void
Blast_SeqIdGetDefLine(SeqId* sip, char** buffer_ptr, Boolean ncbi_gi,
Boolean accession_only, Boolean search_for_id)
{
char* seqid_buffer = NULL;
Int4 gi = 0;
Boolean numeric_id_type = FALSE;
*buffer_ptr = NULL;
if (sip == NULL)
return;
/* Check for ad hoc ID's generated by formatdb if the user does not provide
any. */
if (search_for_id && (sip->choice != SEQID_GENERAL ||
StringCmp(((Dbtag*)sip->data.ptrvalue)->db, "BL_ORD_ID")))
{
if ((!accession_only && !ncbi_gi) || sip->choice == SEQID_LOCAL) {
seqid_buffer = (char*) malloc(BUFFER_LENGTH + 1);
SeqIdWrite(sip, seqid_buffer, PRINTID_FASTA_LONG, BUFFER_LENGTH);
} else if (accession_only) {
seqid_buffer = (char*) malloc(BUFFER_LENGTH + 1);
SeqIdWrite(SeqIdFindBestAccession(sip), seqid_buffer,
PRINTID_TEXTID_ACC_VER, BUFFER_LENGTH);
} else if (ncbi_gi) {
numeric_id_type =
GetAccessionFromSeqId(SeqIdFindBest(sip, SEQID_GI),
&gi, &seqid_buffer);
} else {
numeric_id_type =
GetAccessionFromSeqId(SeqIdFindBestAccession(sip),
&gi, &seqid_buffer);
}
}
if (numeric_id_type && gi > 0) {
seqid_buffer = (char*) malloc(16);
sprintf(seqid_buffer, "%ld", (long) gi);
}
if (!seqid_buffer) {
/* If it's still NULL make a last ditch effort to get info. */
char* title=NULL;
Bioseq* bsp = BioseqLockById(sip);
if (bsp) {
if (BioseqGetTitle(bsp) != NULL)
title = strdup(BioseqGetTitle(bsp));
else
title = strdup("No definition line found");
}
BioseqUnlock(bsp);
if (title) /* Use first token as id. */
seqid_buffer = StringTokMT(title, " \t\n\r", &title);
}
*buffer_ptr = seqid_buffer;
}
static int LIBCALLBACK
MegaBlastPrintEndpoints(VoidPtr ptr)
{
BlastSearchBlkPtr search = (BlastSearchBlkPtr) ptr;
CharPtr subject_descr;
SeqIdPtr sip, query_id;
CharPtr query_buffer, title;
CharPtr subject_buffer;
Int4 query_length, q_start, q_end, q_shift=0, s_shift=0;
Int4 subject_end;
Int4 hsp_index;
Boolean numeric_sip_type = FALSE;
BLAST_HSPPtr hsp;
Int2 context;
Char context_sign;
Int4 subject_gi, score;
FILE *fp = (FILE *) search->output;
if (search->current_hitlist == NULL || search->current_hitlist->hspcnt <= 0) {
search->subject_info = BLASTSubjectInfoDestruct(search->subject_info);
return 0;
}
if (search->rdfp)
readdb_get_descriptor(search->rdfp, search->subject_id, &sip,
&subject_descr);
else
sip = SeqIdSetDup(search->subject_info->sip);
if (sip->choice != SEQID_GENERAL ||
StringCmp(((DbtagPtr)sip->data.ptrvalue)->db, "BL_ORD_ID")) {
if (search->pbp->mb_params->full_seqids) {
subject_buffer = (CharPtr) Malloc(BUFFER_LENGTH + 1);
SeqIdWrite(sip, subject_buffer, PRINTID_FASTA_LONG, BUFFER_LENGTH);
} else
numeric_sip_type = GetAccessionFromSeqId(SeqIdFindBest(sip, SEQID_GI),
&subject_gi, &subject_buffer);
} else {
DbtagPtr db_tag = (DbtagPtr) sip->data.ptrvalue;
if (db_tag->db &&
(!StringCmp(db_tag->db, "THC") ||
!StringICmp(db_tag->db, "TI")) &&
db_tag->tag->id != 0) {
subject_buffer = (CharPtr) Malloc(16);
sprintf(subject_buffer, "%ld", (long) db_tag->tag->id);
} else {
subject_buffer = StringTokMT(subject_descr, " \t", &subject_descr);
subject_descr = subject_buffer;
}
}
search->current_hitlist->hspcnt_max = search->current_hitlist->hspcnt;
/* Only for the two sequences case, get offset shift if subject
is a subsequence */
if (!search->rdfp && search->query_slp->next) {
s_shift = SeqLocStart(search->query_slp->next);
subject_end = SeqLocStop(search->query_slp->next);
} else {
s_shift = 0;
subject_end =
readdb_get_sequence_length(search->rdfp, search->subject_id);
}
/* Get offset shift if query is a subsequence */
q_shift = SeqLocStart(search->query_slp);
for (hsp_index=0; hsp_index<search->current_hitlist->hspcnt; hsp_index++) {
hsp = search->current_hitlist->hsp_array[hsp_index];
if (hsp==NULL || (search->pbp->cutoff_e > 0 &&
hsp->evalue > search->pbp->cutoff_e))
continue;
/* Correct query context is already found in BlastGetNonSumStatsEvalue */
context = hsp->context;
query_id = search->qid_array[context/2];
if (query_id == NULL) /* Bad hsp, something wrong */
continue;
hsp->context = context & 1;
query_length = search->query_context_offsets[context+1] -
search->query_context_offsets[context] - 1;
hsp->subject.end = hsp->subject.offset + hsp->subject.length;
if (hsp->context) {
hsp->query.end = query_length - hsp->query.offset;
hsp->query.offset =
hsp->query.end - hsp->query.length + 1;
context_sign = '-';
} else {
hsp->query.end = (++hsp->query.offset) + hsp->query.length - 1;
if (hsp->query.end > query_length) {
hsp->subject.end -= (hsp->query.end - query_length);
hsp->query.end = query_length;
}
context_sign = '+';
}
if (hsp->subject.end > subject_end) {
hsp->query.end -= (hsp->subject.end - subject_end);
hsp->subject.end = subject_end;
}
hsp->subject.offset++;
query_buffer = NULL;
if (query_id->choice == SEQID_LOCAL &&
search->pbp->mb_params->full_seqids) {
BioseqPtr query_bsp = BioseqLockById(query_id);
title = StringSave(BioseqGetTitle(query_bsp));
if (title)
query_buffer = StringTokMT(title, " ", &title);
else {
Int4 query_gi;
GetAccessionFromSeqId(query_bsp->id, &query_gi,
&query_buffer);
}
BioseqUnlock(query_bsp);
} else {
query_buffer = (CharPtr) Malloc(BUFFER_LENGTH + 1);
if (!search->pbp->mb_params->full_seqids)
SeqIdWrite(query_id, query_buffer, PRINTID_TEXTID_ACCESSION,
BUFFER_LENGTH);
else
SeqIdWrite(query_id, query_buffer, PRINTID_FASTA_LONG,
BUFFER_LENGTH);
}
if (search->pbp->gap_open==0 && search->pbp->gap_extend==0)
score = ((hsp->subject.length + hsp->query.length)*
search->sbp->reward / 2 - hsp->score) /
(search->sbp->reward - search->sbp->penalty);
else
score = hsp->score;
if (context_sign == '+') {
q_start = hsp->query.offset;
q_end = hsp->query.end;
} else {
q_start = hsp->query.end;
q_end = hsp->query.offset;
}
/* Adjust offsets if query is a subsequence, only for first query */
if (context < 2) {
q_start += q_shift;
q_end += q_shift;
}
hsp->subject.offset += s_shift;
hsp->subject.end += s_shift;
if (numeric_sip_type)
fprintf(fp, "'%ld'=='%c%s' (%d %d %d %d) %d\n", (long) subject_gi,
context_sign, query_buffer, hsp->subject.offset, q_start,
hsp->subject.end, q_end, score);
else
fprintf(fp, "'%s'=='%c%s' (%d %d %d %d) %d\n",
subject_buffer, context_sign, query_buffer,
hsp->subject.offset, q_start,
hsp->subject.end, q_end, score);
MemFree(query_buffer);
}
if (!numeric_sip_type && subject_buffer != subject_descr)
MemFree(subject_buffer);
MemFree(subject_descr);
sip = SeqIdSetFree(sip);
return 0;
}
static int LIBCALLBACK
MegaBlastPrintSegments(VoidPtr ptr)
{
BlastSearchBlkPtr search = (BlastSearchBlkPtr) ptr;
ReadDBFILEPtr rdfp = search->rdfp;
BLAST_HSPPtr hsp;
Int4 i, subject_gi;
Int2 context;
CharPtr query_buffer, title;
SeqIdPtr sip, query_id;
Int4 hsp_index, score;
Uint1Ptr query_seq, subject_seq = NULL;
FloatHi perc_ident;
Char strand;
GapXEditScriptPtr esp;
Int4 q_start, q_end, s_start, s_end, query_length, numseg;
Int4 q_off, num_ident, align_length, total_ident, q_shift=0, s_shift=0;
Int4Ptr length, start;
Uint1Ptr strands;
CharPtr subject_descr, subject_buffer, buffer;
Char tmp_buffer[BUFFER_LENGTH];
Int4 buffer_size, max_buffer_size = LARGE_BUFFER_LENGTH;
Boolean numeric_sip_type = FALSE;
FILE *fp = (FILE *) search->output;
if (search->current_hitlist == NULL || search->current_hitlist->hspcnt <= 0) {
search->subject_info = BLASTSubjectInfoDestruct(search->subject_info);
return 0;
}
subject_seq = search->subject->sequence_start + 1;
if (rdfp)
readdb_get_descriptor(rdfp, search->subject_id, &sip, &subject_descr);
else
sip = SeqIdSetDup(search->subject_info->sip);
if (sip->choice != SEQID_GENERAL ||
StringCmp(((DbtagPtr)sip->data.ptrvalue)->db, "BL_ORD_ID")) {
if (search->pbp->mb_params->full_seqids) {
subject_buffer = (CharPtr) Malloc(BUFFER_LENGTH + 1);
SeqIdWrite(sip, subject_buffer, PRINTID_FASTA_LONG, BUFFER_LENGTH);
} else
numeric_sip_type = GetAccessionFromSeqId(SeqIdFindBest(sip, SEQID_GI),
&subject_gi, &subject_buffer);
} else {
subject_buffer = StringTokMT(subject_descr, " \t", &subject_descr);
subject_descr = subject_buffer;
}
buffer = (CharPtr) Malloc(LARGE_BUFFER_LENGTH);
/* Only for the two sequences case, get offset shift if subject
is a subsequence */
if (!rdfp && search->query_slp->next)
s_shift = SeqLocStart(search->query_slp->next);
/* Get offset shift if query is a subsequence */
q_shift = SeqLocStart(search->query_slp);
for (hsp_index=0; hsp_index<search->current_hitlist->hspcnt; hsp_index++) {
hsp = search->current_hitlist->hsp_array[hsp_index];
if (hsp==NULL || (search->pbp->cutoff_e > 0 &&
hsp->evalue > search->pbp->cutoff_e)) {
continue;
}
context = hsp->context;
query_id = search->qid_array[context/2];
if (query_id == NULL) /* Bad hsp, something wrong */
continue;
hsp->context = context & 1;
if (search->pbp->gap_open==0 && search->pbp->gap_extend==0)
score = ((hsp->subject.length + hsp->query.length)*
search->sbp->reward / 2 - hsp->score) /
(search->sbp->reward - search->sbp->penalty);
else
score = hsp->score;
query_length = search->query_context_offsets[context+1] -
search->query_context_offsets[context] - 1;
q_off = hsp->query.offset;
if (hsp->context) {
strand = '-';
hsp->query.end = query_length - hsp->query.offset;
hsp->query.offset =
hsp->query.end - hsp->query.length;
} else {
strand = '+';
hsp->query.end = hsp->query.offset + hsp->query.length;
}
if (strand == '+') {
q_start = hsp->query.offset + 1;
q_end = hsp->query.end;
} else {
q_start = hsp->query.end;
q_end = hsp->query.offset + 1;
}
s_start = hsp->subject.offset + 1;
s_end = hsp->subject.offset + hsp->subject.length;
/* Adjust offsets if query is a subsequence, only for first query */
if (context < 2) {
q_start += q_shift;
q_end += q_shift;
}
s_start += s_shift;
s_end += s_shift;
if (query_id->choice == SEQID_LOCAL &&
search->pbp->mb_params->full_seqids) {
BioseqPtr query_bsp = BioseqLockById(query_id);
title = StringSave(BioseqGetTitle(query_bsp));
if (title)
query_buffer = StringTokMT(title, " ", &title);
else {
Int4 query_gi;
GetAccessionFromSeqId(query_bsp->id, &query_gi,
&query_buffer);
}
BioseqUnlock(query_bsp);
} else {
query_buffer = (CharPtr) Malloc(BUFFER_LENGTH + 1);
if (!search->pbp->mb_params->full_seqids)
SeqIdWrite(query_id, query_buffer, PRINTID_TEXTID_ACCESSION,
BUFFER_LENGTH);
else
SeqIdWrite(query_id, query_buffer, PRINTID_FASTA_LONG,
BUFFER_LENGTH);
}
if (numeric_sip_type)
sprintf(buffer, "\n#'>%ld'=='%c%s' (%d %d %d %d) %d\na {\n s %d\n b %d %d\n e %d %d\n",
(long) subject_gi, strand, query_buffer,
s_start, q_start, s_end, q_end, score, score,
s_start, q_start, s_end, q_end);
else
sprintf(buffer, "\n#'>%s'=='%c%s' (%d %d %d %d) %d\na {\n s %d\n b %d %d\n e %d %d\n",
subject_buffer, strand, query_buffer,
s_start, q_start, s_end, q_end, score, score,
s_start, q_start, s_end, q_end);
buffer_size = StringLen(buffer);
query_seq = search->context[context].query->sequence;
esp = hsp->gap_info->esp;
for (numseg=0; esp; esp = esp->next, numseg++);
GXECollectDataForSeqalign(hsp->gap_info, hsp->gap_info->esp, numseg,
&start, &length, &strands,
&q_off, &hsp->subject.offset);
if (start[0] < 0) {
length[0] += start[0];
start[1] -= start[0];
start[0] = 0;
}
if (start[2*(numseg-1)] + length[numseg-1] > query_length)
length[numseg-1] = query_length - start[2*(numseg-1)];
total_ident = 0;
align_length = 0;
for (i=0; i<numseg; i++) {
align_length += length[i];
if (strand == '+') {
q_start = start[2*i] + 1;
q_end = q_start + length[i] - 1;
} else {
q_start = query_length - start[2*i];
q_end = q_start - length[i] + 1;
}
if (start[2*i] != -1 && start[2*i+1] != -1) {
num_ident = MegaBlastGetNumIdentical(query_seq, subject_seq,
start[2*i], start[2*i+1],
length[i], FALSE);
perc_ident = (FloatHi) num_ident / length[i] * 100;
total_ident += num_ident;
sprintf(tmp_buffer, " l %d %d %d %d (%.0f)\n", start[2*i+1]+1,
q_start, start[2*i+1]+length[i],
q_end, perc_ident);
if ((buffer_size += StringLen(tmp_buffer)) > max_buffer_size - 2) {
max_buffer_size *= 2;
buffer = (CharPtr) Realloc(buffer, max_buffer_size);
}
StringCat(buffer, tmp_buffer);
}
}
if (100*total_ident >=
align_length*search->pbp->mb_params->perc_identity) {
StringCat(buffer, "}");
fprintf(fp, "%s\n", buffer);
}
MemFree(start);
MemFree(length);
MemFree(strands);
MemFree(query_buffer);
} /* End loop on hsp's */
if (!numeric_sip_type && subject_buffer != subject_descr)
MemFree(subject_buffer);
MemFree(subject_descr);
MemFree(buffer);
sip = SeqIdSetFree(sip);
fflush(fp);
return 1;
}
