undefined or invalid likelihood */ #define smoothings 4 /* number of passes through smoothing algorithm */ #define iterations 8 /* number of iterates for each branch */ #define epsilon 0.0001 /* small number used in makenewv */ #define EPSILON 0.00001 /* small number used in hermite root-finding */ #define initialv 0.1 /* starting branch length unless otherwise */ #define INSERT_MIN_TYME 0.0001 /* Minimum tyme between nodes during inserts */ #define over 60 /* maximum width all branches of tree on screen */ #define LIKE_EPSILON 1e-10 /* Estimate of round-off error in likelihood * calculations. */ /*** Math constants ***/ #define SQRTPI 1.7724538509055160273 #define SQRT2 1.4142135623730950488 /*** Rearrangement parameters ***/ #define NLRSAVES 5 /* number of views that need to be saved during local * * rearrangement */ /*** Output options ***/ /* Number of significant figures to display in numeric output */ #define PRECISION 6 /* Maximum line length of matrix output - 0 for unlimited */ #define OUTPUT_TEXTWIDTH 78 /** output_matrix() flags **/ /* Block output: Matrices are vertically split into blocks that * fit within OUTPUT_TEXTWIDTH columns */ #define MAT_BLOCK 0x1 /* Lower triangle: Values on or above the diagonal are not printed */ #define MAT_LOWER 0x2 /* Print a border between headings and data */ #define MAT_BORDER 0x4 /* Do not print the column header */ #define MAT_NOHEAD 0x8 /* Output the number of columns before the matrix */ #define MAT_PCOLS 0x10 /* Do not enforce maximum line width */ #define MAT_NOBREAK 0x20 /* Pad row header with spaces to 10 char */ #define MAT_PADHEAD 0x40 /* Human-readable format. */ #define MAT_HUMAN MAT_BLOCK /* Machine-readable format. */ #define MAT_MACHINE (MAT_PCOLS | MAT_NOHEAD | MAT_PADHEAD) typedef long *steptr; typedef long longer[6]; typedef char naym[MAXNCH]; typedef long *bitptr; typedef double raterootarray[maxcategs2][maxcategs2]; typedef struct bestelm { long *btree; boolean gloreange; boolean locreange; boolean collapse; } bestelm; extern FILE *infile, *outfile, *intree, *intree2, *outtree, *weightfile, *catfile, *ancfile, *mixfile, *factfile; extern long spp, words, bits; extern boolean ibmpc, ansi, tranvsp; extern naym *nayme; /* names of species */ #define ebcdic EBCDIC typedef Char plotstring[MAXNCH]; /* Approx. 1GB, used to test for memory request errors */ #define TOO_MUCH_MEMORY 1000000000 /* The below pre-processor commands define the type used to store group arrays. We can't use #elif for metrowerks, so we use cascaded if statements */ #include /* minimum double we feel safe with, anything less will be considered underflow */ #define MIN_DOUBLE 10e-100 /* K&R says that there should be a plus in front of the number, but no machine we've seen actually uses one; we'll include it just in case. */ #define MAX_32BITS 2147483647 #define MAX_32BITS_PLUS +2147483647 /* If ints are 4 bytes, use them */ #if INT_MAX == MAX_32BITS typedef int group_type; #else #if INT_MAX == MAX_32BITS_PLUS typedef int group_type; #else /* Else, if longs are 4 bytes, use them */ #if LONG_MAX == MAX_32BITS typedef long group_type; #else #if LONG_MAX == MAX_32BITS_PLUS typedef long group_type; /* Default to longs */ #else typedef long group_type; #endif #endif #endif #endif /* for many programs */ #define maxuser 1000 /* maximum number of user-defined trees */ typedef Char **sequence; typedef enum { A, C, G, T, O } bases; typedef enum { alanine, arginine, asparagine, aspartic, cysteine, glutamine, glutamic, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine } acids; /* for Pars */ typedef enum { zero = 0, one, two, three, four, five, six, seven } discbases; /* for Protpars */ typedef enum { ala, arg, asn, asp, cys, gln, glu, gly, his, ileu, leu, lys, met, phe, pro, ser1, ser2, thr, trp, tyr, val, del, stop, asx, glx, ser, unk, quest } aas; typedef double sitelike[(long)T - (long)A + 1]; /* used in dnaml, dnadist */ typedef double psitelike[(long)valine - (long)alanine + 1]; /* used in proml */ typedef long *baseptr; /* baseptr used in dnapars, dnacomp & dnapenny */ typedef long *baseptr2; /* baseptr used in dnamove */ typedef unsigned char *discbaseptr; /* discbaseptr used in pars */ typedef sitelike *ratelike; /* used in dnaml ... */ typedef psitelike *pratelike; /* used in proml */ typedef ratelike *phenotype; /* phenotype used in dnaml, dnamlk, dnadist */ typedef pratelike *pphenotype; /* phenotype used in proml */ typedef double *sitelike2; typedef sitelike2 *phenotype2; /* phenotype2 used in restml */ typedef double *phenotype3; /* for continuous char programs */ typedef double *vector; /* used in distance programs */ typedef long nucarray[(long)O - (long)A + 1]; typedef long discnucarray[(long)seven - (long)zero + 1]; typedef enum { nocollap, tocollap, undefined } collapstates; typedef enum { bottom, nonbottom, hslength, tip, iter, length, hsnolength, treewt, unittrwt } initops; typedef double **transmatrix; typedef transmatrix *transptr; /* transptr used in restml */ typedef long sitearray[3]; typedef sitearray *seqptr; /* seqptr used in protpars */ typedef struct node { struct node *next, *back; plotstring nayme; long naymlength, tipsabove, index; double times_in_tree; /* Previously known as cons_index */ double xcoord, ycoord; long long_xcoord, long_ycoord; /* for use in cons. */ double oldlen, length, r, theta, oldtheta, width, depth, tipdist, lefttheta, righttheta; group_type *nodeset; /* used by accumulate -plc */ long ymin, ymax; /* used by printree -plc */ boolean haslength; /* haslength used in dnamlk */ boolean iter; /* iter used in dnaml, fitch & restml */ boolean initialized; /* initialized used in dnamlk & restml */ long branchnum; /* branchnum used in restml */ phenotype x; /* x used in dnaml, dnamlk, dnadist */ phenotype2 x2; /* x2 used in restml */ phenotype3 view; /* contml etc */ pphenotype protx; /* protx used in proml */ aas *seq; /* the sequence used in protpars */ seqptr siteset; /* temporary storage for aa's used in protpars*/ double v, deltav, ssq; /* ssq used only in contrast */ double bigv; /* bigv used in contml */ double tyme, oldtyme; /* used in dnamlk */ double t; /* time in kitsch */ boolean sametime; /* bookkeeps scrunched nodes in kitsch */ double weight; /* weight of node used by scrunch in kitsch */ boolean processed; /* used by evaluate in kitsch */ boolean deleted; /* true if node is deleted (retree) */ boolean hasname; /* true if tip has a name (retree) */ double beyond; /* distance beyond this node to most distant tip */ /* (retree) */ boolean deadend; /* true if no undeleted nodes beyond this node */ /* (retree) */ boolean onebranch; /* true if there is one undeleted node beyond */ /* this node (retree) */ struct node *onebranchnode; /* if there is, a pointer to that node (retree)*/ double onebranchlength; /* if there is, the distance from here to there*/ /* (retree) */ boolean onebranchhaslength; /* true if there is a valid combined length*/ /* from here to there (retree) */ collapstates collapse; /* used in dnapars & dnacomp */ boolean tip; boolean bottom; /* used in dnapars & dnacomp, disc char */ boolean visited; /* used in dnapars & dnacomp disc char */ baseptr base; /* the sequence in dnapars/comp/penny */ discbaseptr discbase; /* the sequence in pars */ baseptr2 base2; /* the sequence in dnamove */ baseptr oldbase; /* record previous sequence */ discbaseptr olddiscbase; /* record previous sequence */ long numdesc; /* number of immediate descendants */ nucarray *numnuc; /* bookkeeps number of nucleotides */ discnucarray *discnumnuc; /* bookkeeps number of nucleotides */ steptr numsteps; /* bookkeeps steps */ steptr oldnumsteps; /* record previous steps */ double sumsteps; /* bookkeeps sum of steps */ nucarray cumlengths; /* bookkeeps cummulative minimum lengths */ discnucarray disccumlengths; /* bookkeeps cummulative minimum lengths */ nucarray numreconst; /* bookkeeps number of reconstructions */ discnucarray discnumreconst; /* bookkeeps number of reconstructions */ vector d, w; /* for distance matrix programs */ double dist; /* dist used in fitch */ bitptr stateone, statezero; /* discrete char programs */ long maxpos; /* maxpos used in Clique */ Char state; /* state used in Dnamove, Dolmove & Move */ double* underflows; /* used to record underflow */ } node; typedef node **pointarray; /*** tree structure ***/ typedef struct tree { /* An array of pointers to nodes. Each tip node and ring of nodes has a * unique index starting from one. The nodep array contains pointers to each * one, starting from 0. In the case of internal nodes, the entries in nodep * point to the rootward node in the group. Since the trees are otherwise * entirely symmetrical, except at the root, this is the only way to resolve * parent, child, and sibling relationships. * * Indices in range [0, spp) point to tips, while indices [spp, nonodes) * point to fork nodes */ pointarray nodep; /* A pointer to the first node. Typically, root is used when the tree is rooted, * and points to an internal node with no back link. */ node *root; /* start is used when trees are unrooted. It points to an internal node whose * back link typically points to the outgroup leaf. */ node *start; /* In maximum likelihood programs, the most recent evaluation is stored here */ double likelihood; /* Branch transition matrices for restml */ transptr trans; /* all transition matrices */ long *freetrans; /* an array of indexes of free matrices */ long transindex; /* index of last valid entry in freetrans[] */ } tree; typedef void (*initptr)(node **, node **, node *, long, long, long *, long *, initops, pointarray, pointarray, Char *, Char *, FILE *); #ifndef OLDC /* function prototypes */ void scan_eoln(FILE *); boolean eoff(FILE *); boolean eoln(FILE *); int filexists(char *); const char* get_command_name (const char *); void EOF_error(void); void getstryng(char *); void openfile(FILE **,const char *,const char *,const char *,const char *, char *); void cleerhome(void); void loopcount(long *, long); double randum(longer); void randumize(longer, long *); double normrand(longer); long readlong(const char *); void uppercase(Char *); void initseed(long *, long *, longer); void initjumble(long *, long *, longer, long *); void initoutgroup(long *, long); void initthreshold(double *); void initcatn(long *); void initcategs(long, double *); void initprobcat(long, double *, double *); double logfac (long); double halfroot(double (*func)(long , double), long, double, double); double hermite(long, double); void initlaguerrecat(long, double, double *, double *); void root_hermite(long, double *); void hermite_weight(long, double *, double *); void inithermitcat(long, double, double *, double *); void lgr(long, double, raterootarray); double glaguerre(long, double, double); void initgammacat(long, double, double *, double *); void inithowmany(long *, long); void inithowoften(long *); void initlambda(double *); void initfreqs(double *, double *, double *, double *); void initratio(double *); void initpower(double *); void initdatasets(long *); void justweights(long *); void initterminal(boolean *, boolean *); void initnumlines(long *); void initbestrees(bestelm *, long, boolean); void newline(FILE *, long, long, long); void inputnumbers(long *, long *, long *, long); void inputnumbersold(long *, long *, long *, long); void inputnumbers2(long *, long *, long n); void inputnumbers3(long *, long *); void samenumsp(long *, long); void samenumsp2(long); void readoptions(long *, const char *); void matchoptions(Char *, const char *); void inputweights(long, steptr, boolean *); void inputweightsold(long, steptr, boolean *); void inputweights2(long, long, long *, steptr, boolean *, const char *); void printweights(FILE *, long, long, steptr, const char *); void inputcategs(long, long, steptr, long, const char *); void printcategs(FILE *, long, steptr, const char *); void inputfactors(long, Char *, boolean *); void inputfactorsnew(long, Char *, boolean *); void printfactors(FILE *, long, Char *, const char *); void headings(long, const char *, const char *); void initname(long); void findtree(boolean *,long *,long,long *,bestelm *); void addtree(long,long *,boolean,long *,bestelm *); long findunrearranged(bestelm *, long, boolean); boolean torearrange(bestelm *, long); void reducebestrees(bestelm *, long *); void shellsort(double *, long *, long); void getch(Char *, long *, FILE *); void getch2(Char *, long *); void findch(Char, Char *, long); void findch2(Char, long *, long *, Char *); void findch3(Char, Char *, long, long); void processlength(double *,double *,Char *,boolean *,FILE *,long *); void writename(long, long, long *); void memerror(void); void odd_malloc(long); void gnu(node **, node **); void chuck(node **, node *); void zeronumnuc(node *, long); void zerodiscnumnuc(node *, long); void allocnontip(node *, long *, long); void allocdiscnontip(node *, long *, unsigned char *, long ); void allocnode(node **, long *, long); void allocdiscnode(node **, long *, unsigned char *, long ); void gnutreenode(node **, node **, long, long, long *); void gnudisctreenode(node **, node **, long , long, long *, unsigned char *); void setupnode(node *, long); node * pnode(tree *t, node *p); long count_sibs (node *); void inittrav (node *); void commentskipper(FILE ***, long *); long countcomma(FILE **, long *); long countsemic(FILE **); void hookup(node *, node *); void unhookup(node *, node *); void link_trees(long, long , long, pointarray); void allocate_nodep(pointarray *, FILE **, long *); void malloc_pheno(node *, long, long); void malloc_ppheno(node *, long, long); long take_name_from_tree (Char *, Char *, FILE *); void match_names_to_data (Char *, pointarray, node **, long); void addelement(node **, node *, Char *, long *, FILE *, pointarray, boolean *, boolean *, pointarray, long *, long *, boolean *, node **, initptr,boolean,long); void treeread (FILE *, node **, pointarray, boolean *, boolean *, pointarray, long *, boolean *, node **, initptr,boolean,long); void addelement2(node *, Char *, long *, FILE *, pointarray, boolean, double *, boolean *, long *, long *, long, boolean *,boolean, long); void treeread2 (FILE *, node **, pointarray, boolean, double *, boolean *, boolean *, long *,boolean,long); void exxit (int); void countup(long *loopcount, long maxcount); char gettc(FILE* file); void unroot_r(node* p,node ** nodep, long nonodes); void unroot(tree* t,long nonodes); void unroot_here(node* root, node** nodep, long nonodes); void clear_connections(tree *t, long nonodes); void init(int argc, char** argv); char **stringnames_new(void); void stringnames_delete(char **names); int fieldwidth_double(double val, unsigned int precision); void output_matrix_d(FILE *fp, double **matrix, unsigned long rows, unsigned long cols, char **row_head, char **col_head, int flags); void debugtree (tree *, FILE *); void debugtree2 (pointarray, long, FILE *); #endif /* OLDC */ #endif /* _PHYLIP_H_ */