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view rDiff/src/locfit/Source/locf.h @ 2:233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
author | vipints <vipin@cbio.mskcc.org> |
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date | Tue, 08 Oct 2013 07:15:44 -0400 |
parents | 0f80a5141704 |
children |
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/* * Copyright 1996-2006 Catherine Loader. */ #ifndef I_LOCF_H #define I_LOCF_H #include "stdlib.h" #include "ctype.h" #include "mut.h" #ifdef WARN #undef WARN #endif #define LERR(args) {mut_printf("Error: "); mut_printf args; mut_printf("\n"); lf_error=1;} #define WARN(args) {mut_printf("Warning: "); mut_printf args; mut_printf("\n"); } extern int lf_error; #define LOGPI 1.144729885849400174143427 #define HUBERC 2.0 #define NOSLN 0.1278433 #define GFACT 2.5 #define EFACT 3.0 #define ISWAP(a,b) { int zz; zz = a; a = b; b = zz; } #define MAX(a,b) (((a)>(b)) ? (a) : (b)) #define MIN(a,b) (((a)<(b)) ? (a) : (b)) #define SGN(x) (((x)>0) ? 1 : -1) #define SQR(x) ((x)*(x)) extern int lf_error; typedef struct { double *wk, *coef, *xbar, *f; jacobian xtwx; int lwk, haspc; } paramcomp; #define haspc(pc) ((pc)->haspc) /* * MXDIM and MXDEG are maximum dimension and local polynomial * degree for Locfit. Note that some parts of the code may be * more restrictive. */ #define MXDIM 15 #define MXDEG 7 typedef struct { double *x[MXDIM]; double *y; double *w; double *b; double *c; double sca[MXDIM]; double xl[2*MXDIM]; int n, d, ord; int sty[MXDIM]; } lfdata; #define resp(lfd,i) (((lfd)->y==NULL) ? 0.0 : (lfd)->y[i]) #define base(lfd,i) (((lfd)->b==NULL) ? 0.0 : (lfd)->b[i]) #define prwt(lfd,i) (((lfd)->w==NULL) ? 1.0 : (lfd)->w[i]) #define cens(lfd,i) (((lfd)->c==NULL) ? 0 : (int)(lfd)->c[i]) #define datum(lfd,i,j) ((lfd)->x[i][j]) #define dvari(lfd,i) ((lfd)->x[i]) /* * The design structure used in Locfit, and associated macro definitions. */ typedef struct { int des_init_id; double *wk; int *ind; int lwk, lind; double *xev; /* fitting point, length p */ double *X; /* design matrix, length n*p */ double *w, *di, *res, *th, *wd, h; double *V, *P; /* matrices with length p*p */ double *f1, *ss, *oc, *cf; /* work vectors, length p */ double llk, smwt; double tr0, tr1, tr2; /* traces for local df computation */ jacobian xtwx; /* to store X'WVX and decomposition */ int cfn[1+MXDIM], ncoef; int *fix; /* integer vector for fixed coefficients. */ int (*itype)(); /* density integration function */ int n, p; } design; #define cfn(des,i) (des->cfn[i]) #define d_x(des) ((des)->X) #define d_xi(des,i) (&(des)->X[i*((des)->p)]) #define d_xij(des,i,j) ((des)->X[i*((des)->p)+j]) #define is_fixed(des,i) ((des)->fix[i]==1) #define wght(des,i) ((des)->w[i]) #define dist(des,i) ((des)->di[i]) #define fitv(des,i) ((des)->th[i]) #define DES_INIT_ID 34988372 extern int des_reqd(), des_reqi(); typedef struct { int deflink, canlink, quasi, robust; int (*vallink)(), (*family)(), (*initial)(), (*like)(), (*pcheck)(); } family; #define isquasi(fam) ((fam)->quasi) #define isrobust(fam) ((fam)->robust) extern int inllmix; /* flag needed to ensure correct behavior in llmix. */ typedef struct { double nn, fixh, adpen; int ker, kt; int deg, deg0, p; int acri; int fam, lin; family fami; int ubas; double (*vb)(); void (*vbasis)(); } smpar; #define nn(sp) ((sp)->nn) #define fixh(sp) ((sp)->fixh) #define pen(sp) ((sp)->adpen) #define ker(sp) ((sp)->ker) #define kt(sp) ((sp)->kt) #define deg(sp) ((sp)->deg) #define deg0(sp) ((sp)->deg0) #define npar(sp) ((sp)->p) #define acri(sp) ((sp)->acri) #define ubas(sp) ((sp)->ubas) #define fam(sp) ((sp)->fam) #define fami(sp) (&(sp)->fami) #define link(sp) ((sp)->lin) typedef struct { int deriv[MXDEG+2]; int nd; } deriv; /* * Criteria for adaptive local fitting mi[MACRI] * 1: localized CP; 2: ICI (katkovnik); 3: curvature model index * 4: Increase bandwidth until locfit returns LF_OK */ #define ANONE 0 #define ACP 1 #define AKAT 2 #define AMDI 3 #define AOK 4 /* * weight functions mi[MKER]. * see Table 3.1 or the function W() in weights.c for definitions. */ #define WRECT 1 #define WEPAN 2 #define WBISQ 3 #define WTCUB 4 #define WTRWT 5 #define WGAUS 6 #define WTRIA 7 #define WQUQU 8 #define W6CUB 9 #define WMINM 10 #define WEXPL 11 #define WMACL 12 #define WPARM 13 /* * type of multivariate weight function mi[MKT] * KSPH (spherical) KPROD (product) * others shouldn't be used at present. */ #define KSPH 1 #define KPROD 2 #define KCE 3 #define KLM 4 #define KZEON 5 /* * Local likelihood family mi[MTG] * for quasi-likelihood, add 64. */ #define TNUL 0 #define TDEN 1 #define TRAT 2 #define THAZ 3 #define TGAUS 4 #define TLOGT 5 #define TPOIS 6 #define TGAMM 7 #define TGEOM 8 #define TCIRC 9 #define TROBT 10 #define TRBIN 11 #define TWEIB 12 #define TCAUC 13 #define TPROB 14 #define TQUANT 15 /* * Link functions mi[MLINK]. * Mostly as in table 4.1 of the book. * LDEFAU and LCANON are used to select default and canonical * links respectively. LINIT shouldn't be selected by user... */ #define LINIT 0 #define LDEFAU 1 #define LCANON 2 #define LIDENT 3 #define LLOG 4 #define LLOGIT 5 #define LINVER 6 #define LSQRT 7 #define LASIN 8 /* * components of vector returned by the links() function * in family.c. ZLIK the likelihood; ZMEAN = estimated mean; * ZDLL = derivative of log-likelihood; ZDDLL = - second derivative */ #define LLEN 4 #define ZLIK 0 #define ZMEAN 1 #define ZDLL 2 #define ZDDLL 3 /* * return status for the locfit() function */ #define LF_OK 0 #define LF_DONE 1 /* done - forced break from iterations */ #define LF_OOB 2 /* out of bounds, or large unstable parameter */ #define LF_PF 3 /* perfect fit; interpolation; deviance=0 */ #define LF_NCON 4 /* not converged */ #define LF_NSLN 5 /* no solution - eg separation in binomial. */ #define LF_NOPT 6 /* no or insufficient points with non-zero wt */ #define LF_INFA 7 /* initial failure e.g. log(0) */ #define LF_DEMP 10 /* density -- empty integration region */ #define LF_XOOR 11 /* density -- fit point outside xlim region */ #define LF_DNOP 12 /* density version of 6 */ #define LF_BADP 81 /* bad parameters e.g. neg prob for binomial */ #define LF_LNK 82 /* invalid link */ #define LF_FAM 83 /* invalid family */ #define LF_ERR 99 /* error */ #define STANGL 4 #define STLEFT 5 #define STRIGH 6 #define STCPAR 7 /* * Integration type mi[MIT] for integration in * density estimation. */ #define INVLD 0 #define IDEFA 1 #define IMULT 2 #define IPROD 3 #define IMLIN 4 #define IHAZD 5 #define ISPHR 6 #define IMONT 7 /* density.c */ extern int densinit(), likeden(), deitype(); extern int fact[]; extern void prodintresp(), prresp(); extern int de_mint, de_itype, de_renorm; /* dens_haz.c */ extern void haz_init(); extern int hazint(); /* dens_odi.c */ extern int onedint(); extern void recurint(); /* famquant.c */ extern void lfquantile(); /* family.c */ extern int lffamily(), lflink(); extern int links(), stdlinks(), defaultlink(), validlinks(); extern double b2(), b3(), b4(), lf_link(), invlink(); extern void setfamily(); /* lf_adap.c */ extern int alocfit(), lfacri(); /* lf_fitfun.c */ extern void fitfun(), makecfn(), designmatrix(); extern int calcp(), coefnumber(); /* lf_nbhd.c */ extern double kordstat(), rho(); extern void nbhd(); /* lf_robust.c */ extern double median(); extern void lf_robust(); /* lfstr.c */ extern int pmatch(); /* lf_vari.c */ extern void lf_vcov(), comp_vari(), local_df(); /* lf_wdiag.c */ extern int wdiag(), wdiagp(); /* locfit.c */ extern int locfit(), des_reqd(), des_reqi(), likereg(); extern int reginit(); extern void lfdata_init(), smpar_init(), deriv_init(), des_init(), lfiter(); extern int lf_maxit, lf_debug; extern void lf_status_msg(); /* minmax.c */ extern double ipower(), minmax(); /* weight.c */ extern int lfkernel(), lfketype(); extern double W(), weight(), weightd(), Wd(), Wdd(), wint(); extern double Wconv(), Wconv1(), Wconv4(), Wconv5(), Wconv6(), Wikk(); extern int iscompact(), wtaylor(); #endif /* define I_LOCF_H */