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* HMMER - Biological sequence analysis with profile HMMs
* Copyright (C) 1992-2003 Washington University School of Medicine
* All Rights Reserved
*
* This source code is distributed under the terms of the
* GNU General Public License. See the files COPYING and LICENSE
* for details.
************************************************************/
/* structs.h
*
* Data structures used in HMMER.
* Also, a few miscellaneous macros and global variable declarations.
*
* RCS $Id: structs.h,v 1.28 2003/10/01 13:06:05 eddy Exp $
*/
#ifndef STRUCTSH_INCLUDED
#define STRUCTSH_INCLUDED
#include "config.h"
#include "squid.h"
#include "ssi.h"
/* Miscellaneous math macros used in the package
*/
#define sreLOG2(x) ((x) > 0 ? log(x) * 1.44269504 : -9999.)
#define sreEXP2(x) (exp((x) * 0.69314718 ))
#define SQR(x) ((x) * (x))
/* an idiom for determining a symbol's position in the array
* by pointer arithmetic.
* does no error checking, so caller must already be damned sure x is
* valid in the alphabet!
*/
#define SYMIDX(x) (strchr(Alphabet, (x)) - Alphabet)
/* The symbol alphabet.
* Must deal with IUPAC degeneracies. Nondegenerate symbols
* come first in Alphabet[], followed by degenerate symbols.
* Nucleic alphabet also must deal with other common symbols
* like U (in RNA) and X (often misused for N).
* Example:
* Nucleic: "ACGTUNRYMKSWHBVDX" size=4 iupac=17
* Amino: "ACDEFGHIKLMNPQRSTVWYBZX" size=20 iupac=23
*
* Parts of the code assume that the last symbol is a
* symbol for an unknown residue, i.e. 'X'.
*
* MAXCODE and MAXABET constants are defined in config.h
*/
extern char Alphabet[MAXCODE+1]; /* "ACDEFGHIKLMNPQRSTVWYBZX" for example */
extern int Alphabet_type; /* hmmNUCLEIC or hmmAMINO */
extern int Alphabet_size; /* uniq alphabet size: 4 or 20 */
extern int Alphabet_iupac; /* total size of alphabet + IUPAC degen. */
extern char Degenerate[MAXCODE][MAXABET];
extern int DegenCount[MAXCODE];
#define hmmNOTSETYET 0
#define hmmNUCLEIC 2 /* compatibility with squid's kRNA */
#define hmmAMINO 3 /* compatibility with squid's kAmino */
/**********************************************************************
*
* Plan7
* Implementation of the new Plan7 HMM architecture.
* Fully probabilistic even for hmmsw, hmmls, and hmmfs;
* No insert->delete or delete->insert transitions;
* Improved structure layout.
*
* The strategy is to infiltrate plan7 code into HMMER in
* an evolutionary rather than revolutionary manner.
*
**********************************************************************/
/* Plan 7 construction strategies.
*/
enum p7_construction {
P7_MAP_CONSTRUCTION, /* maximum a posteriori architecture */
P7_HAND_CONSTRUCTION, /* hand specified architecture */
P7_FAST_CONSTRUCTION /* fast ad hoc architecture */
};
/* Plan 7 parameter optimization strategies
*/
enum p7_param {
P7_MAP_PARAM, /* standard maximum a posteriori */
P7_MD_PARAM, /* maximum discrimination */
P7_MRE_PARAM, /* maximum relative entropy */
P7_WMAP_PARAM /* ad hoc weighted MAP */
};
/* Structure: plan7_s
*
* Declaration of a Plan 7 profile-HMM.
*/
struct plan7_s {
/* Annotation on the model. A name is mandatory.
* Other fields are optional; whether they are present is
* flagged in the stateflags bit array.
*
* desc is only valid if PLAN7_DESC is set in flags.
* acc is only valid if PLAN7_ACC is set in flags.
* rf is only valid if PLAN7_RF is set in flags.
* cs is only valid if PLAN7_CS is set in flags.
* ca is only valid if PLAN7_CA is set in flags.
* map is only valid if PLAN7_MAP is set in flags.
*/
char *name; /* name of the model +*/
char *acc; /* accession number of model (Pfam) +*/
char *desc; /* brief description of model +*/
char *rf; /* reference line from alignment 0..M +*/
char *cs; /* consensus structure line 0..M +*/
char *ca; /* consensus accessibility line 0..M */
char *comlog; /* command line(s) that built model +*/
int nseq; /* number of training sequences +*/
char *ctime; /* creation date +*/
int *map; /* map of alignment cols onto model 1..M+*/
int checksum; /* checksum of training sequences +*/
/* The following are annotations added to support work by Michael Asman,
* CGR Stockholm. They are not stored in model files; they are only
* used in model construction.
*
* #=GC X-PRM (PRT,PRI) annotation is picked up by hmmbuild and interpreted
* as specifying which mixture Dirichlet component to use. If these flags
* are non-NULL, the normal mixture Dirichlet code is bypassed, and a
* single specific Dirichlet is used at each position.
*/
int *tpri; /* which transition mixture prior to use */
int *mpri; /* which match mixture prior to use */
int *ipri; /* which insert mixture prior to use */
/* Pfam-specific score cutoffs.
*
* ga1, ga2 are valid if PLAN7_GA is set in flags.
* tc1, tc2 are valid if PLAN7_TC is set in flags.
* nc1, nc2 are valid if PLAN7_NC is set in flags.
*/
float ga1, ga2; /* per-seq/per-domain gathering thresholds (bits) +*/
float tc1, tc2; /* per-seq/per-domain trusted cutoff (bits) +*/
float nc1, nc2; /* per-seq/per-domain noise cutoff (bits) +*/
/* The main model in probability form: data-dependent probabilities.
* This is the core Krogh/Haussler model.
* Transition probabilities are usually accessed as a
* two-D array: hmm->t[k][TMM], for instance. They are allocated
* such that they can also be stepped through in 1D by pointer
* manipulations, for efficiency in DP algorithms.
*/
int M; /* length of the model (# nodes) +*/
float **t; /* transition prob's. t[1..M-1][0..6] +*/
float **mat; /* match emissions. mat[1..M][0..19] +*/
float **ins; /* insert emissions. ins[1..M-1][0..19] +*/
float tbd1; /* B->D1 prob (data dependent) +*/
/* The unique states of Plan 7 in probability form.
* These are the algorithm-dependent, data-independent probabilities.
* Some parts of the code may briefly use a trick of copying tbd1
* into begin[0]; this makes it easy to call FChoose() or FNorm()
* on the resulting vector. However, in general begin[0] is not
* a valid number.
*/
float xt[4][2]; /* N,E,C,J extra states: 2 transitions +*/
float *begin; /* 1..M B->M state transitions +*/
float *end; /* 1..M M->E state transitions (!= a dist!) +*/
/* The null model probabilities.
*/
float null[MAXABET]; /* "random sequence" emission prob's +*/
float p1; /* null model loop probability +*/
/* The model in log-odds score form.
* These are created from the probabilities by LogoddsifyHMM().
* By definition, null[] emission scores are all zero.
* Note that emission distributions are over 26 upper-case letters,
* not just the unambiguous protein or DNA alphabet: we
* precalculate the scores for all IUPAC degenerate symbols we
* may see. Non-IUPAC symbols simply have a -INFTY score.
*
* Note the reversed indexing on msc, isc, tsc -- for efficiency reasons.
* They're not probability vectors any more so we can reorder them
* without wildly complicating our life.
*
* The _mem ptrs are where the real memory is alloc'ed and free'd,
* as opposed to where it is accessed.
* This came in with Erik Lindahl's altivec port; it allows alignment on
* 16-byte boundaries. In the non-altivec code, this is just a little
* redundancy; tsc and tsc_mem point to the same thing, for example.
*
* Only valid if PLAN7_HASBITS is set.
*/
int **tsc; /* transition scores [0.6][1.M-1] -*/
int **msc; /* match emission scores [0.MAXCODE-1][1.M] -*/
int **isc; /* ins emission scores [0.MAXCODE-1][1.M-1] -*/
int xsc[4][2]; /* N,E,C,J transitions -*/
int *bsc; /* begin transitions [1.M] -*/
int *esc; /* end transitions [1.M] -*/
int *tsc_mem, *msc_mem, *isc_mem, *bsc_mem, *esc_mem;
/* DNA translation scoring parameters
* For aligning protein Plan7 models to DNA sequence.
* Lookup value for a codon is calculated by pos1 * 16 + pos2 * 4 + pos3,
* where 'pos1' is the digitized value of the first nucleotide position;
* if any of the positions are ambiguous codes, lookup value 64 is used
* (which will generally have a score of zero)
*
* Only valid if PLAN7_HASDNA is set.
*/
int **dnam; /* triplet match scores [0.64][1.M] -*/
int **dnai; /* triplet insert scores [0.64][1.M] -*/
int dna2; /* -1 frameshift, doublet emission, M or I -*/
int dna4; /* +1 frameshift, doublet emission, M or I -*/
/* P-value and E-value statistical parameters
* Only valid if PLAN7_STATS is set.
*/
float mu; /* EVD mu +*/
float lambda; /* EVD lambda +*/
int flags; /* bit flags indicating state of HMM, valid data +*/
};
/* Flags for plan7->flags.
* Note: Some models have scores but no probabilities (for instance,
* after reading from an HMM save file). Other models have
* probabilities but no scores (for instance, during training
* or building). Since it costs time to convert either way,
* I use PLAN7_HASBITS and PLAN7_HASPROB flags to defer conversion
* until absolutely necessary. This means I have to be careful
* about keeping these flags set properly when I fiddle a model.
*/
#define PLAN7_HASBITS (1<<0) /* raised if model has log-odds scores */
#define PLAN7_DESC (1<<1) /* raised if description exists */
#define PLAN7_RF (1<<2) /* raised if #RF annotation available */
#define PLAN7_CS (1<<3) /* raised if #CS annotation available */
#define PLAN7_XRAY (1<<4) /* raised if structural data available */
#define PLAN7_HASPROB (1<<5) /* raised if model has probabilities */
#define PLAN7_HASDNA (1<<6) /* raised if protein HMM->DNA seq params set*/
#define PLAN7_STATS (1<<7) /* raised if EVD parameters are available */
#define PLAN7_MAP (1<<8) /* raised if alignment map is available */
#define PLAN7_ACC (1<<9) /* raised if accession number is available */
#define PLAN7_GA (1<<10) /* raised if gathering thresholds available */
#define PLAN7_TC (1<<11) /* raised if trusted cutoffs available */
#define PLAN7_NC (1<<12) /* raised if noise cutoffs available */
#define PLAN7_CA (1<<13) /* raised if surface accessibility avail. */
/* Indices for special state types, I: used for dynamic programming xmx[][]
* mnemonic: eXtra Matrix for B state = XMB
*/
#define XMB 0
#define XME 1
#define XMC 2
#define XMJ 3
#define XMN 4
/* Indices for special state types, II: used for hmm->xt[] indexing
* mnemonic: eXtra Transition for N state = XTN
*/
#define XTN 0
#define XTE 1
#define XTC 2
#define XTJ 3
/* Indices for Plan7 main model state transitions.
* Used for indexing hmm->t[k][]
* mnemonic: Transition from Match to Match = TMM
*/
#define TMM 0
#define TMI 1
#define TMD 2
#define TIM 3
#define TII 4
#define TDM 5
#define TDD 6
/* Indices for extra state transitions
* Used for indexing hmm->xt[][].
*/
#define MOVE 0 /* trNB, trEC, trCT, trJB */
#define LOOP 1 /* trNN, trEJ, trCC, trJJ */
/* Declaration of Plan7 dynamic programming matrix structure.
*/
struct dpmatrix_s {
int **xmx; /* special scores [0.1..N][BECJN] */
int **mmx; /* match scores [0.1..N][0.1..M] */
int **imx; /* insert scores [0.1..N][0.1..M-1.M] */
int **dmx; /* delete scores [0.1..N][0.1..M-1.M] */
/* Hidden ptrs where the real memory is kept; this trick was
* introduced by Erik Lindahl with the Altivec port; it's used to
* align xmx, etc. on 16-byte boundaries for cache optimization.
*/
void *xmx_mem, *mmx_mem, *imx_mem, *dmx_mem;
/* The other trick brought in w/ the Lindahl Altivec port; dp matrix
* is retained and grown, rather than reallocated for every HMM or sequence.
* Keep track of current allocated-for size in rows (sequence length N)
* and columns (HMM length M). Also keep track of pad sizes: how much
* we should overallocate rows or columns when we reallocate. If pad = 0,
* then we're not growable in this dimension.
*/
int maxN; /* alloc'ed for seq of length N; N+1 rows */
int maxM; /* alloc'ed for HMM of length M; M+1 cols */
int padN; /* extra pad in sequence length/rows */
int padM; /* extra pad in HMM length/columns */
};
/* Declaration of Plan7 shadow matrix structure.
* In general, allowed values are STM, STI, etc.
* However, E state has M possible sources, from 1..M match states;
* hence the esrc array.
*/
struct dpshadow_s {
char **xtb; /* special state traces [0.1..N][BECJN] */
char **mtb; /* match state traces [0.1..N][0.1..M] */
char **itb; /* insert state traces [0.1..N][0.1..M-1.M] */
char **dtb; /* delete state traces [0.1..N][0.1..M-1.M] */
int *esrc; /* E trace is special; must store a M state number 1..M */
};
/* Structure: HMMFILE
*
* Purpose: An open HMM file or HMM library. See hmmio.c.
*/
struct hmmfile_s {
FILE *f; /* pointer to file opened for reading */
SSIFILE *ssi; /* pointer to open SSI index, or NULL */
int (*parser)(struct hmmfile_s *, struct plan7_s **); /* parsing function */
int is_binary; /* TRUE if format is a binary one */
int byteswap; /* TRUE if binary and byteswapped */
/* Ewan (GeneWise) needs the input API to know the offset of each
* HMM on the disk, as it's being read. This might be enough
* support for him. hmmindex also uses this. Ewan, see
* HMMFilePositionByIndex() for an example of how to use this
* opaque offset type in the SSI API - the call you need
* is SSISetFilePosition().
*/
int is_seekable; /* TRUE if we use offsets in this HMM file */
int mode; /* type of offset */
SSIOFFSET offset; /* Disk offset for beginning of the current HMM */
};
typedef struct hmmfile_s HMMFILE;
/* Plan 7 model state types
* used in traceback structure
*/
#define STBOGUS 0
#define STM 1
#define STD 2
#define STI 3
#define STS 4
#define STN 5
#define STB 6
#define STE 7
#define STC 8
#define STT 9
#define STJ 10
/* Structure: p7trace_s
*
* Traceback structure for alignments of model to sequence.
* Each array in a trace_s is 0..tlen-1.
* Element 0 is always to STATE_S. Element tlen-1 is always to STATE_T.
*/
struct p7trace_s {
int tlen; /* length of traceback */
char *statetype; /* state type used for alignment */
int *nodeidx; /* index of aligned node, 1..M (if M,D,I), or 0 */
int *pos; /* position in dsq, 1..L, or 0 if none */
};
/* Structure: p7prior_s
*
* Dirichlet priors on HMM parameters.
*/
struct p7prior_s {
int strategy; /* PRI_DCHLET, etc. */
int tnum; /* number of transition Dirichlet mixtures */
float tq[MAXDCHLET]; /* probabilities of tnum components */
float t[MAXDCHLET][7]; /* transition terms per mix component */
int mnum; /* number of mat emission Dirichlet mixtures */
float mq[MAXDCHLET]; /* probabilities of mnum components */
float m[MAXDCHLET][MAXABET]; /* match emission terms per mix component */
int inum; /* number of insert emission Dirichlet mixes */
float iq[MAXDCHLET]; /* probabilities of inum components */
float i[MAXDCHLET][MAXABET]; /* insert emission terms */
};
#define PRI_DCHLET 0 /* simple or mixture Dirichlets */
#define PRI_PAM 1 /* PAM prior hack */
/**********************************************************************
* Other structures, not having to do with HMMs.
**********************************************************************/
/* Structure: histogram_s
*
* Keep a score histogram.
*
* The main implementation issue here is that the range of
* scores is unknown, and will go negative. histogram is
* a 0..max-min array that represents the range min..max.
* A given score is indexed in histogram array as score-min.
* The AddToHistogram() function deals with dynamically
* resizing the histogram array when necessary.
*/
struct histogram_s {
int *histogram; /* counts of hits */
int min; /* elem 0 of histogram == min */
int max; /* last elem of histogram == max */
int highscore; /* highest active elem has this score */
int lowscore; /* lowest active elem has this score */
int lumpsize; /* when resizing, overalloc by this */
int total; /* total # of hits counted */
float *expect; /* expected counts of hits */
int fit_type; /* flag indicating distribution type */
float param[3]; /* parameters used for fits */
float chisq; /* chi-squared val for goodness of fit*/
float chip; /* P value for chisquared */
};
#define HISTFIT_NONE 0 /* no fit done yet */
#define HISTFIT_EVD 1 /* fit type = extreme value dist */
#define HISTFIT_GAUSSIAN 2 /* fit type = Gaussian */
#define EVD_MU 0 /* EVD fit parameter mu */
#define EVD_LAMBDA 1 /* EVD fit parameter lambda */
#define EVD_WONKA 2 /* EVD fit fudge factor */
#define GAUSS_MEAN 0 /* Gaussian parameter mean */
#define GAUSS_SD 1 /* Gaussian parameter std. dev. */
/* Structure: fancyali_s
*
* Alignment of a hit to an HMM, for printing.
*/
struct fancyali_s {
char *rfline; /* reference coord info */
char *csline; /* consensus structure info */
char *model; /* aligned query consensus sequence */
char *mline; /* "identities", conservation +'s, etc. */
char *aseq; /* aligned target sequence */
int len; /* length of strings */
char *query; /* name of query HMM */
char *target; /* name of target sequence */
int sqfrom; /* start position on sequence (1..L) */
int sqto; /* end position on sequence (1..L) */
};
/* Structure: hit_s
*
* Info about a high-scoring database hit.
* We keep this info in memory, so we can output a
* sorted list of high hits at the end.
*
* sqfrom and sqto are the coordinates that will be shown
* in the results, not coords in arrays... therefore, reverse
* complements have sqfrom > sqto
*/
struct hit_s {
double sortkey; /* number to sort by; big is better */
float score; /* score of the hit */
double pvalue; /* P-value of the hit */
float mothersc; /* score of whole sequence */
double motherp; /* P-value of whole sequence */
char *name; /* name of the target */
char *acc; /* accession of the target */
char *desc; /* description of the target */
int sqfrom; /* start position in seq (1..N) */
int sqto; /* end position in seq (1..N) */
int sqlen; /* length of sequence (N) */
int hmmfrom; /* start position in HMM (1..M) */
int hmmto; /* end position in HMM (1..M) */
int hmmlen; /* length of HMM (M) */
int domidx; /* index of this domain */
int ndom; /* total # of domains in this seq */
struct fancyali_s *ali; /* ptr to optional alignment info */
};
/* Structure: tophit_s
*
* Array of high scoring hits, suitable for efficient sorting
* when we prepare to output results. "hit" list is NULL and
* unavailable until after we do a sort.
*/
struct tophit_s {
struct hit_s **hit; /* array of ptrs to top scoring hits */
struct hit_s *unsrt; /* unsorted array */
int alloc; /* current allocation size */
int num; /* number of hits in list now */
int lump; /* allocation lumpsize */
};
/* struct threshold_s
* Contains score/evalue threshold settings.
*
* made first for hmmpfam:
* Since we're going to loop over all HMMs in a Pfam (or pfam-like)
* database in main_loop_{serial,pvm}, and we're going to
* allow autocutoffs using Pfam GA, NC, TC lines, we will need
* to reset those cutoffs with each HMM in turn. Therefore the
* main loops need to know whether they're supposed to be
* doing autocutoff. This amount of info was unwieldy enough
* to pass through the argument list that I put it
* in a structure.
*/
struct threshold_s {
float globT; /* T parameter: keep only hits > globT bits */
double globE; /* E parameter: keep hits < globE E-value */
float domT; /* T parameter for individual domains */
double domE; /* E parameter for individual domains */
/* autosetting of cutoffs using Pfam annot: */
enum { CUT_NONE, CUT_GA, CUT_NC, CUT_TC } autocut;
int Z; /* nseq to base E value calculation on */
};
/**********************************************************
* PVM parallelization
**********************************************************/
#ifdef HMMER_PVM
/* Message tags
*/
#define HMMPVM_INIT 0 /* an initialization packet to all slaves */
#define HMMPVM_WORK 1 /* a work packet sent to a slave */
#define HMMPVM_RESULTS 2 /* a results packet sent back to master */
#define HMMPVM_TASK_TROUBLE 3 /* a notification of bad things in a slave task */
#define HMMPVM_HOST_TROUBLE 4 /* a notification of bad things in a PVM host */
/* error codes
*/
#define HMMPVM_OK 0
#define HMMPVM_NO_HMMFILE 1
#define HMMPVM_NO_INDEX 2
#define HMMPVM_BAD_INIT 3 /* failed to initialize a slave somehow */
#endif
/**********************************************************
* Plan 9: obsolete HMMER1.x code. We still need these structures
* for reading old HMM files (e.g. backwards compatibility)
**********************************************************/
/* We define a "basic" state, which covers the basic match, insert, and
* delete states from the Haussler paper. Numbers are stored as
* pre-calculated negative logs.
*/
struct basic_state {
float t[3]; /* state transitions to +1 M, +0 I, +1 D */
float p[MAXABET]; /* symbol emission probabilities */
};
/* A complete hidden Markov model
*/
struct plan9_s {
int M; /* length of the model */
struct basic_state *ins; /* insert states 0..M+1 */
struct basic_state *mat; /* match 0..M+1; 0 = BEGIN, M+1 = END */
struct basic_state *del; /* delete 0..M+1 */
float null[MAXABET]; /* the *suggested* null model */
/* Optional annotation on the HMM, taken from alignment
*/
char *name; /* a name for the HMM */
char *ref; /* reference coords and annotation */
char *cs; /* consensus structure annotation */
float *xray; /* Structural annotation: xray[0..M+1][NINPUTS], indexed manually */
int flags; /* flags for what optional info is in HMM */
};
/* Flags for optional info in an HMM structure
*/
#define HMM_REF (1<<0)
#define HMM_CS (1<<1)
#define HMM_XRAY (1<<2)
#define MATCH 0
#define INSERT 1
#define DELETE 2
#define BEGIN MATCH
#define END MATCH
#endif /* STRUCTSH_INCLUDED */
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