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msa.c
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msa.c
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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.
*****************************************************************/
/* msa.c
* SRE, Mon May 17 10:48:47 1999
*
* SQUID's interface for multiple sequence alignment
* manipulation: access to the MSA object.
*
* CVS $Id: msa.c,v 1.20 2003/05/26 16:21:50 eddy Exp $
*/
#include "squidconf.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "squid.h"
#include "msa.h" /* multiple sequence alignment object support */
#include "gki.h" /* string indexing hashtable code */
#include "ssi.h" /* SSI sequence file indexing code */
/* Function: MSAAlloc()
* Date: SRE, Tue May 18 10:45:47 1999 [St. Louis]
*
* Purpose: Allocate an MSA structure, return a pointer
* to it.
*
* Designed to be used in three ways:
* 1) We know exactly the dimensions of the alignment:
* both nseq and alen.
* msa = MSAAlloc(nseq, alen);
*
* 2) We know the number of sequences but not alen.
* (We add sequences later.)
* msa = MSAAlloc(nseq, 0);
*
* 3) We even don't know the number of sequences, so
* we'll have to dynamically expand allocations.
* We provide a blocksize for the allocation expansion,
* and expand when needed.
* msa = MSAAlloc(10, 0);
* if (msa->nseq == msa->nseqalloc) MSAExpand(msa);
*
* Args: nseq - number of sequences, or nseq allocation blocksize
* alen - length of alignment in columns, or 0
*
* Returns: pointer to new MSA object, w/ all values initialized.
* Note that msa->nseq is initialized to 0, though space
* is allocated.
*
* Diagnostics: "always works". Die()'s on memory allocation failure.
*
*/
MSA *
MSAAlloc(int nseq, int alen)
{
MSA *msa;
int i;
msa = MallocOrDie(sizeof(MSA));
msa->aseq = MallocOrDie(sizeof(char *) * nseq);
msa->sqname = MallocOrDie(sizeof(char *) * nseq);
msa->sqlen = MallocOrDie(sizeof(int) * nseq);
msa->wgt = MallocOrDie(sizeof(float) * nseq);
for (i = 0; i < nseq; i++)
{
msa->sqname[i] = NULL;
msa->sqlen[i] = 0;
msa->wgt[i] = -1.0;
if (alen != 0) msa->aseq[i] = MallocOrDie(sizeof(char) * (alen+1));
else msa->aseq[i] = NULL;
}
msa->alen = alen;
msa->nseq = 0;
msa->nseqalloc = nseq;
msa->nseqlump = nseq;
msa->flags = 0;
msa->type = kOtherSeq;
msa->name = NULL;
msa->desc = NULL;
msa->acc = NULL;
msa->au = NULL;
msa->ss_cons = NULL;
msa->sa_cons = NULL;
msa->rf = NULL;
msa->sqacc = NULL;
msa->sqdesc = NULL;
msa->ss = NULL;
msa->sslen = NULL;
msa->sa = NULL;
msa->salen = NULL;
msa->index = GKIInit();
msa->lastidx = 0;
for (i = 0; i < MSA_MAXCUTOFFS; i++) {
msa->cutoff[i] = 0.;
msa->cutoff_is_set[i] = FALSE;
}
/* Initialize unparsed optional markup
*/
msa->comment = NULL;
msa->ncomment = 0;
msa->alloc_ncomment = 0;
msa->gf_tag = NULL;
msa->gf = NULL;
msa->ngf = 0;
msa->gs_tag = NULL;
msa->gs = NULL;
msa->gs_idx = NULL;
msa->ngs = 0;
msa->gc_tag = NULL;
msa->gc = NULL;
msa->gc_idx = NULL;
msa->ngc = 0;
msa->gr_tag = NULL;
msa->gr = NULL;
msa->gr_idx = NULL;
msa->ngr = 0;
/* Done. Return the alloced, initialized structure
*/
return msa;
}
/* Function: MSAExpand()
* Date: SRE, Tue May 18 11:06:53 1999 [St. Louis]
*
* Purpose: Increase the sequence allocation in an MSA
* by msa->nseqlump. (Typically used when we're reading
* in an alignment sequentially from a file,
* so we don't know nseq until we're done.)
*
* Args: msa - the MSA object
*
* Returns: (void)
*
*/
void
MSAExpand(MSA *msa)
{
int i,j;
msa->nseqalloc += msa->nseqlump;
msa->aseq = ReallocOrDie(msa->aseq, sizeof(char *) * msa->nseqalloc);
msa->sqname = ReallocOrDie(msa->sqname, sizeof(char *) * msa->nseqalloc);
msa->sqlen = ReallocOrDie(msa->sqlen, sizeof(char *) * msa->nseqalloc);
msa->wgt = ReallocOrDie(msa->wgt, sizeof(float) * msa->nseqalloc);
if (msa->ss != NULL) {
msa->ss = ReallocOrDie(msa->ss, sizeof(char *) * msa->nseqalloc);
msa->sslen = ReallocOrDie(msa->sslen, sizeof(int) * msa->nseqalloc);
}
if (msa->sa != NULL) {
msa->sa = ReallocOrDie(msa->sa, sizeof(char *) * msa->nseqalloc);
msa->salen = ReallocOrDie(msa->salen, sizeof(int) * msa->nseqalloc);
}
if (msa->sqacc != NULL)
msa->sqacc = ReallocOrDie(msa->sqacc, sizeof(char *) * msa->nseqalloc);
if (msa->sqdesc != NULL)
msa->sqdesc =ReallocOrDie(msa->sqdesc,sizeof(char *) * msa->nseqalloc);
for (i = msa->nseqalloc-msa->nseqlump; i < msa->nseqalloc; i++)
{
msa->sqname[i] = NULL;
msa->wgt[i] = -1.0;
if (msa->sqacc != NULL) msa->sqacc[i] = NULL;
if (msa->sqdesc != NULL) msa->sqdesc[i] = NULL;
if (msa->alen != 0)
msa->aseq[i] = ReallocOrDie(msa->aseq[i], sizeof(char) * (msa->alen+1));
else msa->aseq[i] = NULL;
msa->sqlen[i] = 0;
if (msa->ss != NULL) {
if (msa->alen != 0)
msa->ss[i] = ReallocOrDie(msa->ss[i], sizeof(char) * (msa->alen+1));
else msa->ss[i] = NULL;
msa->sslen[i] = 0;
}
if (msa->sa != NULL) {
if (msa->alen != 0)
msa->sa[i] = ReallocOrDie(msa->ss[i], sizeof(char) * (msa->alen+1));
else
msa->sa[i] = NULL;
msa->salen[i] = 0;
}
}
/* Reallocate and re-init for unparsed #=GS tags, if we have some.
* gs is [0..ngs-1][0..nseq-1][], so we're reallocing the middle
* set of pointers.
*/
if (msa->gs != NULL)
for (i = 0; i < msa->ngs; i++)
{
if (msa->gs[i] != NULL)
{
msa->gs[i] = ReallocOrDie(msa->gs[i], sizeof(char *) * msa->nseqalloc);
for (j = msa->nseqalloc-msa->nseqlump; j < msa->nseqalloc; j++)
msa->gs[i][j] = NULL;
}
}
/* Reallocate and re-init for unparsed #=GR tags, if we have some.
* gr is [0..ngs-1][0..nseq-1][], so we're reallocing the middle
* set of pointers.
*/
if (msa->gr != NULL)
for (i = 0; i < msa->ngr; i++)
{
if (msa->gr[i] != NULL)
{
msa->gr[i] = ReallocOrDie(msa->gr[i], sizeof(char *) * msa->nseqalloc);
for (j = msa->nseqalloc-msa->nseqlump; j < msa->nseqalloc; j++)
msa->gr[i][j] = NULL;
}
}
return;
}
/* Function: MSAFree()
* Date: SRE, Tue May 18 11:20:16 1999 [St. Louis]
*
* Purpose: Free a multiple sequence alignment structure.
*
* Args: msa - the alignment
*
* Returns: (void)
*/
void
MSAFree(MSA *msa)
{
Free2DArray((void **) msa->aseq, msa->nseq);
Free2DArray((void **) msa->sqname, msa->nseq);
Free2DArray((void **) msa->sqacc, msa->nseq);
Free2DArray((void **) msa->sqdesc, msa->nseq);
Free2DArray((void **) msa->ss, msa->nseq);
Free2DArray((void **) msa->sa, msa->nseq);
if (msa->sqlen != NULL) free(msa->sqlen);
if (msa->wgt != NULL) free(msa->wgt);
if (msa->name != NULL) free(msa->name);
if (msa->desc != NULL) free(msa->desc);
if (msa->acc != NULL) free(msa->acc);
if (msa->au != NULL) free(msa->au);
if (msa->ss_cons != NULL) free(msa->ss_cons);
if (msa->sa_cons != NULL) free(msa->sa_cons);
if (msa->rf != NULL) free(msa->rf);
if (msa->sslen != NULL) free(msa->sslen);
if (msa->salen != NULL) free(msa->salen);
Free2DArray((void **) msa->comment, msa->ncomment);
Free2DArray((void **) msa->gf_tag, msa->ngf);
Free2DArray((void **) msa->gf, msa->ngf);
Free2DArray((void **) msa->gs_tag, msa->ngs);
Free3DArray((void ***)msa->gs, msa->ngs, msa->nseq);
Free2DArray((void **) msa->gc_tag, msa->ngc);
Free2DArray((void **) msa->gc, msa->ngc);
Free2DArray((void **) msa->gr_tag, msa->ngr);
Free3DArray((void ***)msa->gr, msa->ngr, msa->nseq);
GKIFree(msa->index);
GKIFree(msa->gs_idx);
GKIFree(msa->gc_idx);
GKIFree(msa->gr_idx);
free(msa);
}
/* Function: MSASetSeqAccession()
* Date: SRE, Mon Jun 21 04:13:33 1999 [Sanger Centre]
*
* Purpose: Set a sequence accession in an MSA structure.
* Handles some necessary allocation/initialization.
*
* Args: msa - multiple alignment to add accession to
* seqidx - index of sequence to attach accession to
* acc - accession
*
* Returns: void
*/
void
MSASetSeqAccession(MSA *msa, int seqidx, char *acc)
{
int x;
if (msa->sqacc == NULL) {
msa->sqacc = MallocOrDie(sizeof(char *) * msa->nseqalloc);
for (x = 0; x < msa->nseqalloc; x++)
msa->sqacc[x] = NULL;
}
msa->sqacc[seqidx] = sre_strdup(acc, -1);
}
/* Function: MSASetSeqDescription()
* Date: SRE, Mon Jun 21 04:21:09 1999 [Sanger Centre]
*
* Purpose: Set a sequence description in an MSA structure.
* Handles some necessary allocation/initialization.
*
* Args: msa - multiple alignment to add accession to
* seqidx - index of sequence to attach accession to
* desc - description
*
* Returns: void
*/
void
MSASetSeqDescription(MSA *msa, int seqidx, char *desc)
{
int x;
if (msa->sqdesc == NULL) {
msa->sqdesc = MallocOrDie(sizeof(char *) * msa->nseqalloc);
for (x = 0; x < msa->nseqalloc; x++)
msa->sqdesc[x] = NULL;
}
msa->sqdesc[seqidx] = sre_strdup(desc, -1);
}
/* Function: MSAAddComment()
* Date: SRE, Tue Jun 1 17:37:21 1999 [St. Louis]
*
* Purpose: Add an (unparsed) comment line to the MSA structure,
* allocating as necessary.
*
* Args: msa - a multiple alignment
* s - comment line to add
*
* Returns: (void)
*/
void
MSAAddComment(MSA *msa, char *s)
{
/* If this is our first recorded comment, we need to malloc();
* and if we've filled available space, we need to realloc().
* Note the arbitrary lumpsize of 10 lines per allocation...
*/
if (msa->comment == NULL) {
msa->comment = MallocOrDie (sizeof(char *) * 10);
msa->alloc_ncomment = 10;
}
if (msa->ncomment == msa->alloc_ncomment) {
msa->alloc_ncomment += 10;
msa->comment = ReallocOrDie(msa->comment, sizeof(char *) * msa->alloc_ncomment);
}
msa->comment[msa->ncomment] = sre_strdup(s, -1);
msa->ncomment++;
return;
}
/* Function: MSAAddGF()
* Date: SRE, Wed Jun 2 06:53:54 1999 [bus to Madison]
*
* Purpose: Add an unparsed #=GF markup line to the MSA
* structure, allocating as necessary.
*
* Args: msa - a multiple alignment
* tag - markup tag (e.g. "AU")
* value - free text markup (e.g. "Alex Bateman")
*
* Returns: (void)
*/
void
MSAAddGF(MSA *msa, char *tag, char *value)
{
/* If this is our first recorded unparsed #=GF line, we need to malloc();
* if we've filled availabl space If we already have a hash index, and the GF
* Note the arbitrary lumpsize of 10 lines per allocation...
*/
if (msa->gf_tag == NULL) {
msa->gf_tag = MallocOrDie (sizeof(char *) * 10);
msa->gf = MallocOrDie (sizeof(char *) * 10);
msa->alloc_ngf = 10;
}
if (msa->ngf == msa->alloc_ngf) {
msa->alloc_ngf += 10;
msa->gf_tag = ReallocOrDie(msa->gf_tag, sizeof(char *) * msa->alloc_ngf);
msa->gf = ReallocOrDie(msa->gf, sizeof(char *) * msa->alloc_ngf);
}
msa->gf_tag[msa->ngf] = sre_strdup(tag, -1);
msa->gf[msa->ngf] = sre_strdup(value, -1);
msa->ngf++;
return;
}
/* Function: MSAAddGS()
* Date: SRE, Wed Jun 2 06:57:03 1999 [St. Louis]
*
* Purpose: Add an unparsed #=GS markup line to the MSA
* structure, allocating as necessary.
*
* It's possible that we could get more than one
* of the same type of GS tag per sequence; for
* example, "DR PDB;" structure links in Pfam.
* Hack: handle these by appending to the string,
* in a \n separated fashion.
*
* Args: msa - multiple alignment structure
* tag - markup tag (e.g. "AC")
* sqidx - index of sequence to assoc markup with (0..nseq-1)
* value - markup (e.g. "P00666")
*
* Returns: 0 on success
*/
void
MSAAddGS(MSA *msa, char *tag, int sqidx, char *value)
{
int tagidx;
int i;
/* Is this an unparsed tag name that we recognize?
* If not, handle adding it to index, and reallocating
* as needed.
*/
if (msa->gs_tag == NULL) /* first tag? init w/ malloc */
{
msa->gs_idx = GKIInit();
tagidx = GKIStoreKey(msa->gs_idx, tag);
SQD_DASSERT1((tagidx == 0));
msa->gs_tag = MallocOrDie(sizeof(char *));
msa->gs = MallocOrDie(sizeof(char **));
msa->gs[0] = MallocOrDie(sizeof(char *) * msa->nseqalloc);
for (i = 0; i < msa->nseqalloc; i++)
msa->gs[0][i] = NULL;
}
else
{
/* new tag? */
tagidx = GKIKeyIndex(msa->gs_idx, tag);
if (tagidx < 0) { /* it's a new tag name; realloc */
tagidx = GKIStoreKey(msa->gs_idx, tag);
/* since we alloc in blocks of 1,
we always realloc upon seeing
a new tag. */
SQD_DASSERT1((tagidx == msa->ngs));
msa->gs_tag = ReallocOrDie(msa->gs_tag, (msa->ngs+1) * sizeof(char *));
msa->gs = ReallocOrDie(msa->gs, (msa->ngs+1) * sizeof(char **));
msa->gs[msa->ngs] = MallocOrDie(sizeof(char *) * msa->nseqalloc);
for (i = 0; i < msa->nseqalloc; i++)
msa->gs[msa->ngs][i] = NULL;
}
}
if (tagidx == msa->ngs) {
msa->gs_tag[tagidx] = sre_strdup(tag, -1);
msa->ngs++;
}
if (msa->gs[tagidx][sqidx] == NULL) /* first annotation of this seq with this tag? */
msa->gs[tagidx][sqidx] = sre_strdup(value, -1);
else {
/* >1 annotation of this seq with this tag; append */
int len;
if ((len = sre_strcat(&(msa->gs[tagidx][sqidx]), -1, "\n", 1)) < 0)
Die("failed to sre_strcat()");
if (sre_strcat(&(msa->gs[tagidx][sqidx]), len, value, -1) < 0)
Die("failed to sre_strcat()");
}
return;
}
/* Function: MSAAppendGC()
* Date: SRE, Thu Jun 3 06:25:14 1999 [Madison]
*
* Purpose: Add an unparsed #=GC markup line to the MSA
* structure, allocating as necessary.
*
* When called multiple times for the same tag,
* appends value strings together -- used when
* parsing multiblock alignment files, for
* example.
*
* Args: msa - multiple alignment structure
* tag - markup tag (e.g. "CS")
* value - markup, one char per aligned column
*
* Returns: (void)
*/
void
MSAAppendGC(MSA *msa, char *tag, char *value)
{
int tagidx;
/* Is this an unparsed tag name that we recognize?
* If not, handle adding it to index, and reallocating
* as needed.
*/
if (msa->gc_tag == NULL) /* first tag? init w/ malloc */
{
msa->gc_tag = MallocOrDie(sizeof(char *));
msa->gc = MallocOrDie(sizeof(char *));
msa->gc_idx = GKIInit();
tagidx = GKIStoreKey(msa->gc_idx, tag);
SQD_DASSERT1((tagidx == 0));
msa->gc[0] = NULL;
}
else
{ /* new tag? */
tagidx = GKIKeyIndex(msa->gc_idx, tag);
if (tagidx < 0) { /* it's a new tag name; realloc */
tagidx = GKIStoreKey(msa->gc_idx, tag);
/* since we alloc in blocks of 1,
we always realloc upon seeing
a new tag. */
SQD_DASSERT1((tagidx == msa->ngc));
msa->gc_tag = ReallocOrDie(msa->gc_tag, (msa->ngc+1) * sizeof(char **));
msa->gc = ReallocOrDie(msa->gc, (msa->ngc+1) * sizeof(char **));
msa->gc[tagidx] = NULL;
}
}
if (tagidx == msa->ngc) {
msa->gc_tag[tagidx] = sre_strdup(tag, -1);
msa->ngc++;
}
sre_strcat(&(msa->gc[tagidx]), -1, value, -1);
return;
}
/* Function: MSAGetGC()
* Date: SRE, Fri Aug 13 13:25:57 1999 [St. Louis]
*
* Purpose: Given a tagname for a miscellaneous #=GC column
* annotation, return a pointer to the annotation
* string.
*
* Args: msa - alignment and its annotation
* tag - name of the annotation
*
* Returns: ptr to the annotation string. Caller does *not*
* free; is managed by msa object still.
*/
char *
MSAGetGC(MSA *msa, char *tag)
{
int tagidx;
if (msa->gc_idx == NULL) return NULL;
if ((tagidx = GKIKeyIndex(msa->gc_idx, tag)) < 0) return NULL;
return msa->gc[tagidx];
}
/* Function: MSAAppendGR()
* Date: SRE, Thu Jun 3 06:34:38 1999 [Madison]
*
* Purpose: Add an unparsed #=GR markup line to the
* MSA structure, allocating as necessary.
*
* When called multiple times for the same tag,
* appends value strings together -- used when
* parsing multiblock alignment files, for
* example.
*
* Args: msa - multiple alignment structure
* tag - markup tag (e.g. "SS")
* sqidx - index of seq to assoc markup with (0..nseq-1)
* value - markup, one char per aligned column
*
* Returns: (void)
*/
void
MSAAppendGR(MSA *msa, char *tag, int sqidx, char *value)
{
int tagidx;
int i;
/* Is this an unparsed tag name that we recognize?
* If not, handle adding it to index, and reallocating
* as needed.
*/
if (msa->gr_tag == NULL) /* first tag? init w/ malloc */
{
msa->gr_tag = MallocOrDie(sizeof(char *));
msa->gr = MallocOrDie(sizeof(char **));
msa->gr[0] = MallocOrDie(sizeof(char *) * msa->nseqalloc);
for (i = 0; i < msa->nseqalloc; i++)
msa->gr[0][i] = NULL;
msa->gr_idx = GKIInit();
tagidx = GKIStoreKey(msa->gr_idx, tag);
SQD_DASSERT1((tagidx == 0));
}
else
{
/* new tag? */
tagidx = GKIKeyIndex(msa->gr_idx, tag);
if (tagidx < 0) { /* it's a new tag name; realloc */
tagidx = GKIStoreKey(msa->gr_idx, tag);
/* since we alloc in blocks of 1,
we always realloc upon seeing
a new tag. */
SQD_DASSERT1((tagidx == msa->ngr));
msa->gr_tag = ReallocOrDie(msa->gr_tag, (msa->ngr+1) * sizeof(char *));
msa->gr = ReallocOrDie(msa->gr, (msa->ngr+1) * sizeof(char **));
msa->gr[msa->ngr] = MallocOrDie(sizeof(char *) * msa->nseqalloc);
for (i = 0; i < msa->nseqalloc; i++)
msa->gr[msa->ngr][i] = NULL;
}
}
if (tagidx == msa->ngr) {
msa->gr_tag[tagidx] = sre_strdup(tag, -1);
msa->ngr++;
}
sre_strcat(&(msa->gr[tagidx][sqidx]), -1, value, -1);
return;
}
/* Function: MSAVerifyParse()
* Date: SRE, Sat Jun 5 14:24:24 1999 [Madison, 1999 worm mtg]
*
* Purpose: Last function called after a multiple alignment is
* parsed. Checks that parse was successful; makes sure
* required information is present; makes sure required
* information is consistent. Some fields that are
* only use during parsing may be freed (sqlen, for
* example).
*
* Some fields in msa may be modified (msa->alen is set,
* for example).
*
* Args: msa - the multiple alignment
* sqname, aseq must be set
* nseq must be correct
* alen need not be set; will be set here.
* wgt will be set here if not already set
*
* Returns: (void)
* Will Die() here with diagnostics on error.
*
* Example:
*/
void
MSAVerifyParse(MSA *msa)
{
int idx;
if (msa->nseq == 0) Die("Parse error: no sequences were found for alignment %s",
msa->name != NULL ? msa->name : "");
msa->alen = msa->sqlen[0];
/* We can rely on msa->sqname[] being valid for any index,
* because of the way the line parsers always store any name
* they add to the index.
*/
for (idx = 0; idx < msa->nseq; idx++)
{
/* aseq is required. */
if (msa->aseq[idx] == NULL)
Die("Parse error: No sequence for %s in alignment %s", msa->sqname[idx],
msa->name != NULL ? msa->name : "");
/* either all weights must be set, or none of them */
if ((msa->flags & MSA_SET_WGT) && msa->wgt[idx] == -1.0)
Die("Parse error: some weights are set, but %s doesn't have one in alignment %s",
msa->sqname[idx],
msa->name != NULL ? msa->name : "");
/* all aseq must be same length. */
if (msa->sqlen[idx] != msa->alen)
Die("Parse error: sequence %s: length %d, expected %d in alignment %s",
msa->sqname[idx], msa->sqlen[idx], msa->alen,
msa->name != NULL ? msa->name : "");
/* if SS is present, must have length right */
if (msa->ss != NULL && msa->ss[idx] != NULL && msa->sslen[idx] != msa->alen)
Die("Parse error: #=GR SS annotation for %s: length %d, expected %d in alignment %s",
msa->sqname[idx], msa->sslen[idx], msa->alen,
msa->name != NULL ? msa->name : "");
/* if SA is present, must have length right */
if (msa->sa != NULL && msa->sa[idx] != NULL && msa->salen[idx] != msa->alen)
Die("Parse error: #=GR SA annotation for %s: length %d, expected %d in alignment %s",
msa->sqname[idx], msa->salen[idx], msa->alen,
msa->name != NULL ? msa->name : "");
}
/* if cons SS is present, must have length right */
if (msa->ss_cons != NULL && strlen(msa->ss_cons) != msa->alen)
Die("Parse error: #=GC SS_cons annotation: length %d, expected %d in alignment %s",
strlen(msa->ss_cons), msa->alen,
msa->name != NULL ? msa->name : "");
/* if cons SA is present, must have length right */
if (msa->sa_cons != NULL && strlen(msa->sa_cons) != msa->alen)
Die("Parse error: #=GC SA_cons annotation: length %d, expected %d in alignment %s",
strlen(msa->sa_cons), msa->alen,
msa->name != NULL ? msa->name : "");
/* if RF is present, must have length right */
if (msa->rf != NULL && strlen(msa->rf) != msa->alen)
Die("Parse error: #=GC RF annotation: length %d, expected %d in alignment %s",
strlen(msa->rf), msa->alen,
msa->name != NULL ? msa->name : "");
/* Check that all or no weights are set */
if (!(msa->flags & MSA_SET_WGT))
FSet(msa->wgt, msa->nseq, 1.0); /* default weights */
/* Clean up a little from the parser */
if (msa->sqlen != NULL) { free(msa->sqlen); msa->sqlen = NULL; }
if (msa->sslen != NULL) { free(msa->sslen); msa->sslen = NULL; }
if (msa->salen != NULL) { free(msa->salen); msa->salen = NULL; }
return;
}
/* Function: MSAFileOpen()
* Date: SRE, Tue May 18 13:22:01 1999 [St. Louis]
*
* Purpose: Open an alignment database file and prepare
* for reading one alignment, or sequentially
* in the (rare) case of multiple MSA databases
* (e.g. Stockholm format).
*
* Args: filename - name of file to open
* if "-", read stdin
* if it ends in ".gz", read from pipe to gunzip -dc
* format - format of file (e.g. MSAFILE_STOCKHOLM)
* env - environment variable for path (e.g. BLASTDB)
*
* Returns: opened MSAFILE * on success.
* NULL on failure:
* usually, because the file doesn't exist;
* for gzip'ed files, may also mean that gzip isn't in the path.
*/
MSAFILE *
MSAFileOpen(char *filename, int format, char *env)
{
MSAFILE *afp;
afp = MallocOrDie(sizeof(MSAFILE));
if (strcmp(filename, "-") == 0)
{
afp->f = stdin;
afp->do_stdin = TRUE;
afp->do_gzip = FALSE;
afp->fname = sre_strdup("[STDIN]", -1);
afp->ssi = NULL; /* can't index stdin because we can't seek*/
}
#ifndef SRE_STRICT_ANSI
/* popen(), pclose() aren't portable to non-POSIX systems; disable */
else if (Strparse("^.*\\.gz$", filename, 0))
{
char cmd[256];
/* Note that popen() will return "successfully"
* if file doesn't exist, because gzip works fine
* and prints an error! So we have to check for
* existence of file ourself.
*/
if (! FileExists(filename))
Die("%s: file does not exist", filename);
if (strlen(filename) + strlen("gzip -dc ") >= 256)
Die("filename > 255 char in MSAFileOpen()");
sprintf(cmd, "gzip -dc %s", filename);
if ((afp->f = popen(cmd, "r")) == NULL)
return NULL;
afp->do_stdin = FALSE;
afp->do_gzip = TRUE;
afp->fname = sre_strdup(filename, -1);
/* we can't index a .gz file, because we can't seek in a pipe afaik */
afp->ssi = NULL;
}
#endif /*SRE_STRICT_ANSI*/
else
{
char *ssifile;
char *dir;
/* When we open a file, it may be either in the current
* directory, or in the directory indicated by the env
* argument - and we have to construct the SSI filename accordingly.
*/
if ((afp->f = fopen(filename, "r")) != NULL)
{
ssifile = MallocOrDie(sizeof(char) * (strlen(filename) + 5));
sprintf(ssifile, "%s.ssi", filename);
}
else if ((afp->f = EnvFileOpen(filename, env, &dir)) != NULL)
{
char *full;
full = FileConcat(dir, filename);
ssifile = MallocOrDie(sizeof(char) * (strlen(full) + strlen(filename) + 5));
sprintf(ssifile, "%s.ssi", full);
free(dir);
}
else return NULL;
afp->do_stdin = FALSE;
afp->do_gzip = FALSE;
afp->fname = sre_strdup(filename, -1);
afp->ssi = NULL;
/* Open the SSI index file. If it doesn't exist, or
* it's corrupt, or some error happens, afp->ssi stays NULL.
*/
SSIOpen(ssifile, &(afp->ssi));
free(ssifile);
}
/* Invoke autodetection if we haven't already been told what
* to expect.
*/
if (format == MSAFILE_UNKNOWN)
{
if (afp->do_stdin == TRUE || afp->do_gzip)
Die("Can't autodetect alignment file format from a stdin or gzip pipe");
format = MSAFileFormat(afp);
if (format == MSAFILE_UNKNOWN)
Die("Can't determine format of multiple alignment file %s", afp->fname);
}
afp->format = format;
afp->linenumber = 0;
afp->buf = NULL;
afp->buflen = 0;
return afp;
}
/* Function: MSAFilePositionByKey()
* MSAFilePositionByIndex()
* MSAFileRewind()
*
* Date: SRE, Tue Nov 9 19:02:54 1999 [St. Louis]
*
* Purpose: Family of functions for repositioning in
* open MSA files; analogous to a similarly
* named function series in HMMER's hmmio.c.
*
* Args: afp - open alignment file
* offset - disk offset in bytes
* key - key to look up in SSI indices
* idx - index of alignment.
*
* Returns: 0 on failure.
* 1 on success.
* If called on a non-fseek()'able file (e.g. a gzip'ed
* or pipe'd alignment), returns 0 as a failure flag.
*/
int
MSAFileRewind(MSAFILE *afp)
{
if (afp->do_gzip || afp->do_stdin) return 0;
rewind(afp->f);
return 1;
}
int
MSAFilePositionByKey(MSAFILE *afp, char *key)
{
int fh; /* filehandle is ignored */
SSIOFFSET offset; /* offset of the key alignment */
if (afp->ssi == NULL) return 0;
if (SSIGetOffsetByName(afp->ssi, key, &fh, &offset) != 0) return 0;
if (SSISetFilePosition(afp->f, &offset) != 0) return 0;
return 1;
}
int
MSAFilePositionByIndex(MSAFILE *afp, int idx)
{
int fh; /* filehandled is passed but ignored */
SSIOFFSET offset; /* disk offset of desired alignment */
if (afp->ssi == NULL) return 0;
if (SSIGetOffsetByNumber(afp->ssi, idx, &fh, &offset) != 0) return 0;
if (SSISetFilePosition(afp->f, &offset) != 0) return 0;
return 1;
}
/* Function: MSAFileRead()
* Date: SRE, Fri May 28 16:01:43 1999 [St. Louis]
*
* Purpose: Read the next msa from an open alignment file.
* This is a wrapper around format-specific calls.
*
* Args: afp - open alignment file
*
* Returns: next alignment, or NULL if out of alignments
*/
MSA *
MSAFileRead(MSAFILE *afp)
{
MSA *msa = NULL;
switch (afp->format) {
case MSAFILE_STOCKHOLM: msa = ReadStockholm(afp); break;
case MSAFILE_MSF: msa = ReadMSF(afp); break;
case MSAFILE_A2M: msa = ReadA2M(afp); break;
case MSAFILE_CLUSTAL: msa = ReadClustal(afp); break;
case MSAFILE_SELEX: msa = ReadSELEX(afp); break;
case MSAFILE_PHYLIP: msa = ReadPhylip(afp); break;
default:
Die("MSAFILE corrupted: bad format index");
}
return msa;
}
/* Function: MSAFileClose()
* Date: SRE, Tue May 18 14:05:28 1999 [St. Louis]
*
* Purpose: Close an open MSAFILE.
*
* Args: afp - ptr to an open MSAFILE.
*
* Returns: void
*/
void
MSAFileClose(MSAFILE *afp)
{
#ifndef SRE_STRICT_ANSI /* gzip functionality only on POSIX systems */
if (afp->do_gzip) pclose(afp->f);
#endif
if (! afp->do_stdin) fclose(afp->f);
if (afp->buf != NULL) free(afp->buf);
if (afp->ssi != NULL) SSIClose(afp->ssi);
if (afp->fname != NULL) free(afp->fname);
free(afp);
}
char *
MSAFileGetLine(MSAFILE *afp)
{
char *s;
if ((s = sre_fgets(&(afp->buf), &(afp->buflen), afp->f)) == NULL)
return NULL;
afp->linenumber++;
return afp->buf;
}
void
MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline)
{
switch (outfmt) {
case MSAFILE_A2M: WriteA2M(fp, msa); break;
case MSAFILE_CLUSTAL: WriteClustal(fp, msa); break;
case MSAFILE_MSF: WriteMSF(fp, msa); break;
case MSAFILE_PHYLIP: WritePhylip(fp, msa); break;
case MSAFILE_SELEX: WriteSELEX(fp, msa); break;
case MSAFILE_STOCKHOLM:
if (do_oneline) WriteStockholmOneBlock(fp, msa);
else WriteStockholm(fp, msa);
break;
default:
Die("can't write. no such alignment format %d\n", outfmt);
}
}
/* Function: MSAGetSeqidx()
* Date: SRE, Wed May 19 15:08:25 1999 [St. Louis]
*
* Purpose: From a sequence name, return seqidx appropriate
* for an MSA structure.
*
* 1) try to guess the index. (pass -1 if you can't guess)
* 2) Look up name in msa's hashtable.
* 3) If it's a new name, store in msa's hashtable;
* expand allocs as needed;
* save sqname.
*
* Args: msa - alignment object
* name - a sequence name
* guess - a guess at the right index, or -1 if no guess.
*
* Returns: seqidx
*/
int
MSAGetSeqidx(MSA *msa, char *name, int guess)