extern SeqLocPtr SeqLocDup (SeqLocPtr slpold)
{
SeqLocPtr slpnew, slpn, slp;
SeqIdPtr id;
if (slpold == NULL)
return NULL;
slpnew = (SeqLocPtr) AsnIoMemCopy ((Pointer) slpold,
(AsnReadFunc) SeqLocAsnRead,
(AsnWriteFunc) SeqLocAsnWrite);
slp = slpnew->next;
while (slp != NULL)
{
slpn = slp->next;
id = SeqLocId (slp);
if (id != NULL)
id->next = SeqIdSetFree (id->next);
SeqLocFree (slp);
slp = slpn;
}
slpnew->next = NULL;
return slpnew;
}
extern SeqLocPtr SeqLocDupAll (SeqLocPtr slpold)
{
SeqLocPtr slpnew;
if (slpold == NULL)
return NULL;
slpnew = (SeqLocPtr) AsnIoMemCopy ((Pointer) slpold,
(AsnReadFunc) SeqLocAsnRead,
(AsnWriteFunc) SeqLocAsnWrite);
return slpnew;
}
/*---------------- To put Local_id in segs for Vastsearch - Ken -----------*/
void AssignLocaIdToSeqAlignMaster(SeqIdPtr sip, SeqAlignPtr salpHead)
{
DenseDiagPtr ddp;
SeqIdPtr sipTemp = NULL;
ddp = salpHead->segs;
while(ddp)
{
if(ddp->id!=NULL) {
sipTemp = ddp->id->next;
SeqIdFree(ddp->id);
ddp->id = AsnIoMemCopy(sip, (AsnReadFunc) SeqIdAsnRead, (AsnWriteFunc) SeqIdAsnWrite);
ddp->id->next = sipTemp;
} else
ErrPostEx(SEV_ERROR,0,0,"AssignLocalIdToSeqAlignMaster: No SeqId on SeqALign\n");
ddp = ddp->next;
}
}
SeqIdPtr CpySeqIdList(SeqIdPtr sip) {
SeqIdPtr sipNew = NULL, sipNewHead = NULL, sipLast = NULL;
if(!sip) {
return sipNewHead;
}
while(sip) {
sipNew = (SeqIdPtr)AsnIoMemCopy(sip, (AsnReadFunc)SeqIdAsnRead, (AsnWriteFunc)SeqIdAsnWrite);
if(sipNewHead == NULL) {
sipNewHead = sipNew;
sipLast = sipNew;
}
else {
sipLast->next = sipNew;
sipLast = sipNew;
}
sip = sip->next;
}
return sipNewHead;
}
BiomolDescrPtr CpyBiomolDescrList(BiomolDescrPtr bdp) {
BiomolDescrPtr bdpNew = NULL, bdpNewHead = NULL, bdpLast = NULL;
if(bdp == NULL) {
return bdpNewHead;
}
while(bdp != NULL) {
bdpNew = (BiomolDescrPtr)AsnIoMemCopy(bdp, (AsnReadFunc)BiomolDescrAsnRead, (AsnWriteFunc)BiomolDescrAsnWrite);
if(bdpNewHead == NULL) {
bdpNewHead = bdpNew;
bdpLast = bdpNew;
}
else {
bdpLast->next = bdpNew;
bdpLast = bdpNew;
}
bdp = bdp->next;
}
return bdpNewHead;
}
static BioseqPtr
BioseqFromAccession(CharPtr accver, Boolean is_na)
{
CharPtr accession, version_str;
Int4 version=0, gi, number;
SeqIdPtr sip = NULL;
TextSeqIdPtr tsip;
PDBSeqIdPtr psip;
BioseqPtr bsp = NULL, bsp_tmp = NULL;
SeqPortPtr spp;
Int2 retval, buf_length=512;
Uint1 buf[512];
char* defline = NULL;
char* dummy_ptr = NULL;
if (!ID1BioseqFetchEnable ("bl2seq", TRUE))
ErrPostEx(SEV_FATAL, 1, 0,
"Entrez access interface currently unavailable\n");
if (!IS_DIGIT(*accver)) {
accession = StringTokMT(accver, ".", &version_str);
if (version_str)
version = atoi(version_str);
if((sip = ValNodeNew (NULL)) == NULL)
return NULL;
if((tsip = TextSeqIdNew ()) == NULL)
return NULL;
tsip->accession = StringSave(accession);
tsip->version = version;
/* GenBank, EMBL, and DDBJ. */
sip->choice = SEQID_GENBANK;
sip->data.ptrvalue = (Pointer) tsip;
gi = ID1FindSeqId (sip);
if (gi == 0) {
/* SwissProt. */
sip->choice = SEQID_SWISSPROT;
gi = ID1FindSeqId (sip);
}
if (gi == 0) {
/* PIR */
sip->choice = SEQID_PIR;
gi = ID1FindSeqId (sip);
}
if (gi == 0) {
/* PRF */
sip->choice = SEQID_PRF;
gi = ID1FindSeqId (sip);
}
if (gi == 0) {
/* OTHER, probably 'ref' */
sip->choice = SEQID_OTHER;
gi = ID1FindSeqId (sip);
}
if(gi == 0) {
/* OK. We failed to find gi using string as TextSeqId. Now trying
last time - with PDBSeqIdPtr */
if((psip = PDBSeqIdNew()) == NULL)
return NULL;
sip->choice = SEQID_PDB;
tsip = TextSeqIdFree(tsip);
sip->data.ptrvalue = psip;
psip->mol = accession;
psip->chain = version;
gi = ID1FindSeqId (sip);
}
if (gi == 0) {
ErrPostEx(SEV_WARNING, 0, 0, "Sequence %s not found\n", accver);
return NULL;
}
sip = SeqIdFree(sip);
} else
gi = atoi(accver);
ID1BioseqFetchDisable();
if (gi > 0) {
/* First attempt to retrieve Bioseq from BLAST databases. */
char* db_name = (is_na ? "nucl_dbs" : "prot_dbs");
ValNodeAddInt(&sip, SEQID_GI, gi);
ReadDBBioseqFetchEnable ("bl2seq", db_name, is_na, TRUE);
bsp_tmp = BioseqLockById(sip);
ReadDBBioseqFetchDisable();
if (!bsp_tmp) {
/* Try ID1 again as a last resort. */
ID1BioseqFetchEnable("bl2seq", TRUE);
bsp_tmp = BioseqLockById(sip);
ID1BioseqFetchDisable();
}
sip = SeqIdFree(sip);
}
if (!bsp_tmp) {
ErrPostEx(SEV_WARNING, 0, 0, "Gi %ld not found", gi);
return NULL;
}
if (ISA_na(bsp_tmp->mol) != is_na) {
BioseqUnlock(bsp_tmp);
if (is_na)
ErrPostEx(SEV_FATAL, 1, 0,
"%s is a protein sequence, program requires nucleotide",
accver);
else
ErrPostEx(SEV_FATAL, 1, 0,
"%s is a nucleotide sequence, program requires protein",
accver);
return NULL;
}
bsp = AsnIoMemCopy(bsp_tmp, (AsnReadFunc) BioseqAsnRead, (AsnWriteFunc) BioseqAsnWrite);
SeqMgrDeleteFromBioseqIndex(bsp_tmp);
BioseqUnlock(bsp_tmp);
BioseqPack(bsp);
return bsp;
}
