/* 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: 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: 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: 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)
{
int seqidx;
/* can we guess? */
if (guess >= 0 && guess < msa->nseq && strcmp(name, msa->sqname[guess]) == 0)
return guess;
/* else, a lookup in the index */
if ((seqidx = GKIKeyIndex(msa->index, name)) >= 0)
return seqidx;
/* else, it's a new name */
seqidx = GKIStoreKey(msa->index, name);
if (seqidx >= msa->nseqalloc) MSAExpand(msa);
msa->sqname[seqidx] = sre_strdup(name, -1);
msa->nseq++;
return seqidx;
}
/* 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: ReadMSF()
* Date: SRE, Tue Jun 1 08:07:22 1999 [St. Louis]
*
* Purpose: Parse an alignment read from an open MSF format
* alignment file. (MSF is a single-alignment format.)
* Return the alignment, or NULL if we've already
* read the alignment.
*
* Args: afp - open alignment file
*
* Returns: MSA * - an alignment object
* caller responsible for an MSAFree()
* NULL if no more alignments
*
* Diagnostics:
* Will Die() here with a (potentially) useful message
* if a parsing error occurs.
*/
MSA *
ReadMSF(MSAFILE *afp)
{
MSA *msa;
char *s;
int alleged_alen;
int alleged_type;
int alleged_checksum;
char *tok;
char *sp;
int slen;
int sqidx;
char *name;
char *seq;
if (feof(afp->f)) return NULL;
if ((s = MSAFileGetLine(afp)) == NULL) return NULL;
/* The first line is the header.
* This is a new-ish GCG feature. Don't count on it, so
* we can be a bit more tolerant towards non-GCG software
* generating "MSF" files.
*/
msa = MSAAlloc(10, 0);
if (strncmp(s, "!!AA_MULTIPLE_ALIGNMENT", 23) == 0) {
msa->type = kAmino;
if ((s = MSAFileGetLine(afp)) == NULL) return NULL;
} else if (strncmp(s, "!!NA_MULTIPLE_ALIGNMENT", 23) == 0) {
msa->type = kRNA;
if ((s = MSAFileGetLine(afp)) == NULL) return NULL;
}
/* Now we're in the free text comment section of the MSF file.
* It ends when we see the "MSF: Type: Check: .." line.
* This line must be present.
*/
do
{
if ((strstr(s, "..") != NULL && strstr(s, "MSF:") != NULL) &&
Strparse("^.+MSF: +([0-9]+) +Type: +([PNX]).+Check: +([0-9]+) +\\.\\.", s, 3))
{
alleged_alen = atoi(sqd_parse[0]);
switch (*(sqd_parse[1])) {
case 'N' : alleged_type = kRNA; break;
case 'P' : alleged_type = kAmino; break;
case 'X' : alleged_type = kOtherSeq; break;
default : alleged_type = kOtherSeq;
}
alleged_checksum = atoi(sqd_parse[3]);
if (msa->type == kOtherSeq) msa->type = alleged_type;
break; /* we're done with comment section. */
}
if (! IsBlankline(s))
MSAAddComment(msa, s);
} while ((s = MSAFileGetLine(afp)) != NULL);
/* Now we're in the name section.
* GCG has a relatively poorly documented feature: only sequences that
* appear in this list will be read from the alignment section. Commenting
* out sequences in the name list (by preceding them with "!") is
* allowed as a means of manually defining subsets of sequences in
* the alignment section. We can support this feature reasonably
* easily because of the hash table for names in the MSA: we
* only add names to the hash table when we see 'em in the name section.
*/
while ((s = MSAFileGetLine(afp)) != NULL)
{
while ((*s == ' ' || *s == '\t') && *s) s++; /* skip leading whitespace */
if (*s == '\n') continue; /* skip blank lines */
else if (*s == '!') MSAAddComment(msa, s);
else if ((sp = strstr(s, "Name:")) != NULL)
{
/* We take the name and the weigh, and that's it */
sp += 5;
tok = sre_strtok(&sp, " \t", &slen); /* <sequence name> */
sqidx = GKIStoreKey(msa->index, tok);
if (sqidx >= msa->nseqalloc) MSAExpand(msa);
msa->sqname[sqidx] = sre_strdup(tok, slen);
msa->nseq++;
if ((sp = strstr(sp, "Weight:")) == NULL)
Die("No Weight: on line %d for %s in name section of MSF file %s\n",
afp->linenumber, msa->sqname[sqidx], afp->fname);
sp += 7;
tok = sre_strtok(&sp, " \t", &slen);
msa->wgt[sqidx] = atof(tok);
msa->flags |= MSA_SET_WGT;
}
else if (strncmp(s, "//", 2) == 0)
break;
else
{
Die("Invalid line (probably %d) in name section of MSF file %s:\n%s\n",
afp->linenumber, afp->fname, s);
squid_errno = SQERR_FORMAT; /* NOT THREADSAFE */
return NULL;
}
}
/* And now we're in the sequence section.
* As discussed above, if we haven't seen a sequence name, then we
* don't include the sequence in the alignment.
* Also, watch out for coordinate-only lines.
*/
while ((s = MSAFileGetLine(afp)) != NULL)
{
sp = s;
if ((name = sre_strtok(&sp, " \t", NULL)) == NULL) continue;
if ((seq = sre_strtok(&sp, "\n", &slen)) == NULL) continue;
/* The test for a coord line: digits starting both fields
*/
if (isdigit((int) *name) && isdigit((int) *seq))
continue;
/* It's not blank, and it's not a coord line: must be sequence
*/
sqidx = GKIKeyIndex(msa->index, name);
if (sqidx < 0) continue; /* not a sequence we recognize */
msa->sqlen[sqidx] = sre_strcat(&(msa->aseq[sqidx]), msa->sqlen[sqidx], seq, slen);
}
/* We've left blanks in the aseqs; take them back out.
*/
for (sqidx = 0; sqidx < msa->nseq; sqidx++)
{
if (msa->aseq[sqidx] == NULL)
Die("Didn't find a sequence for %s in MSF file %s\n", msa->sqname[sqidx], afp->fname);
for (s = sp = msa->aseq[sqidx]; *s != '\0'; s++)
{
if (*s == ' ' || *s == '\t') {
msa->sqlen[sqidx]--;
} else {
*sp = *s;
sp++;
}
}
*sp = '\0';
}
MSAVerifyParse(msa); /* verifies, and also sets alen and wgt. */
return msa;
}
