/* Function: MSAFromAINFO()
* Date: SRE, Mon Jun 14 11:22:24 1999 [St. Louis]
*
* Purpose: Convert the old aseq/ainfo alignment structure
* to new MSA structure. Enables more rapid conversion
* of codebase to the new world order.
*
* Args: aseq - [0..nseq-1][0..alen-1] alignment
* ainfo - old-style optional info
*
* Returns: MSA *
*/
MSA *
MSAFromAINFO(char **aseq, AINFO *ainfo)
{
MSA *msa;
int i, j;
msa = MSAAlloc(ainfo->nseq, ainfo->alen);
for (i = 0; i < ainfo->nseq; i++)
{
strcpy(msa->aseq[i], aseq[i]);
msa->wgt[i] = ainfo->wgt[i];
msa->sqname[i] = sre_strdup(ainfo->sqinfo[i].name, -1);
msa->sqlen[i] = msa->alen;
GKIStoreKey(msa->index, msa->sqname[i]);
if (ainfo->sqinfo[i].flags & SQINFO_ACC)
MSASetSeqAccession(msa, i, ainfo->sqinfo[i].acc);
if (ainfo->sqinfo[i].flags & SQINFO_DESC)
MSASetSeqDescription(msa, i, ainfo->sqinfo[i].desc);
if (ainfo->sqinfo[i].flags & SQINFO_SS) {
if (msa->ss == NULL) {
msa->ss = MallocOrDie(sizeof(char *) * msa->nseqalloc);
msa->sslen = MallocOrDie(sizeof(int) * msa->nseqalloc);
for (j = 0; j < msa->nseqalloc; j++) {
msa->ss[j] = NULL;
msa->sslen[j] = 0;
}
}
MakeAlignedString(msa->aseq[i], msa->alen, ainfo->sqinfo[i].ss, &(msa->ss[i]));
msa->sslen[i] = msa->alen;
}
if (ainfo->sqinfo[i].flags & SQINFO_SA) {
if (msa->sa == NULL) {
msa->sa = MallocOrDie(sizeof(char *) * msa->nseqalloc);
msa->salen = MallocOrDie(sizeof(int) * msa->nseqalloc);
for (j = 0; j < msa->nseqalloc; j++) {
msa->sa[j] = NULL;
msa->salen[j] = 0;
}
}
MakeAlignedString(msa->aseq[i], msa->alen, ainfo->sqinfo[i].sa, &(msa->sa[i]));
msa->salen[i] = msa->alen;
}
}
/* note that sre_strdup() returns NULL when passed NULL */
msa->name = sre_strdup(ainfo->name, -1);
msa->desc = sre_strdup(ainfo->desc, -1);
msa->acc = sre_strdup(ainfo->acc, -1);
msa->au = sre_strdup(ainfo->au, -1);
msa->ss_cons = sre_strdup(ainfo->cs, -1);
msa->rf = sre_strdup(ainfo->rf, -1);
if (ainfo->flags & AINFO_TC) {
msa->cutoff[MSA_CUTOFF_TC1] = ainfo->tc1; msa->cutoff_is_set[MSA_CUTOFF_TC1] = TRUE;
msa->cutoff[MSA_CUTOFF_TC2] = ainfo->tc2; msa->cutoff_is_set[MSA_CUTOFF_TC2] = TRUE;
}
if (ainfo->flags & AINFO_NC) {
msa->cutoff[MSA_CUTOFF_NC1] = ainfo->nc1; msa->cutoff_is_set[MSA_CUTOFF_NC1] = TRUE;
msa->cutoff[MSA_CUTOFF_NC2] = ainfo->nc2; msa->cutoff_is_set[MSA_CUTOFF_NC2] = TRUE;
}
if (ainfo->flags & AINFO_GA) {
msa->cutoff[MSA_CUTOFF_GA1] = ainfo->ga1; msa->cutoff_is_set[MSA_CUTOFF_GA1] = TRUE;
msa->cutoff[MSA_CUTOFF_GA2] = ainfo->ga2; msa->cutoff_is_set[MSA_CUTOFF_GA2] = TRUE;
}
msa->nseq = ainfo->nseq;
msa->alen = ainfo->alen;
return msa;
}
/* Function: WriteSELEX()
*
* Write aligned sequences to an open file pointer,
* breaking into multiple blocks if the sequences are
* long. Number of symbols written per line is set by cpl.
* The alignment must be flushed (all aseqs the same length).
*
* cpl cannot exceed 32767.
*
* May also write optional information from ainfo;
* ainfo may be NULL.
*
* Return: (void)
*/
void
WriteSELEX(FILE *fp, char **aseqs, AINFO *ainfo, int cpl)
{
int idx; /* counter for sequences */
int namelen; /* maximum name length used */
int len; /* tmp variable for name lengths */
char buffer[32768]; /* buffer for writing seq */
int currpos;
char **ss; /* aligned secondary structure strings */
char **sa; /* aligned accessibility strings */
if (cpl > 32767)
Die("You can't WriteSELEX() with lines as long as %d, pal.\n", cpl);
/* calculate max namelen used */
namelen = 0;
for (idx = 0; idx < ainfo->nseq; idx++)
if ((len = strlen(ainfo->sqinfo[idx].name)) > namelen)
namelen = len;
if (namelen < 6) namelen = 6;
/* Make aligned secondary structure strings
*/
ss = (char **) MallocOrDie(sizeof(char *) * ainfo->nseq);
sa = (char **) MallocOrDie(sizeof(char *) * ainfo->nseq);
for (idx = 0; idx < ainfo->nseq; idx++)
{
if (ainfo->sqinfo[idx].flags & SQINFO_SS)
MakeAlignedString(aseqs[idx], ainfo->alen, ainfo->sqinfo[idx].ss, &(ss[idx]));
if (ainfo->sqinfo[idx].flags & SQINFO_SA)
MakeAlignedString(aseqs[idx], ainfo->alen, ainfo->sqinfo[idx].sa, &(sa[idx]));
}
/* Write header info
*/
if (ainfo->name != NULL)
fprintf(fp, "#=ID %s\n", ainfo->name);
if (ainfo->acc != NULL)
fprintf(fp, "#=AC %s\n", ainfo->acc);
if (ainfo->desc != NULL)
fprintf(fp, "#=DE %s\n", ainfo->desc);
if (ainfo->au != NULL)
fprintf(fp, "#=AU %s\n", ainfo->au);
if (ainfo->flags & AINFO_GA)
fprintf(fp, "#=GA %.1f %.1f\n", ainfo->ga1, ainfo->ga2);
if (ainfo->flags & AINFO_TC)
fprintf(fp, "#=TC %.1f %.1f\n", ainfo->tc1, ainfo->tc2);
if (ainfo->flags & AINFO_NC)
fprintf(fp, "#=NC %.1f %.1f\n", ainfo->nc1, ainfo->nc2);
for (idx = 0; idx < ainfo->nseq; idx++)
fprintf(fp, "#=SQ %-*.*s %6.4f %s %s %d..%d::%d %s\n",
namelen, namelen, ainfo->sqinfo[idx].name,
ainfo->wgt[idx],
(ainfo->sqinfo[idx].flags & SQINFO_ID) ? ainfo->sqinfo[idx].id : "-",
(ainfo->sqinfo[idx].flags & SQINFO_ACC) ? ainfo->sqinfo[idx].acc : "-",
(ainfo->sqinfo[idx].flags & SQINFO_START) ? ainfo->sqinfo[idx].start : 0,
(ainfo->sqinfo[idx].flags & SQINFO_STOP) ? ainfo->sqinfo[idx].stop : 0,
(ainfo->sqinfo[idx].flags & SQINFO_OLEN) ? ainfo->sqinfo[idx].olen : 0,
(ainfo->sqinfo[idx].flags & SQINFO_DESC) ? ainfo->sqinfo[idx].desc : "-");
fprintf(fp, "\n");
/* main loop: write seqs in blocks. */
for (currpos = 0; currpos < ainfo->alen; currpos += cpl)
{
/* Reference coord system */
if (ainfo->rf != NULL)
{
strncpy(buffer, ainfo->rf + currpos, cpl);
buffer[cpl] = '\0';
fprintf(fp, "%-*.*s %s\n", namelen, namelen, "#=RF", buffer);
}
/* Consensus secondary structure */
if (ainfo->cs != NULL)
{
strncpy(buffer, ainfo->cs + currpos, cpl);
buffer[cpl] = '\0';
fprintf(fp, "%-*.*s %s\n", namelen, namelen, "#=CS", buffer);
}
for (idx = 0; idx < ainfo->nseq; idx++)
{
/* Aligned sequence */
strncpy(buffer, aseqs[idx] + currpos, cpl);
buffer[cpl] = '\0';
fprintf(fp, "%-*.*s %s\n", namelen, namelen,
ainfo->sqinfo[idx].name, buffer);
/* Individual secondary structure */
if (ainfo->sqinfo[idx].flags & SQINFO_SS)
{
strncpy(buffer, ss[idx] + currpos, cpl);
buffer[cpl] = '\0';
fprintf(fp, "%-*.*s %s\n", namelen, namelen, "#=SS", buffer);
}
/* Surface accessibility */
if (ainfo->sqinfo[idx].flags & SQINFO_SA)
{
strncpy(buffer, sa[idx] + currpos, cpl);
buffer[cpl] = '\0';
fprintf(fp, "%-*.*s %s\n", namelen, namelen, "#=SA", buffer);
}
}
/* put blank line between blocks */
fprintf(fp, "\n");
}
/* Garbage collection
*/
for (idx = 0; idx < ainfo->nseq; idx++)
{
if (ainfo->sqinfo[idx].flags & SQINFO_SS) free(ss[idx]);
if (ainfo->sqinfo[idx].flags & SQINFO_SA) free(sa[idx]);
}
free(ss);
free(sa);
}
