static ValNodePtr CollectBioseqLineValues (BioseqPtr bsp, ValNodePtr field_list, Boolean want_gi)
{
SeqDescrPtr sdp;
SeqMgrDescContext dcontext;
Char id_txt[255], id_txt2[255];
SeqIdPtr sip, sip_gi = NULL, sip_gb = NULL;
ValNodePtr line_list = NULL, line_values;
if (bsp == NULL) {
return NULL;
}
for (sip = bsp->id; sip != NULL; sip = sip->next) {
if (sip->choice == SEQID_GENBANK
|| (sip->choice == SEQID_EMBL && sip_gb == NULL)
|| (sip->choice == SEQID_SWISSPROT && sip_gb == NULL)
|| (sip->choice == SEQID_DDBJ && sip_gb == NULL)
|| (sip->choice == SEQID_PIR && sip_gb == NULL)) {
sip_gb = sip;
} else if (sip->choice == SEQID_GI) {
sip_gi = sip;
}
}
if (sip_gb == NULL && sip_gi == NULL) {
SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_txt, PRINTID_REPORT, sizeof (id_txt) - 1);
id_txt2[0] = 0;
} else {
if (sip_gb == NULL) {
id_txt[0] = 0;
} else {
SeqIdWrite (sip_gb, id_txt, PRINTID_REPORT, sizeof (id_txt) - 1);
}
if (sip_gi == NULL) {
id_txt2[0] = 0;
} else {
SeqIdWrite (sip_gi, id_txt2, PRINTID_REPORT, sizeof (id_txt2) - 1);
}
}
for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
sdp != NULL;
sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &dcontext)) {
line_values = NULL;
ValNodeAddPointer (&line_values, 0, StringSave (id_txt));
if (want_gi) {
ValNodeAddPointer (&line_values, 0, StringSave (id_txt2));
}
ValNodeLink (&line_values, CollectBioSourceValues (sdp->data.ptrvalue, field_list));
ValNodeAddPointer (&line_list, 0, line_values);
}
return line_list;
}
static Boolean
BL2SEQ_MakeSeqLoc(const BioseqPtr bsp1, const BioseqPtr bsp2, SeqLocPtr *slp1, SeqLocPtr *slp2, Uint1 strand_option)
{
const char* k_delimiters = " ,;";
CharPtr location;
Int4 from, to;
*slp1 = NULL;
*slp2 = NULL;
location = myargs[ARG_LOC1].strvalue;
if (location) {
from = atoi(StringTokMT(location, k_delimiters, &location)) - 1;
to = atoi(location) - 1;
from = MAX(from, 0);
if (to < 0)
to = bsp1->length - 1;
to = MIN(to, bsp1->length - 1);
if (from >= bsp1->length) {
ErrPostEx(SEV_FATAL, 1, 0,
"Location outside of the first sequence range\n");
return FALSE;
}
*slp1 = SeqLocIntNew(from, to, strand_option,
SeqIdFindBestAccession(bsp1->id));
} else if (strand_option != Seq_strand_both) {
*slp1 = SeqLocIntNew(0, bsp1->length-1, strand_option,
SeqIdFindBestAccession(bsp1->id));
} else
ValNodeAddPointer(slp1, SEQLOC_WHOLE, SeqIdDup(SeqIdFindBestAccession(bsp1->id)));
location = myargs[ARG_LOC2].strvalue;
if (location) {
from = atoi(StringTokMT(location, k_delimiters, &location)) - 1;
to = atoi(location) - 1;
from = MAX(from, 0);
if (to < 0)
to = bsp2->length - 1;
to = MIN(to, bsp2->length - 1);
if (from >= bsp2->length) {
ErrPostEx(SEV_FATAL, 1, 0,
"Location outside of the second sequence range\n");
return FALSE;
}
*slp2 = SeqLocIntNew(from, to, Seq_strand_plus, SeqIdFindBestAccession(bsp2->id));
} else
ValNodeAddPointer(slp2, SEQLOC_WHOLE, SeqIdDup(SeqIdFindBestAccession(bsp2->id)));
return TRUE;
}
static void CommentFieldsToDialog (DialoG d, Pointer data)
{
TagListPtr tlp;
ValNodePtr fields, vnp;
CharPtr str;
tlp = (TagListPtr) GetObjectExtra (d);
if (tlp == NULL) {
return;
}
fields = (ValNodePtr) data;
tlp->vnp = ValNodeFreeData (tlp->vnp);
SendMessageToDialog (tlp->dialog, VIB_MSG_RESET);
for (vnp = fields; vnp != NULL; vnp = vnp->next) {
str = TagStringFromFieldRule (vnp->data.ptrvalue);
if (str != NULL) {
ValNodeAddPointer (&(tlp->vnp), 0, str);
}
}
SendMessageToDialog (tlp->dialog, VIB_MSG_REDRAW);
tlp->max = MAX ((Int2) 0, (Int2) (ValNodeLen (tlp->vnp) - tlp->rows));
CorrectBarMax (tlp->bar, tlp->max);
CorrectBarPage (tlp->bar, tlp->rows - 1, tlp->rows - 1);
if (tlp->max > 0) {
SafeShow (tlp->bar);
} else {
SafeHide (tlp->bar);
}
}
static ValNodePtr CollectBioSourceValues (BioSourcePtr biop, ValNodePtr field_list)
{
Char taxid_buf[30];
ValNodePtr field_values = NULL;
CharPtr txt;
sprintf (taxid_buf, "%d", GetTaxIdFromOrgRef(biop->org));
ValNodeAddPointer (&field_values, 0, StringSave (taxid_buf));
while (field_list != NULL) {
txt = GetSourceQualFromBioSource (biop, field_list->data.ptrvalue, NULL);
ValNodeAddPointer (&field_values, 0, txt);
field_list = field_list->next;
}
return field_values;
}
static Boolean GetGraphsProc (GatherObjectPtr gop)
{
GphGetPtr ggp;
GphItemPtr gip;
SeqGraphPtr sgp;
if (gop == NULL || gop->itemtype != OBJ_SEQGRAPH) return TRUE;
ggp = (GphGetPtr) gop->userdata;
sgp = (SeqGraphPtr) gop->dataptr;
if (ggp == NULL || sgp == NULL) return TRUE;
/* only phrap or gap4 currently allowed */
if (StringICmp (sgp->title, "Phrap Quality") == 0 ||
StringICmp (sgp->title, "Gap4") == 0) {
/* data type must be bytes */
if (sgp->flags[2] == 3) {
if (SeqIdForSameBioseq (SeqLocId (sgp->loc), SeqLocId (ggp->slp))) {
gip = (GphItemPtr) MemNew (sizeof (GphItem));
if (gip == NULL) return TRUE;
gip->sgp = sgp;
gip->left = GetOffsetInBioseq (sgp->loc, ggp->bsp, SEQLOC_LEFT_END);
gip->right = GetOffsetInBioseq (sgp->loc, ggp->bsp, SEQLOC_RIGHT_END);
ValNodeAddPointer (&(ggp->vnp), 0, (Pointer) gip);
}
}
}
return TRUE;
}
static void RecordThesis (ScanDataPtr sdp, CharPtr str)
{
StringSetPtr ssp;
ValNodePtr vnp;
if (sdp == NULL || StringHasNoText (str)) return;
for (vnp = sdp->lcList; vnp != NULL; vnp = vnp->next) {
ssp = (StringSetPtr) vnp->data.ptrvalue;
if (ssp == NULL) continue;
if (StringCmp (ssp->text, str) == 0) {
(ssp->count)++;
return;
}
}
ssp = MemNew (sizeof (StringSet));
if (ssp == NULL) return;
StringCpy (ssp->firstID, sdp->buf);
StringNCpy_0 (ssp->text, str, sizeof (ssp->text));
ssp->count = 1;
ValNodeAddPointer (&(sdp->lcList), 0, (Pointer) ssp);
}
static void GetProtListCallback (BioseqPtr bsp, Pointer userdata)
{
ValNodePtr PNTR pList;
SeqFeatPtr sfp;
SeqMgrFeatContext fcontext;
ProtRefPtr prp;
AlphaProtPtr app;
if (bsp == NULL || userdata == NULL || ! ISA_aa (bsp->mol)) return;
pList = (ValNodePtr PNTR) userdata;
app = (AlphaProtPtr) MemNew (sizeof (AlphaProtData));
if (app == NULL) return;
app->bsp = bsp;
app->prot_name = NULL;
sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_PROT, 0, &fcontext);
if (sfp != NULL && sfp->data.value.ptrvalue != NULL)
{
prp = (ProtRefPtr) sfp->data.value.ptrvalue;
if (prp->name != NULL)
{
app->prot_name = StringSave (prp->name->data.ptrvalue);
}
else
{
app->prot_name = StringSave (fcontext.label);
}
}
ValNodeAddPointer (pList, 0, app);
}
PVNMB CpyPVNMBList(PVNMB pvnmb, PDNMG pdnmgNewHead, Pointer parentPtr) {
PDNMG pdnmg, pdnmgNew, pdnmgPmadFrom = NULL, pdnmgPmadTo = NULL;
PMGD pmgd, pmgdNew, pmgdTmp = NULL;
PVNMB pvnmbNew, pvnmbNewHead = NULL, pvnmbLast = NULL;
PMBD pmbd, pmbdNew;
while(pvnmb) {
pmbd = (PMBD)(pvnmb->data.ptrvalue);
pvnmbNew = ValNodeNew(NULL);
pvnmbNew->choice = pvnmb->choice;
pmbdNew = NewMBD();
pmbdNew->pfbParent = (PFB)parentPtr;
pmbdNew->pvnmbLink = pvnmbNew;
pmbdNew->bWhat = pmbd->bWhat;
pmgdTmp = (PMGD)(pmbd->pmadFrom->pfbParent);
pdnmgPmadFrom = GetPDNMGFromIndex(pdnmgNewHead, ((PDNMG)(pmgdTmp->pdnmgLink))->choice);
pmbdNew->pmadFrom = GetPMADFromName(((PMGD)(pdnmgPmadFrom->data.ptrvalue))->pvnmaAHead, pmbd->pmadFrom->pcAName);
pmgdTmp = (PMGD)(pmbd->pmadTo->pfbParent);
pdnmgPmadTo = GetPDNMGFromIndex(pdnmgNewHead, ((PDNMG)(pmgdTmp->pdnmgLink))->choice);
pmbdNew->pmadTo = GetPMADFromName(((PMGD)(pdnmgPmadTo->data.ptrvalue))->pvnmaAHead, pmbd->pmadTo->pcAName);
/* Add PMBD to the appropriate PMADs */
ValNodeAddPointer(&pmbdNew->pmadFrom->pvnBonds, 0, (VoidPtr)pmbdNew);
ValNodeAddPointer(&pmbdNew->pmadTo->pvnBonds, 0, (VoidPtr)pmbdNew);
pvnmbNew->data.ptrvalue = (VoidPtr)pmbdNew;
if(pvnmbNewHead == NULL) {
pvnmbNewHead = pvnmbNew;
pvnmbLast = pvnmbNew;
}
else {
pvnmbLast->next = pvnmbNew;
pvnmbLast = pvnmbNew;
}
pvnmb = pvnmb->next;
}
return pvnmbNewHead;
}
static Boolean AddToSaveList (GatherContextPtr gcp)
{
ValNodePtr PNTR list;
list = (ValNodePtr PNTR) gcp->userdata;
if (list == NULL) return TRUE;
ValNodeAddPointer (list, gcp->thistype, gcp->thisitem);
return TRUE;
}
static ValNodePtr FieldsFromFieldListString (CharPtr str)
{
CharPtr cpy, val, comma;
Int4 qual;
ValNodePtr field_list = NULL, qc;
if (StringHasNoText (str)) {
return NULL;
}
cpy = StringSave (str);
val = cpy;
comma = StringChr(val, ',');
while (comma != NULL) {
*comma = 0;
qual = GetSourceQualTypeByName(val);
if (qual < 0) {
Message (MSG_ERROR, "%s is not a recognized source field name", val);
} else {
qc = ValNodeNew (NULL);
qc->choice = SourceQualChoice_textqual;
qc->data.intvalue = qual;
ValNodeAddPointer (&field_list, FieldType_source_qual, qc);
}
*comma = ',';
val = comma + 1;
comma = StringChr (val, ',');
}
qual = GetSourceQualTypeByName(val);
if (qual < 0) {
Message (MSG_ERROR, "%s is not a recognized source field name", val);
} else {
qc = ValNodeNew (NULL);
qc->choice = SourceQualChoice_textqual;
qc->data.intvalue = qual;
ValNodeAddPointer (&field_list, FieldType_source_qual, qc);
}
cpy = MemFree (cpy);
return field_list;
}
static void CollectBioseqsForConversion (BioseqPtr bsp, Pointer userdata)
{
ValNodePtr PNTR list;
if (bsp == NULL || bsp->repr != Seq_repr_raw || ISA_aa (bsp->mol)) return;
if (userdata == NULL)
{
return;
}
list = (ValNodePtr PNTR) userdata;
ValNodeAddPointer (list, 0, bsp);
}
NLM_EXTERN ValNodePtr LIBCALL AsnGenericValNodeSetAsnRead (
AsnIoPtr aip,
AsnModulePtr amp,
AsnTypePtr orig,
BoolPtr isError,
AsnReadFunc readfunc,
AsnOptFreeFunc freefunc
)
{
AsnTypePtr atp = orig, start_atp;
DataVal av;
Pointer val;
ValNodePtr vnp, head = NULL, last = NULL;
if (isError != NULL) {
*isError = FALSE;
}
if (aip == NULL || readfunc == NULL || freefunc == NULL) return NULL;
if (AsnReadVal (aip, atp, &av) <= 0) goto erret; /* read START STRUCT */
start_atp = orig;
atp = start_atp;
while ((atp = AsnReadId (aip, amp, atp)) != start_atp) {
val = (Pointer) readfunc (aip, atp);
if (val == NULL) goto erret;
vnp = ValNodeAddPointer (&last, 0, val);
if (head == NULL) {
head = vnp;
}
last = vnp;
}
if (AsnReadVal (aip, atp, &av) <= 0) goto erret; /* read END STRUCT */
ret:
return (Pointer) head;
erret:
head = AsnGenericValNodeSetFree (head, freefunc);
if (isError != NULL) {
*isError = TRUE;
}
goto ret;
}
/* This constructs an ASN.1 SeqGraph that contains the quality scores from the consensus sequence */
static SeqGraphPtr SeqGraphFromContig (TContigPtr contig, BioseqPtr bsp)
{
SeqGraphPtr sgp;
ByteStorePtr bs;
Uint1 bytes[128];
Int2 max = INT2_MIN;
Int2 min = INT2_MAX;
Int4 q_pos, b_pos;
SeqIntPtr sintp;
if (contig == NULL || contig->num_qual_scores == 0 || contig->qual_scores == NULL
|| bsp == NULL) {
return NULL;
}
sgp = SeqGraphNew ();
bs = BSNew (1000);
q_pos = 0;
while (q_pos < contig->num_qual_scores) {
b_pos = 0;
while (b_pos < sizeof (bytes) && q_pos < contig->num_qual_scores) {
max = MAX (max, (Int2) contig->qual_scores[q_pos]);
min = MIN (min, (Int2) contig->qual_scores[q_pos]);
bytes[b_pos++] = (Uint1) contig->qual_scores[q_pos++];
}
BSWrite (bs, (Pointer) bytes, (Int4) b_pos);
}
sgp->numval = BSLen (bs);
BSPutByte (bs, EOF);
sgp->title = StringSave ("Phrap Quality");
sgp->flags [0] = 0;
sgp->compr = 1;
sgp->flags [1] = 0;
sgp->flags [2] = 3;
sgp->axis.intvalue = 0;
sgp->min.intvalue = min;
sgp->max.intvalue = max;
sgp->a = 1.0;
sgp->b = 0;
sgp->values = (Pointer) bs;
sintp = SeqIntNew ();
sintp->from = 0;
sintp->to = bsp->length - 1;
sintp->id = SeqIdDup (bsp->id);
ValNodeAddPointer (&(sgp->loc), SEQLOC_INT, (Pointer) sintp);
return sgp;
}
/** Creates a list of SeqLoc structures with data about PHI BLAST pattern
* occurrences, to be used as features on Query Seq-locs.
* @param pattern_info Pattern information structure. [in]
* @param query_seqloc Query SeqLoc, needed to retrieve Seq-id. [in]
* @param seed_seqloc_ptr List of SeqLoc's with pattern data. [out]
*/
static Int2
s_PHIBlastCreateSeedSeqLoc(const SPHIQueryInfo* pattern_info,
SeqLoc* query_seqloc,
SeqLoc** seed_seqloc_ptr)
{
Int4 index;
for (index = 0; index < pattern_info->num_patterns; ++index) {
const SPHIPatternInfo* this_occurrence =
&pattern_info->occurrences[index];
SeqInt* si = SeqIntNew();
si->id = SeqIdDup(SeqLocId(query_seqloc));
si->from = this_occurrence->offset;
si->to = this_occurrence->offset + this_occurrence->length - 1;
ValNodeAddPointer(seed_seqloc_ptr, SEQLOC_INT, si);
}
return 0;
}
static Pointer CommentFieldsFromDialog (DialoG d)
{
TagListPtr tlp;
ValNodePtr fields = NULL, vnp;
FieldRulePtr rule;
tlp = (TagListPtr) GetObjectExtra (d);
if (tlp == NULL) {
return NULL;
}
for (vnp = tlp->vnp; vnp != NULL; vnp = vnp->next) {
rule = FieldRuleFromTagString (vnp->data.ptrvalue);
if (rule != NULL) {
ValNodeAddPointer (&fields, 0, rule);
}
}
return fields;
}
/** Splits the PHI BLAST results corresponding to different pattern occurrences
* in query, converts them to Seq-aligns and puts in a list of ValNodes.
* @param results All results from different pattern occurrences
* mixed together. On return points to NULL. [in]
* @param pattern_info Query pattern occurrences information [in]
* @param program Program type (phiblastp or phiblastn) [in]
* @param query_seqloc List of query locations [in]
* @param rdfp blast db object [in]
* @param phivnps List of ValNodes containing Seq-aligns. [out]
* @return Status, 0 on success, -1 on failure.
*/
static Int2
s_PHIResultsToSeqAlign(const BlastHSPResults* results,
const SPHIQueryInfo* pattern_info,
EBlastProgramType program, SeqLoc* query_seqloc,
ReadDBFILE* rdfp, ValNode* *phivnps)
{
Int2 status = 0;
/* Split results into an array of BlastHSPResults structures corresponding
to different pattern occurrences. */
BlastHSPResults* *phi_results =
PHIBlast_HSPResultsSplit(results, pattern_info);
if (phi_results) {
int pattern_index; /* Index over pattern occurrences. */
for (pattern_index = 0; pattern_index < pattern_info->num_patterns;
++pattern_index) {
SBlastSeqalignArray* seqalign_arr = NULL;
SeqAlign* seqalign = NULL;
BlastHSPResults* one_phi_results = phi_results[pattern_index];
if (one_phi_results) {
/* PHI BLAST is always gapped, and never out-of-frame, hence
* TRUE and FALSE values for the respective booleans in the next
* call.
*/
status =
BLAST_ResultsToSeqAlign(program, &one_phi_results,
query_seqloc, rdfp, NULL, TRUE,
FALSE, &seqalign_arr);
if (seqalign_arr)
{
seqalign = seqalign_arr->array[0];
seqalign_arr->array[0] = NULL;
SBlastSeqalignArrayFree(seqalign_arr);
}
ValNodeAddPointer(phivnps, pattern_index, seqalign);
}
}
sfree(phi_results);
}
return status;
}
Int2 Main_old (void)
{
AsnIoPtr aip;
BioseqPtr fake_bsp = NULL, fake_subject_bsp = NULL, query_bsp = NULL,
subject_bsp = NULL;
BioseqPtr bsp1, bsp2;
BLAST_KarlinBlkPtr ka_params=NULL, ka_params_gap=NULL;
BLAST_OptionsBlkPtr options=NULL;
Boolean seq1_is_na, seq2_is_na;
CharPtr params_buffer=NULL;
DbtagPtr dbtagptr;
Uint1 align_type;
Uint4 align_options;
SeqAlignPtr seqalign;
SeqAnnotPtr seqannot;
SeqEntryPtr sep = NULL, sep1 = NULL;
CharPtr program_name, blast_outputfile;
FILE *outfp;
ValNodePtr mask_loc, mask_loc_start, vnp, other_returns=NULL, error_returns=NULL;
BLAST_MatrixPtr matrix;
Int4Ptr PNTR txmatrix;
int (LIBCALLBACK *handle_results)PROTO((VoidPtr search)) = NULL;
Boolean entrez_lookup = FALSE;
Boolean html, seqannot_output, believe_query;
Uint1 tabular_output;
Boolean gapped_calculation;
entrez_lookup = (Boolean) myargs[ARG_ACCN].intvalue;
html = (Boolean) myargs[ARG_HTML].intvalue;
seqannot_output = (myargs[ARG_ASNOUT].strvalue != NULL);
blast_outputfile = myargs [ARG_OUT].strvalue;
program_name = StringSave(myargs[ARG_PROGRAM].strvalue);
if (StringCmp(program_name, "blastn") &&
StringCmp(program_name, "blastp") &&
StringCmp(program_name, "blastx") &&
StringCmp(program_name, "tblastn") &&
StringCmp(program_name, "tblastx")) {
ErrPostEx(SEV_FATAL, 1, 0, "Program name must be blastn, blastp, blastx, tblastn or tblastx\n");
return (1);
}
align_type = BlastGetTypes(program_name, &seq1_is_na, &seq2_is_na);
if ((outfp = FileOpen(blast_outputfile, "w")) == NULL)
{
ErrPostEx(SEV_FATAL, 1, 0, "blast: Unable to open output file %s\n", blast_outputfile);
return (1);
}
gapped_calculation = (Boolean) myargs[ARG_GAPPED].intvalue;
believe_query = (seqannot_output || entrez_lookup);
options = BLASTOptionNewEx(program_name, gapped_calculation,
(Boolean) myargs[ARG_USEMEGABLAST].intvalue);
if (BL2SEQ_GetSequences(seq1_is_na, seq2_is_na, &query_bsp, &subject_bsp,
&sep, &sep1, &(options->query_lcase_mask),
believe_query) == FALSE)
{
ErrPostEx(SEV_FATAL, 1, 0, "blast: Unable to get sequences");
return (1);
}
if (!entrez_lookup) {
if (!believe_query)
fake_bsp = BlastMakeFakeBioseq(query_bsp, NULL);
fake_subject_bsp = BioseqNew();
fake_subject_bsp->descr = subject_bsp->descr;
fake_subject_bsp->repr = subject_bsp->repr;
fake_subject_bsp->mol = subject_bsp->mol;
fake_subject_bsp->length = subject_bsp->length;
fake_subject_bsp->seq_data = subject_bsp->seq_data;
fake_subject_bsp->seq_data_type = subject_bsp->seq_data_type;
dbtagptr = DbtagNew();
dbtagptr->db = StringSave("BL_ORD_ID");
dbtagptr->tag = ObjectIdNew();
if (BioseqGetTitle(subject_bsp) != NULL)
dbtagptr->tag->str = StringSave(BioseqGetTitle(subject_bsp));
else
dbtagptr->tag->str = StringSave("No definition line found");
ValNodeAddPointer(&fake_subject_bsp->id, SEQID_GENERAL, dbtagptr);
bsp1 = (believe_query ? query_bsp : fake_bsp);
bsp2 = fake_subject_bsp;
} else {
bsp1 = query_bsp;
bsp2 = subject_bsp;
}
tabular_output = (Uint1) myargs[ARG_FORMAT].intvalue;
if (myargs[ARG_SEARCHSP].floatvalue)
options->searchsp_eff = (Nlm_FloatHi) myargs[ARG_SEARCHSP].floatvalue;
options->filter_string = StringSave(myargs[ARG_FILTER].strvalue);
options->expect_value = (Nlm_FloatHi) myargs [ARG_EVALUE].floatvalue;
if (StringICmp("blastn", program_name) == 0)
{
options->penalty = myargs[ARG_MISMATCH].intvalue;
options->reward = myargs[ARG_MATCH].intvalue;
}
options->db_length = (Int8) myargs[ARG_DBSIZE].floatvalue;
options->discontinuous = FALSE;
if (myargs[ARG_XDROP].intvalue != 0)
{
options->gap_x_dropoff = myargs[ARG_XDROP].intvalue;
}
if (myargs[ARG_WORDSIZE].intvalue != 0)
options->wordsize = (Int2) myargs[ARG_WORDSIZE].intvalue;
if (options->is_megablast_search) {
options->cutoff_s2 = options->wordsize*options->reward;
}
options->matrix = MemFree(options->matrix);
BLASTOptionSetGapParams(options, myargs[ARG_MATRIX].strvalue, 0, 0);
if (myargs[ARG_GAPOPEN].intvalue != -1)
options->gap_open = myargs[ARG_GAPOPEN].intvalue;
if (myargs[ARG_GAPEXT].intvalue != -1)
options->gap_extend = myargs[ARG_GAPEXT].intvalue;
options->strand_option = myargs[ARG_STRAND].intvalue;
/* Input longest intron length is in nucleotide scale; in the lower
level code it will be used in protein scale */
if (myargs[ARG_INTRON].intvalue > 0)
options->longest_intron = myargs[ARG_INTRON].intvalue;
if (!myargs[ARG_LOC1].strvalue && !myargs[ARG_LOC2].strvalue) {
seqalign = BlastTwoSequencesWithCallback(bsp1, bsp2, program_name,
options, &other_returns, &error_returns, handle_results);
} else {
SeqLocPtr slp1=NULL, slp2=NULL;
if (BL2SEQ_MakeSeqLoc(bsp1, bsp2, &slp1, &slp2, options->strand_option) == FALSE)
return 1;
seqalign = BlastTwoSequencesByLocWithCallback(slp1, slp2, program_name, options, &other_returns, &error_returns, handle_results, NULL);
SeqLocFree(slp1);
SeqLocFree(slp2);
}
if (error_returns) {
BlastErrorPrint(error_returns);
for (vnp = error_returns; vnp; vnp = vnp->next) {
BlastDestroyErrorMessage((BlastErrorMsgPtr)vnp->data.ptrvalue);
}
ValNodeFree(error_returns);
}
ka_params = NULL;
ka_params_gap = NULL;
params_buffer = NULL;
mask_loc = NULL;
matrix = NULL;
txmatrix = NULL;
for (vnp=other_returns; vnp; vnp = vnp->next) {
switch (vnp->choice) {
case TXKABLK_NOGAP:
ka_params = vnp->data.ptrvalue;
break;
case TXKABLK_GAP:
ka_params_gap = vnp->data.ptrvalue;
break;
case TXPARAMETERS:
params_buffer = vnp->data.ptrvalue;
break;
case TXMATRIX:
matrix = vnp->data.ptrvalue;
if (matrix && !tabular_output)
txmatrix = BlastMatrixToTxMatrix(matrix);
break;
case SEQLOC_MASKING_NOTSET:
case SEQLOC_MASKING_PLUS1:
case SEQLOC_MASKING_PLUS2:
case SEQLOC_MASKING_PLUS3:
case SEQLOC_MASKING_MINUS1:
case SEQLOC_MASKING_MINUS2:
case SEQLOC_MASKING_MINUS3:
ValNodeAddPointer(&mask_loc, vnp->choice, vnp->data.ptrvalue);
break;
default:
break;
}
}
if (!tabular_output || seqannot_output) {
align_options = 0;
align_options += TXALIGN_MATRIX_VAL;
align_options += TXALIGN_SHOW_QS;
align_options += TXALIGN_COMPRESS;
align_options += TXALIGN_END_NUM;
if (StringICmp("blastx", program_name) == 0) {
align_options += TXALIGN_BLASTX_SPECIAL;
}
if (html)
align_options += TXALIGN_HTML;
seqannot = SeqAnnotNew();
seqannot->type = 2;
AddAlignInfoToSeqAnnot(seqannot, align_type);
seqannot->data = seqalign;
aip = NULL;
if (seqannot_output)
aip = AsnIoOpen (myargs[ARG_ASNOUT].strvalue,"w");
if (aip && seqannot) {
SeqAnnotAsnWrite((SeqAnnotPtr) seqannot, aip, NULL);
AsnIoReset(aip);
aip = AsnIoClose(aip);
}
}
if (!tabular_output) {
AcknowledgeBlastQuery(query_bsp, 70, outfp, believe_query, html);
ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL, NULL, align_options, txmatrix, mask_loc, FormatScoreFunc);
seqannot = SeqAnnotFree(seqannot);
if (txmatrix)
txmatrix = TxMatrixDestruct(txmatrix);
init_buff_ex(85);
if (ka_params) {
PrintKAParameters(ka_params->Lambda, ka_params->K, ka_params->H, 70, outfp, FALSE);
}
if (ka_params_gap) {
PrintKAParameters(ka_params_gap->Lambda, ka_params_gap->K, ka_params_gap->H, 70, outfp, TRUE);
}
PrintTildeSepLines(params_buffer, 70, outfp);
free_buff();
} else {
PrintTabularOutputHeader(NULL, query_bsp, NULL,
program_name, 0, believe_query, outfp);
BlastPrintTabulatedResults(seqalign, query_bsp, NULL,
1, program_name, !gapped_calculation,
believe_query, 0, 0, outfp, FALSE);
SeqAlignSetFree(seqalign);
}
matrix = BLAST_MatrixDestruct(matrix);
MemFree(ka_params);
MemFree(ka_params_gap);
MemFree(params_buffer);
mask_loc_start = mask_loc;
while (mask_loc) {
SeqLocSetFree(mask_loc->data.ptrvalue);
mask_loc = mask_loc->next;
}
ValNodeFree(mask_loc_start);
fake_bsp = BlastDeleteFakeBioseq(fake_bsp);
other_returns = ValNodeFree(other_returns);
options->query_lcase_mask = SeqLocSetFree(options->query_lcase_mask);
options = BLASTOptionDelete(options);
MemFree(program_name);
FileClose(outfp);
if (entrez_lookup) {
BioseqFree(query_bsp);
BioseqFree(subject_bsp);
} else {
SeqEntryFree(sep);
SeqEntryFree(sep1);
}
return 0;
}
Int2 Main_new(void)
{
BioseqPtr query_bsp=NULL, subject_bsp=NULL;
BioseqPtr bsp1=NULL, bsp2=NULL;
BioseqPtr fake_bsp=NULL, fake_subject_bsp=NULL;
BlastFormattingInfo* format_info = NULL;
BLAST_SummaryOptions* options=NULL;
Blast_SummaryReturn* extra_returns = Blast_SummaryReturnNew();
Boolean believe_query= FALSE;
Boolean seq1_is_na, seq2_is_na; /* seq1/2 is DNA if TRUE. */
Boolean seqannot_output; /* SeqAlign will be output. */
Boolean entrez_lookup; /* QUery/subject fetched from Entrez. */
Boolean mask_at_hash=FALSE; /* masking only on lookup table if TRUE. */
DbtagPtr dbtagptr;
EBlastProgramType program_number;
Int2 status; /* return value */
EAlignView align_view = eAlignViewPairwise; /* Used for formatting */
SeqAlignPtr seqalign=NULL;
SeqEntryPtr sep=NULL, sep1=NULL;
SeqLocPtr slp1, slp2; /* Used for actual search. */
SeqLocPtr filter_loc=NULL; /* Location of regions filtered (returned by engine) */
SeqLocPtr lcase_mask=NULL; /* For lower-case masking info from query FASTA. */
SeqLoc* repeat_mask = NULL; /* Repeat mask locations */
Uint1 strand_option = 0; /* FIXME */
SBlastOptions* search_options = NULL; /* Needed for formatting. */
SBlastSeqalignArray* seqalign_arr = NULL;
GeneticCodeSingletonInit();
strand_option = (Uint1) myargs[ARG_STRAND].intvalue;
entrez_lookup = (Boolean) myargs[ARG_ACCN].intvalue;
seqannot_output = (myargs[ARG_ASNOUT].strvalue != NULL);
believe_query = (seqannot_output || entrez_lookup);
/* Non-zero value for -m option means tabular output. */
if (myargs[ARG_FORMAT].intvalue != 0)
align_view = eAlignViewTabularWithComments;
BlastProgram2Number(myargs[ARG_PROGRAM].strvalue, &program_number);
seq1_is_na = (program_number == eBlastTypeBlastn ||
program_number == eBlastTypeBlastx ||
program_number == eBlastTypeRpsTblastn ||
program_number == eBlastTypeTblastx);
seq2_is_na = (program_number == eBlastTypeBlastn ||
program_number == eBlastTypeTblastn ||
program_number == eBlastTypeTblastx);
if (BL2SEQ_GetSequences(seq1_is_na, seq2_is_na, &query_bsp, &subject_bsp,
&sep, &sep1, &lcase_mask, believe_query)
== FALSE)
{
ErrPostEx(SEV_FATAL, 1, 0, "blast: Unable to get sequences");
return (1);
}
if (!entrez_lookup) {
if (!believe_query)
fake_bsp = BlastMakeFakeBioseq(query_bsp, NULL);
fake_subject_bsp = BioseqNew();
fake_subject_bsp->descr = subject_bsp->descr;
fake_subject_bsp->repr = subject_bsp->repr;
fake_subject_bsp->mol = subject_bsp->mol;
fake_subject_bsp->length = subject_bsp->length;
fake_subject_bsp->seq_data = subject_bsp->seq_data;
fake_subject_bsp->seq_data_type = subject_bsp->seq_data_type;
dbtagptr = DbtagNew();
dbtagptr->db = StringSave("BL_ORD_ID");
dbtagptr->tag = ObjectIdNew();
if (BioseqGetTitle(subject_bsp) != NULL)
dbtagptr->tag->str = StringSave(BioseqGetTitle(subject_bsp));
else
dbtagptr->tag->str = StringSave("No definition line found");
ValNodeAddPointer(&fake_subject_bsp->id, SEQID_GENERAL, dbtagptr);
bsp1 = (believe_query ? query_bsp : fake_bsp);
bsp2 = fake_subject_bsp;
} else { /* Query and subject Bioseqs are already "fake". */
bsp1 = query_bsp;
bsp2 = subject_bsp;
}
if (BL2SEQ_MakeSeqLoc(bsp1, bsp2, &slp1, &slp2, strand_option) == FALSE)
return 1;
if (Bl2SEQ_SummaryOptionsSet(&options, program_number) == FALSE)
return 1;
/* Find repeat mask, if necessary */
if ((status = Blast_FindRepeatFilterSeqLoc(slp1, myargs[ARG_FILTER].strvalue,
&repeat_mask, &extra_returns->error)) != 0)
{
if (extra_returns && extra_returns->error)
{
ErrSev max_sev = SBlastMessageErrPost(extra_returns->error);
if (max_sev >= SEV_ERROR)
return status;
}
}
/* Combine repeat mask with lower case mask */
if (repeat_mask)
lcase_mask = ValNodeLink(&lcase_mask, repeat_mask);
status = BLAST_TwoSeqLocSets(options, slp1, slp2, lcase_mask, &seqalign_arr,
&filter_loc, &mask_at_hash,
&extra_returns);
/* Free the lower case mask in SeqLoc form. */
lcase_mask = Blast_ValNodeMaskListFree(lcase_mask);
/* Post warning or error messages, no matter what the search status
was. */
SBlastMessageErrPost(extra_returns->error);
if (status != 0)
{
ErrPostEx(SEV_FATAL, 1, 0, "BLAST_TwoSeqLocSets failed");
return status;
}
if (myargs[ARG_ASNOUT].strvalue && seqalign_arr) {
AsnIoPtr asnout =
AsnIoOpen(myargs[ARG_ASNOUT].strvalue, (char*)"w");
GenericSeqAlignSetAsnWrite(seqalign_arr->array[0], asnout);
asnout = AsnIoClose(asnout);
}
/* Pass NULL for the database name, since there is no database. */
BlastFormattingInfoNewBasic(align_view, options, slp1,
myargs[ARG_OUT].strvalue, &search_options,
&format_info);
/* Always show gis in the output, hence pass TRUE for respective
argument. */
BlastFormattingInfoSetUpOptions(format_info, 0, 1,
(Boolean) myargs[ARG_HTML].intvalue,
(Boolean) myargs[ARG_USEMEGABLAST].intvalue,
TRUE, believe_query);
/* If masking was at hash only, free the masking locations,
* to prevent them from being used for formatting.
*/
if (SBlastOptionsGetMaskAtHash(search_options))
filter_loc = Blast_ValNodeMaskListFree(filter_loc);
/* Format the results */
status =
BLAST_FormatResults(seqalign_arr, 1, slp1, filter_loc, format_info,
extra_returns);
status = Blast_PrintOutputFooter(format_info, extra_returns);
/* Free masking locations if they haven't been freed already. */
filter_loc = Blast_ValNodeMaskListFree(filter_loc);
format_info = BlastFormattingInfoFree(format_info);
extra_returns = Blast_SummaryReturnFree(extra_returns);
search_options = SBlastOptionsFree(search_options);
if (entrez_lookup) {
BioseqFree(query_bsp);
BioseqFree(subject_bsp);
} else {
SeqEntryFree(sep);
SeqEntryFree(sep1);
}
options = BLAST_SummaryOptionsFree(options);
seqalign_arr = SBlastSeqalignArrayFree(seqalign_arr);
slp1 = SeqLocSetFree(slp1);
slp2 = SeqLocSetFree(slp2);
fake_bsp = BlastDeleteFakeBioseq(fake_bsp);
GeneticCodeSingletonFini();
return 0;
}
/*******************************************************************************
Function : DDV_GetRulerForEditor()
Purpose : create the ruler for the editor. This new descriptor is created
using the descriptor of the viewer.
Return value : an allocated data block ready for use by the editor. Null if
failure
*******************************************************************************/
NLM_EXTERN ValNodePtr DDV_GetRulerForEditor(ValNodePtr descr_head,Int4 from_disp,
Int4 to_disp)
{
DDVRulerDescrPtr drdp,prev_drdp,new_drdp;
ValNodePtr vnp2,vnp3,vnpDesc;
Int4 cumulDecr,drdp_size,beginCopy,endCopy,drdp_start_ali;
Boolean bPop;
cumulDecr=0;
vnpDesc=NULL;
prev_drdp=NULL;
for(vnp2=descr_head;vnp2!=NULL;vnp2=vnp2->next){
drdp=(DDVRulerDescrPtr)vnp2->data.ptrvalue;
drdp_size=drdp->disp_stop-drdp->disp_start+1;
/*not yet in the region of interest ?*/
if (drdp->disp_stop<from_disp) {
cumulDecr+=drdp_size;
continue;
}
beginCopy=_max_(from_disp,drdp->disp_start);
endCopy=_min_(drdp->disp_stop,to_disp);
if (drdp->bUnAligned==FALSE)
drdp_start_ali=drdp->align_start+(beginCopy-drdp->disp_start);
else
drdp_start_ali=(Int4)-1;
/*in order to merge nodes of same type, i keep track of
the previous populated drdp node. Same style==yes, then
just extend to the right the previous node*/
if (prev_drdp){
if (prev_drdp->bUnAligned==drdp->bUnAligned){
prev_drdp->disp_stop=endCopy;
bPop=TRUE;
}
else{
bPop=FALSE;
}
}
else{
bPop=FALSE;
}
if (!bPop){
new_drdp=(DDVRulerDescrPtr)MemNew(sizeof(DDVRulerDescr));
if (!new_drdp) goto erreur;
new_drdp->disp_start=beginCopy;
new_drdp->disp_stop=endCopy;
new_drdp->align_start=drdp_start_ali;
new_drdp->bUnAligned=drdp->bUnAligned;
if (!vnpDesc){
vnp3=ValNodeAddPointer(&vnpDesc,0,(Pointer)new_drdp);
}
else{
vnp3=ValNodeAddPointer(&vnp3,0,(Pointer)new_drdp);
}
prev_drdp=new_drdp;
}
if (drdp->disp_stop>=to_disp) break;
cumulDecr+=drdp_size;
}
return(vnpDesc);
erreur:
if (vnpDesc)
ValNodeFreeData(vnpDesc);
return(NULL);
}
/*******************************************************************************
Function : DDV_ComputeRuler()
Purpose : compute the Ruler descriptor (usefull for discontinuous align)
Parameters :
Return value : a list of RUler descriptor
*******************************************************************************/
extern ValNodePtr DDV_ComputeRuler(SeqAlignPtr sap,DDV_Disp_OptPtr ddop)
{
DDVRulerDescrPtr drdp;
ValNodePtr vnp=NULL,vnp_head=NULL;
Int4 disp_start=0,length,TotAliLength=0,r=0;
Boolean bUnAligned;
/* make ruler for LEFT_TAIL */
if ((ddop->DispDiscStyle == MSA_TXT_STYLE_2) && (ddop->ShowLeftTail)) {
length = AlnMgrGetMaxTailLength(sap, LEFT_TAIL);
if (length) {
drdp=(DDVRulerDescrPtr)MemNew(sizeof(DDVRulerDescr));
drdp->disp_start=disp_start;
drdp->disp_stop=disp_start+length-1;
drdp->bUnAligned=TRUE;
drdp->align_start = -1;
disp_start += length;
vnp_head=ValNodeAddPointer(NULL,0,(Pointer)drdp);
vnp=vnp_head;
}
}
if (AlnMgrIsSAPDiscAli(sap)){
/* make ruler for multiple blocks */
while(AlnMgrGetNextLengthBit(sap,&length,&r)){
if (length<0){
bUnAligned=TRUE;
switch(ddop->DispDiscStyle){/*user's display choice*/
case MSA_TXT_STYLE_1:
length=ddop->SpacerSize;
break;
case MSA_TXT_STYLE_2:
length=ABS(length);
break;
}
}
else{
bUnAligned=FALSE;
}
drdp=(DDVRulerDescrPtr)MemNew(sizeof(DDVRulerDescr));
drdp->disp_start=disp_start;
drdp->disp_stop=disp_start+length-1;
drdp->bUnAligned=bUnAligned;
if (bUnAligned==FALSE)
drdp->align_start=TotAliLength;/*SeqAlign Coord*/
else
drdp->align_start=-1;/*drdp->disp_start;*//*Disp Coord*/
if (!vnp_head){
vnp_head=ValNodeAddPointer(NULL,0,(Pointer)drdp);
vnp=vnp_head;
}
else{
vnp=ValNodeAddPointer(&vnp,0,(Pointer)drdp);
}
disp_start+=length;
if (bUnAligned==FALSE)
TotAliLength+=length;
}
}
else if (sap->type == SAT_MASTERSLAVE){
/* make ruler for a single block */
drdp=(DDVRulerDescrPtr)MemNew(sizeof(DDVRulerDescr));
drdp->disp_start=disp_start;
length=AlnMgrGetAlnLength(sap,FALSE);
drdp->disp_stop=disp_start+length-1;
drdp->bUnAligned = FALSE;
drdp->align_start=0;
if (!vnp_head){
vnp_head=ValNodeAddPointer(NULL,0,(Pointer)drdp);
vnp=vnp_head;
}
else{
vnp=ValNodeAddPointer(&vnp,0,(Pointer)drdp);
}
}
/* make ruler for RIGHT_TAIL */
if ((ddop->DispDiscStyle == MSA_TXT_STYLE_2) && (ddop->ShowRightTail)) {
length = AlnMgrGetMaxTailLength(sap, RIGHT_TAIL);
if (length) {
drdp=(DDVRulerDescrPtr)MemNew(sizeof(DDVRulerDescr));
drdp->disp_start=disp_start;
drdp->disp_stop=disp_start+length-1;
drdp->bUnAligned=TRUE;
drdp->align_start = -1;
disp_start += length;
vnp = ValNodeAddPointer(&vnp,0,(Pointer)drdp);
}
}
return(vnp_head);
}
static Int2 Main_old (void)
{
AsnIoPtr aip, xml_aip = NULL;
BioseqPtr query_bsp, PNTR query_bsp_array;
BioSourcePtr source;
BLAST_MatrixPtr matrix;
BLAST_OptionsBlkPtr options;
BLAST_KarlinBlkPtr ka_params=NULL, ka_params_gap=NULL;
BlastPruneSapStructPtr prune;
Boolean db_is_na, query_is_na, show_gi, believe_query=FALSE;
Boolean html=FALSE;
CharPtr params_buffer=NULL;
Int4 number_of_descriptions, number_of_alignments;
SeqAlignPtr seqalign, PNTR seqalign_array;
SeqAnnotPtr seqannot;
SeqEntryPtr PNTR sepp;
TxDfDbInfoPtr dbinfo=NULL, dbinfo_head;
Uint1 align_type, align_view, out_type;
Uint4 align_options, print_options;
ValNodePtr mask_loc, mask_loc_start, next_mask_loc;
ValNodePtr vnp, other_returns, error_returns;
CharPtr blast_program, blast_database, blast_inputfile, blast_outputfile;
FILE *infp, *outfp, *mqfp=NULL;
Int4 index, num_bsps, total_length, total_processed = 0;
Int2 ctr = 1;
Char prefix[2];
SeqLocPtr last_mask, mask_slp;
Boolean done, hits_found;
Boolean lcase_masking;
MBXmlPtr mbxp = NULL;
Boolean traditional_formatting;
blast_program = "blastn";
blast_database = myargs [ARG_DB].strvalue;
blast_inputfile = myargs [ARG_QUERY].strvalue;
blast_outputfile = myargs [ARG_OUT].strvalue;
if (myargs[ARG_HTML].intvalue)
html = TRUE;
if ((infp = FileOpen(blast_inputfile, "r")) == NULL) {
ErrPostEx(SEV_FATAL, 1, 0, "mgblast: Unable to open input file %s\n", blast_inputfile);
return (1);
}
align_view = (Int1) myargs[ARG_FORMAT].intvalue;
/* Geo mod:
-- replaced myargs[ARG_OUTTYPE].intvalue with out_type from now on
*/
out_type=(Int1) myargs[ARG_OUTTYPE].intvalue;
if (out_type==MGBLAST_FLTHITS || out_type==MGBLAST_HITGAPS) {
align_view = 12 + (out_type-MGBLAST_FLTHITS );
out_type=MBLAST_ALIGNMENTS;
//Attention: 12 MUST be the -m mgblast tab option for MGBLAST_FLTHITS format
// and MGBLAST_HITGAPS = MGBLAST_FLTHITS+1
if (align_view>12) { // this is MGBLAST_HITGAPS output
gap_Info=TRUE;
if (dbgaps_buf==NULL)
dbgaps_buf=(CharPtr) Malloc(dbgaps_bufsize + 1);
if (qgaps_buf==NULL)
qgaps_buf=(CharPtr) Malloc(qgaps_bufsize + 1);
}
}
outfp = NULL;
traditional_formatting =
(out_type == MBLAST_ALIGNMENTS ||
out_type == MBLAST_DELAYED_TRACEBACK);
if ((!traditional_formatting ||
(align_view != 7 && align_view != 10 && align_view != 11)) &&
blast_outputfile != NULL) {
if ((outfp = FileOpen(blast_outputfile, "w")) == NULL) {
ErrPostEx(SEV_FATAL, 1, 0, "blast: Unable to open output file %s\n", blast_outputfile);
return (1);
}
}
//align_type = BlastGetTypes(blast_program, &query_is_na, &db_is_na);
align_type = BlastGetTypes(blast_program, &query_is_na, &db_is_na);
/*
if (!traditional_formatting)
believe_query = TRUE;
else
believe_query = (Boolean) myargs[ARG_BELIEVEQUERY].intvalue;
*/
//Geo mod:
believe_query=FALSE;
//If ASN.1 output is requested and believe_query is not set to TRUE,
// exit with an error.
if (!believe_query && (myargs[ARG_ASNOUT].strvalue ||
align_view == 10 || align_view == 11)) {
ErrPostEx(SEV_FATAL, 1, 0,
"-J option must be TRUE to produce ASN.1 output; before "
"changing -J to TRUE please also ensure that all query "
"sequence identifiers are unique");
return -1;
}
options = BLASTOptionNewEx(blast_program, TRUE, TRUE);
if (options == NULL)
return 3;
options->do_sum_stats = FALSE;
options->is_neighboring = FALSE;
options->expect_value = (Nlm_FloatHi) myargs [ARG_EVALUE].floatvalue;
number_of_descriptions = myargs[ARG_DESCRIPTIONS].intvalue;
number_of_alignments = myargs[ARG_ALIGNMENTS].intvalue;
options->hitlist_size = MAX(number_of_descriptions, number_of_alignments);
if (myargs[ARG_XDROP].intvalue != 0)
options->gap_x_dropoff = myargs[ARG_XDROP].intvalue;
if (myargs[ARG_XDROP_UNGAPPED].intvalue != 0)
options->dropoff_2nd_pass = myargs[ARG_XDROP_UNGAPPED].intvalue;
if (myargs[ARG_XDROP_FINAL].intvalue != 0)
options->gap_x_dropoff_final = myargs[ARG_XDROP_FINAL].intvalue;
if (StringICmp(myargs[ARG_FILTER].strvalue, "T") == 0)
options->filter_string = StringSave("D");
else
options->filter_string = StringSave(myargs[ARG_FILTER].strvalue);
show_gi = (Boolean) myargs[ARG_SHOWGIS].intvalue;
options->penalty = myargs[ARG_MISMATCH].intvalue;
options->reward = myargs[ARG_MATCH].intvalue;
if (myargs[ARG_GAPOPEN].intvalue >= 0)
options->gap_open = myargs[ARG_GAPOPEN].intvalue;
if (myargs[ARG_GAPEXT].intvalue >= 0)
options->gap_extend = myargs[ARG_GAPEXT].intvalue;
if (options->gap_open == 0 && options->reward % 2 == 0 &&
options->gap_extend == options->reward / 2 - options->penalty)
/* This is the default value */
options->gap_extend = 0;
options->genetic_code = 1;
options->db_genetic_code = 1; /* Default; it's not needed here anyway */
options->number_of_cpus = myargs[ARG_THREADS].intvalue;
if (myargs[ARG_WORDSIZE].intvalue != 0)
options->wordsize = myargs[ARG_WORDSIZE].intvalue;
if (myargs[ARG_MINSCORE].intvalue == 0)
options->cutoff_s2 = options->wordsize*options->reward;
else
options->cutoff_s2 = myargs[ARG_MINSCORE].intvalue;
options->db_length = (Int8) myargs[ARG_DBSIZE].floatvalue;
options->searchsp_eff = (Nlm_FloatHi) myargs[ARG_SEARCHSP].floatvalue;
options->perform_culling = FALSE;
/* Kludge */
options->block_width = myargs[ARG_MAXPOS].intvalue;
options->strand_option = myargs[ARG_STRAND].intvalue;
options->window_size = myargs[ARG_WINDOW].intvalue;
#ifdef DO_NOT_SUPPRESS_BLAST_OP
options->mb_template_length = myargs[ARG_TEMPL_LEN].intvalue;
if (myargs[ARG_TEMPL_LEN].intvalue != 0)
options->mb_one_base_step = (Boolean) myargs[ARG_EVERYBASE].intvalue;
options->mb_disc_type = myargs[ARG_TEMPL_TYPE].intvalue;
#endif
lcase_masking = (Boolean) myargs[ARG_LCASE].intvalue;
/* Allow dynamic programming gapped extension only with affine
gap scores */
if (options->gap_open != 0 || options->gap_extend != 0)
options->mb_use_dyn_prog = (Boolean) myargs[ARG_DYNAMIC].intvalue;
print_options = 0;
align_options = 0;
align_options += TXALIGN_COMPRESS;
align_options += TXALIGN_END_NUM;
if (show_gi) {
align_options += TXALIGN_SHOW_GI;
print_options += TXALIGN_SHOW_GI;
}
if (align_view) {
align_options += TXALIGN_MASTER;
if (align_view == 1 || align_view == 3)
align_options += TXALIGN_MISMATCH;
if (align_view == 3 || align_view == 4 || align_view == 6)
align_options += TXALIGN_FLAT_INS;
if (align_view == 5 || align_view == 6)
align_options += TXALIGN_BLUNT_END;
} else {
align_options += TXALIGN_MATRIX_VAL;
align_options += TXALIGN_SHOW_QS;
}
if (html) {
align_options += TXALIGN_HTML;
print_options += TXALIGN_HTML;
}
if (myargs[ARG_GILIST].strvalue)
options->gifile = StringSave(myargs[ARG_GILIST].strvalue);
if (out_type == MBLAST_ENDPOINTS)
options->no_traceback = 1;
else if (out_type == MBLAST_DELAYED_TRACEBACK)
options->no_traceback = 2;
else
options->no_traceback = 0;
options->megablast_full_deflines = (Boolean) myargs[ARG_FULLID].intvalue;
options->perc_identity = (FloatLo) myargs[ARG_PERC_IDENT].floatvalue;
options->hsp_num_max = myargs[ARG_MAXHSP].intvalue;
if (!believe_query)
options->megablast_full_deflines = TRUE;
/*if (options->megablast_full_deflines)
believe_query = FALSE;*/
query_bsp_array = (BioseqPtr PNTR) MemNew((MAX_NUM_QUERIES+1)*sizeof(BioseqPtr));
sepp = (SeqEntryPtr PNTR) MemNew(MAX_NUM_QUERIES*sizeof(SeqEntryPtr));
StrCpy(prefix, "");
global_fp = outfp;
options->output = outfp;
if (traditional_formatting) {
if (align_view < 7) {
if (html) {
fprintf(outfp, "<HTML>\n<TITLE>MEGABLAST Search Results</TITLE>\n");
fprintf(outfp, "<BODY BGCOLOR=\"#FFFFFF\" LINK=\"#0000FF\" "
"VLINK=\"#660099\" ALINK=\"#660099\">\n");
fprintf(outfp, "<PRE>\n");
}
init_buff_ex(90);
BlastPrintVersionInfo("mgblast", html, outfp);
fprintf(outfp, "\n");
MegaBlastPrintReference(html, 90, outfp);
fprintf(outfp, "\n");
if(!PrintDbInformation(blast_database, !db_is_na, 70, outfp, html))
return 1;
free_buff();
#ifdef OS_UNIX
fprintf(global_fp, "%s", "Searching");
#endif
}
}
aip = NULL;
if (myargs[ARG_ASNOUT].strvalue != NULL) {
if ((aip = AsnIoOpen (myargs[ARG_ASNOUT].strvalue,"w")) == NULL) {
ErrPostEx(SEV_FATAL, 1, 0, "blast: Unable to open output file %s\n", myargs[ARG_ASNOUT].strvalue);
return 1;
}
}
else if (align_view == 10 || align_view == 11)
{
const char* mode = (align_view == 10) ? "w" : "wb";
if ((aip = AsnIoOpen (blast_outputfile, (char*) mode)) == NULL) {
ErrPostEx(SEV_FATAL, 1, 0, "blast: Unable to open output file %s\n", blast_outputfile);
return 1;
}
}
if (align_view == 7) {
xml_aip = AsnIoOpen(blast_outputfile, "wx");
}
if (myargs[ARG_QUERYLOC].strvalue) {
Int4 start, end;
Megablast_GetLoc(myargs[ARG_QUERYLOC].strvalue, &start, &end);
options->required_start = start - 1;
options->required_end = end -1;
}
done = FALSE;
while (!done) {
num_bsps = 0;
total_length = 0;
done = TRUE;
SeqMgrHoldIndexing(TRUE);
mask_slp = last_mask = NULL;
while ((sepp[num_bsps]=FastaToSeqEntryForDb(infp, query_is_na, NULL,
believe_query, prefix, &ctr,
&mask_slp)) != NULL) {
if (!lcase_masking) /* Lower case ignored */
mask_slp = SeqLocFree(mask_slp);
if (mask_slp) {
if (!last_mask)
options->query_lcase_mask = last_mask = mask_slp;
else {
last_mask->next = mask_slp;
last_mask = last_mask->next;
}
mask_slp = NULL;
}
query_bsp = NULL;
SeqEntryExplore(sepp[num_bsps], &query_bsp, FindNuc);
//debug:
/*
char query_buffer[255];
SeqIdWrite(query_bsp->id, query_buffer, PRINTID_FASTA_LONG, BUFFER_LENGTH);
fprintf(stderr, "===> query_buf=%s\n", query_buffer);
*/
if (query_bsp == NULL) {
ErrPostEx(SEV_FATAL, 1, 0, "Unable to obtain bioseq\n");
return 2;
}
source = BioSourceNew();
source->org = OrgRefNew();
source->org->orgname = OrgNameNew();
source->org->orgname->gcode = options->genetic_code;
ValNodeAddPointer(&(query_bsp->descr), Seq_descr_source, source);
query_bsp_array[num_bsps++] = query_bsp;
total_length += query_bsp->length;
if (total_length > myargs[ARG_MAXQUERY].intvalue ||
num_bsps >= MAX_NUM_QUERIES) {
done = FALSE;
break;
}
}
if (num_bsps == 0)
break;
SeqMgrHoldIndexing(FALSE);
other_returns = NULL;
error_returns = NULL;
if (out_type==MBLAST_ENDPOINTS)
seqalign_array = BioseqMegaBlastEngine(query_bsp_array, blast_program,
blast_database, options,
&other_returns, &error_returns,
dummy_callback, NULL, NULL, 0,
MegaBlastPrintEndpoints);
else if (out_type==MBLAST_SEGMENTS)
seqalign_array = BioseqMegaBlastEngine(query_bsp_array, blast_program,
blast_database, options,
&other_returns, &error_returns,
dummy_callback, NULL, NULL, 0,
MegaBlastPrintSegments);
else if (out_type==MBLAST_ALIGN_INFO) {
/* -- Geo mod: do not print header
PrintTabularOutputHeader(blast_database,
(num_bsps==1) ? query_bsp_array[0] : NULL,
NULL, "megablast", 0, believe_query,
global_fp);*/
seqalign_array = BioseqMegaBlastEngine(query_bsp_array, blast_program,
blast_database, options,
&other_returns, &error_returns,
dummy_callback, NULL, NULL, 0,
MegaBlastPrintAlignInfo);
} else if (out_type==MBLAST_ALIGNMENTS) {
seqalign_array = BioseqMegaBlastEngine(query_bsp_array, blast_program,
blast_database, options, &other_returns,
&error_returns, align_view < 7 ? tick_callback : NULL,
NULL, NULL, 0, NULL);
}
#ifdef OS_UNIX
fflush(global_fp);
#endif
if (error_returns) {
BlastErrorPrint(error_returns);
for (vnp = error_returns; vnp; vnp = vnp->next) {
BlastDestroyErrorMessage((BlastErrorMsgPtr)vnp->data.ptrvalue);
}
ValNodeFree(error_returns);
}
if (traditional_formatting) {
dbinfo = NULL;
ka_params = NULL;
ka_params_gap = NULL;
params_buffer = NULL;
mask_loc = NULL;
matrix = NULL;
for (vnp=other_returns; vnp; vnp = vnp->next) {
switch (vnp->choice) {
case TXDBINFO:
dbinfo = vnp->data.ptrvalue;
break;
case TXKABLK_NOGAP:
ka_params = vnp->data.ptrvalue;
break;
case TXKABLK_GAP:
ka_params_gap = vnp->data.ptrvalue;
break;
case TXPARAMETERS:
params_buffer = vnp->data.ptrvalue;
break;
case TXMATRIX:
matrix = vnp->data.ptrvalue;
break;
case SEQLOC_MASKING_NOTSET:
case SEQLOC_MASKING_PLUS1:
case SEQLOC_MASKING_PLUS2:
case SEQLOC_MASKING_PLUS3:
case SEQLOC_MASKING_MINUS1:
case SEQLOC_MASKING_MINUS2:
case SEQLOC_MASKING_MINUS3:
ValNodeAddPointer(&mask_loc, vnp->choice, vnp->data.ptrvalue);
break;
default:
break;
}
}
#ifdef OS_UNIX
if(align_view < 7) {
fprintf(global_fp, "%s\n", " done");
}
#endif
if (myargs[ARG_MASKEDQUERY].strvalue) {
if ((mqfp = FileOpen(myargs[ARG_MASKEDQUERY].strvalue, "w")) == NULL)
ErrPostEx(SEV_WARNING, 1, 0, "Unable to open file %s for masked query\n",
myargs[ARG_MASKEDQUERY].strvalue);
}
hits_found = FALSE;
mask_loc_start = next_mask_loc = mask_loc;
mask_loc = NULL;
if (align_view == 7) {
mbxp = PSIXmlInit(xml_aip, "megablast", blast_database,
options, query_bsp_array[0], 0);
}
if (seqalign_array) { //results returned back for processing
ReadDBBioseqFetchEnable ("megablast", blast_database, db_is_na, TRUE);
for (index=0; index<num_bsps; index++) {
seqalign = seqalign_array[index];
if (next_mask_loc &&
SeqIdComp(SeqLocId((SeqLocPtr)next_mask_loc->data.ptrvalue),
query_bsp_array[index]->id) == SIC_YES) {
mask_loc = (SeqLocPtr)
MemDup(next_mask_loc, sizeof(SeqLoc));
next_mask_loc = next_mask_loc->next;
mask_loc->next = NULL;
}
if (mqfp) {
/* convert mask locations from all sources into
a single seqloc */
mask_slp = NULL;
if (mask_loc)
mask_slp = blastMergeFilterLocs(mask_slp,
(SeqLocPtr)mask_loc->data.ptrvalue,
FALSE, 0, 0);
PrintMaskedSequence(query_bsp_array[index], mask_slp,
mqfp, 50, lcase_masking);
SeqLocSetFree(mask_slp);
}
if (seqalign==NULL) {
mask_loc = MemFree(mask_loc);
continue;
}
hits_found = TRUE;
if (align_view < 7) {
init_buff_ex(70);
AcknowledgeBlastQuery(query_bsp_array[index], 70, outfp,
believe_query, html);
free_buff();
}
if (align_view == 8 || align_view == 9) {
if (align_view == 9)
PrintTabularOutputHeader(blast_database,
query_bsp_array[index], NULL, blast_program, 0,
believe_query, global_fp);
/* debug:
char qbuf[512];
strcpy(qbuf, BioseqGetTitle(query_bsp_array[index]));
fprintf(stderr, "---> Here: query title=%s\n", qbuf);
*/
BlastPrintTabulatedResults(seqalign,
query_bsp_array[index], NULL, number_of_alignments,
blast_program, !options->gapped_calculation,
believe_query, 0, 0,
global_fp, (align_view == 9));
ObjMgrFreeCache(0);
SeqAlignSetFree(seqalign);
mask_loc = MemFree(mask_loc);
continue;
}
//Geo mod:
else if (align_view>=12) {
MGBlastPrintTab(seqalign,
query_bsp_array[index], number_of_alignments,
!options->gapped_calculation,
global_fp);
ObjMgrFreeCache(0);
SeqAlignSetFree(seqalign);
mask_loc = MemFree(mask_loc);
continue;
}
else if(align_view == 7) {
IterationPtr iterp;
iterp = BXMLBuildOneQueryIteration(seqalign,
NULL, FALSE,
!options->gapped_calculation, index,
NULL, query_bsp_array[index], mask_loc);
IterationAsnWrite(iterp, mbxp->aip, mbxp->atp);
AsnIoFlush(mbxp->aip);
IterationFree(iterp);
SeqAlignSetFree(seqalign);
mask_loc = MemFree(mask_loc);
continue;
}
seqannot = SeqAnnotNew();
seqannot->type = 2;
AddAlignInfoToSeqAnnot(seqannot, align_type);
seqannot->data = seqalign;
if (aip) {
SeqAnnotAsnWrite((SeqAnnotPtr) seqannot, aip, NULL);
AsnIoReset(aip);
}
if (outfp) { /* Uncacheing causes problems with ordinal nos. vs. gi's. */
prune = BlastPruneHitsFromSeqAlign(seqalign, number_of_descriptions, NULL);
ObjMgrSetHold();
init_buff_ex(85);
PrintDefLinesFromSeqAlign(prune->sap, 80,
outfp, print_options, FIRST_PASS, NULL);
free_buff();
prune = BlastPruneHitsFromSeqAlign(seqalign, number_of_alignments, prune);
seqannot->data = prune->sap;
if (align_view != 0)
ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL,
NULL, align_options, NULL,
mask_loc, NULL);
else
ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL, NULL, align_options, NULL, mask_loc, FormatScoreFunc);
seqannot->data = seqalign;
prune = BlastPruneSapStructDestruct(prune);
ObjMgrClearHold();
ObjMgrFreeCache(0);
}
seqannot = SeqAnnotFree(seqannot);
mask_loc = MemFree(mask_loc);
} /* End loop on seqaligns for different queries */
ReadDBBioseqFetchDisable();
}
if (mbxp != NULL) {
MBXmlClose(mbxp, other_returns, !options->gapped_calculation);
}
if (mqfp)
FileClose(mqfp);
if (!hits_found && align_view < 7)
fprintf(outfp, "\n\n ***** No hits found ******\n\n");
matrix = BLAST_MatrixDestruct(matrix);
if(html)
fprintf(outfp, "<PRE>\n");
init_buff_ex(85);
dbinfo_head = dbinfo;
if(align_view < 7) {
while (dbinfo) {
PrintDbReport(dbinfo, 70, outfp);
dbinfo = dbinfo->next;
}
}
dbinfo_head = TxDfDbInfoDestruct(dbinfo_head);
if (ka_params) {
if(align_view < 7)
PrintKAParameters(ka_params->Lambda, ka_params->K, ka_params->H, 70, outfp, FALSE);
MemFree(ka_params);
}
if (ka_params_gap) {
if(align_view < 7)
PrintKAParameters(ka_params_gap->Lambda, ka_params_gap->K, ka_params_gap->H, 70, outfp, TRUE);
MemFree(ka_params_gap);
}
if(align_view < 7)
PrintTildeSepLines(params_buffer, 70, outfp);
MemFree(params_buffer);
free_buff();
mask_loc = mask_loc_start;
while (mask_loc) {
SeqLocSetFree(mask_loc->data.ptrvalue);
mask_loc = mask_loc->next;
}
ValNodeFree(mask_loc_start);
} else { //not traditional formatting
/* Just destruct all other_returns parts */
for (vnp=other_returns; vnp; vnp = vnp->next) {
switch (vnp->choice) {
case TXDBINFO:
TxDfDbInfoDestruct(vnp->data.ptrvalue);
break;
case TXKABLK_NOGAP:
case TXKABLK_GAP:
case TXPARAMETERS:
MemFree(vnp->data.ptrvalue);
break;
case TXMATRIX:
BLAST_MatrixDestruct(vnp->data.ptrvalue);
break;
case SEQLOC_MASKING_NOTSET:
case SEQLOC_MASKING_PLUS1:
case SEQLOC_MASKING_PLUS2:
case SEQLOC_MASKING_PLUS3:
case SEQLOC_MASKING_MINUS1:
case SEQLOC_MASKING_MINUS2:
case SEQLOC_MASKING_MINUS3:
mask_loc = vnp->data.ptrvalue;
SeqLocSetFree(mask_loc);
default:
break;
}
}
}
other_returns = ValNodeFree(other_returns);
MemFree(seqalign_array);
options->query_lcase_mask =
SeqLocSetFree(options->query_lcase_mask);
/* Freeing SeqEntries can be very expensive, do this only if
this is not the last iteration of search */
if (!done) {
for (index=0; index<num_bsps; index++) {
sepp[index] = SeqEntryFree(sepp[index]);
query_bsp_array[index] = NULL;
}
}
total_processed += num_bsps;
} /* End of loop on complete searches */
aip = AsnIoClose(aip);
/*if (align_view == 7)
xml_aip = AsnIoClose(xml_aip);*/
if (align_view < 7 && html)
fprintf(outfp, "</PRE>\n</BODY>\n</HTML>\n");
if (align_view < 7 && myargs[ARG_LOGINFO].intvalue)
fprintf(outfp, "Mega BLAST run finished, processed %d queries\n",
total_processed);
MemFree(query_bsp_array);
MemFree(sepp);
MemFree(qgaps_buf);
MemFree(dbgaps_buf);
options = BLASTOptionDelete(options);
FileClose(infp);
FileClose(outfp);
return 0;
}
/******************************************************************
*
* aa_to_codon(sfp, aa_start, aa_stop)
* generate a list of CodonVecotr to show the codons of an
* amino acid sequence
* sfp: the Seq-feat for cds
* aa_start: the start position of protein sequence
* aa_stop the stop position of protein sequence
*
******************************************************************/
NLM_EXTERN ValNodePtr aa_to_codon(SeqFeatPtr sfp, Int4 aa_start, Int4 aa_stop)
{
BioseqPtr bsp;
Int4 frame_offset, start_offset;
SeqLocPtr slp = NULL;
SeqLocPtr cdloc;
CdRegionPtr crp;
Uint1 frame;
Boolean is_end; /**is the end for process reached?**/
Int4 p_start=0, p_stop=0; /**protein start & stop in defined
corresponding CdRegion Seq-loc**/
Int4 line_len;
Int4 cur_pos; /**current protein position in process**/
Int4 cd_len; /**length of the cDNA for the coding region**/
Int2 i, j;
Int2 k, n;
CharPtr PNTR buf;
Boolean is_new; /**Is cur_pos at the begin of new Seq-loc?**/
CharPtr temp;
SeqPortPtr spp;
Uint1 residue;
Boolean end_partial;
Int4 d_start, seq_pos;
Int2 pos;
ValNodePtr head= NULL;
CodonVectorPtr cvp;
Boolean prt_stop_codon;
Uint2 exon;
if(sfp->data.choice !=3)
return NULL;
crp = sfp->data.value.ptrvalue;
if(!crp)
return NULL;
frame = crp->frame;
cdloc = sfp->location;
if(cdloc == NULL )
return NULL;
if(frame>0)
frame_offset = frame-1;
else
frame_offset = 0;
start_offset = frame_offset;
prt_stop_codon = (aa_stop == SeqLocStop(sfp->product));
line_len = (aa_stop - aa_start + 1) + 1;
/* +1 for the possible partial start codon*/
if(prt_stop_codon)/*can be either as a stop codon or partial stop*/
++line_len;
buf = MemNew((size_t)3 * sizeof(CharPtr));
for(i =0; i<3; ++i)
buf[i] = MemNew((size_t)(line_len + 1) * sizeof (Char));
cur_pos= aa_start;
cd_len = 0;
is_end = FALSE;
p_start = 0;
slp = NULL;
exon = 0;
while(!is_end && ((slp = SeqLocFindNext(cdloc, slp))!=NULL))
{
++exon;
cd_len += SeqLocLen(slp);
end_partial = ((cd_len - start_offset)%3 != 0);
p_stop = (cd_len - start_offset)/3 -1;
if(end_partial)
++p_stop;
if(p_stop > aa_stop || (p_stop == aa_stop && !end_partial))
{
p_stop = aa_stop; /**check if the end is reached**/
is_end = TRUE;
}
if(p_stop >= cur_pos) /*get the exon*/
{
bsp = BioseqLockById(SeqLocId(slp));
if(bsp)
{
is_new = (p_start == cur_pos); /*start a new exon?*/
cvp = MemNew(sizeof(CodonVector));
cvp->sip = SeqIdDup(find_sip(bsp->id));
cvp->strand = SeqLocStrand(slp);
cvp->exonCount = exon;
if(is_new)
{
if(frame_offset == 0)
cvp->frame = 0;
else
cvp->frame = 3- (Uint1)frame_offset;
}
else
cvp->frame = 0;
if(cur_pos==0 && frame_offset > 0) /*partial start codon*/
cvp->aa_index = 0;
else
cvp->aa_index = 1;
if(is_new) /**special case of the first partial**/
d_start = SeqLocStart(slp);
else
{
if(frame_offset && p_start >0)
++p_start;
d_start = SeqLocStart(slp) + 3*(cur_pos - p_start) + frame_offset;
}
/**p_start is the start position of aa in the current Seq-loc
cur_pos is the current aa that is in process. The offset will
help to located the position on the DNA Seq-loc for translation
d_start is the position of the starting DNA in the coordinates
of DNA segment, used for mark the sequence
**/
seq_pos = d_start - SeqLocStart(slp); /**the pos in spp**/
if(SeqLocStrand(slp)== Seq_strand_minus)
d_start = SeqLocStop(slp) - seq_pos;
cvp->dna_pos = d_start;
n = (Int2)cur_pos - (Int2)aa_start + cvp->aa_index; /*position in buffer*/
for(i =0; i<3; ++i)
make_empty(buf[i], (Int2)line_len);
spp = SeqPortNewByLoc(slp, Seq_code_iupacna);
SeqPortSeek(spp, seq_pos, SEEK_SET);
/**store the partial codons**/
if(is_new && frame_offset > 0)
{
k = (Int2)frame_offset;
while(k > 0)
{
residue = SeqPortGetResidue(spp);
temp = buf[3-k]; /**the position**/
pos = n;
temp[pos] = TO_LOWER(residue);
--k;
}
++n;
if(cur_pos!=0)
++cur_pos;
}
/**load the codons**/
k =0;
while((residue = SeqPortGetResidue(spp)) != SEQPORT_EOF && cur_pos <= p_stop)
{
j= (Uint1)k%3;
temp = buf[j];
temp[n] = TO_LOWER(residue);
if(j ==2)
{ /**the last base**/
++n;
if(!prt_stop_codon|| !is_end) /*for the last codon*/
/**prt_end controls to print the whole loc**/
++cur_pos;
}
++k;
} /**end of while**/
SeqPortFree(spp);
for(i =0; i<3; ++i)
cvp->buf[i] = StringSave(buf[i]);
ValNodeAddPointer(&head, 0, (Pointer)cvp);
BioseqUnlock(bsp);
}/*end of if(bsp)*/
}/**end of if for matched intervals**/
if(end_partial)
p_start = p_stop;
else
p_start = p_stop +1;
frame_offset = (cd_len - start_offset)%3;
if(frame_offset >0)
frame_offset = 3-frame_offset;
}/**end of while(slp && !is_end) **/
for(i=0; i<3; ++i)
MemFree(buf[i]);
MemFree(buf);
return head;
}
static SeqLocPtr slpDust (SeqPortPtr spp, SeqLocPtr slp, SeqIdPtr id,
ValNodePtr PNTR vnp, DREGION PNTR reg,
Int4 nreg, Int4 loopDustMax)
{
SeqIntPtr sintp;
Int4 i;
Boolean flagNoPack;
/* point to dusted locations */
if (nreg)
{
/* loopDustMax == 1 forces PACKED_INT IN - PACKED_INT OUT as needed */
flagNoPack = FALSE;
if (nreg == 1 && loopDustMax == 1) flagNoPack = TRUE;
if (!slp)
{
if ((slp = ValNodeNew (NULL)) == NULL)
{
ErrPostEx (SEV_ERROR, 6, 1,
"val node new failed");
ErrShow ();
return slp;
}
}
if (flagNoPack)
{
slp->choice = SEQLOC_INT;
}
else
{
slp->choice = SEQLOC_PACKED_INT;
}
for (i = 0; i < nreg; i++)
{
sintp = SeqIntNew ();
if (!sintp)
{
ErrPostEx (SEV_FATAL, 6, 2,
"memory allocation error");
ErrShow ();
return slp;
}
sintp->id = SeqIdDup (id);
sintp->from = reg->from;
sintp->to = reg->to;
if (!flagNoPack) ValNodeAddPointer
(vnp, SEQLOC_INT, sintp);
reg = reg->next;
}
if (flagNoPack)
{
slp->data.ptrvalue = (Pointer) sintp;
}
else
{
slp->data.ptrvalue = *vnp;
}
}
return slp;
}