/* sqnutil3.c * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information (NCBI) * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government do not place any restriction on its use or reproduction. * We would, however, appreciate having the NCBI and the author cited in * any work or product based on this material * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * =========================================================================== * * File Name: sqnutil3.c * * Author: Jonathan Kans * * Version Creation Date: 2/7/00 * * $Revision: 6.13 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include /* CautiousSeqEntryCleanup section */ static Boolean EmptyOrNullString (CharPtr str) { Char ch; if (str == NULL) return TRUE; ch = *str; while (ch != '\0') { if (ch > ' ' && ch <= '~') return FALSE; str++; ch = *str; } return TRUE; } /* RemoveMultipleTitles currently removes FIRST title in chain */ static void RemoveMultipleTitles (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; SeqDescrPtr descr = NULL; SeqDescrPtr lasttitle = NULL; ObjValNodePtr ovp; SeqDescrPtr sdp; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp == NULL) return; descr = bsp->descr; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) return; descr = bssp->descr; } else return; for (sdp = descr; sdp != NULL; sdp = sdp->next) { if (sdp->choice == Seq_descr_title) continue; if (lasttitle != NULL) { if (lasttitle->extended != 0) { ovp = (ObjValNodePtr) lasttitle; ovp->idx.deleteme = TRUE; } lasttitle = sdp; } else { lasttitle = sdp; } } } static void MakeBioSourceCopy (SeqEntryPtr sep, Pointer userdata) { BioSourcePtr biop; OrgRefPtr master; OrgRefPtr orp; SeqDescrPtr sdp; master = (OrgRefPtr) userdata; sdp = SeqEntryGetSeqDescr (sep, Seq_descr_source, NULL); if (sdp != NULL) return; biop = BioSourceNew (); if (biop == NULL) return; orp = OrgRefNew (); if (orp == NULL) return; biop->org = orp; orp->taxname = StringSave (master->taxname); orp->common = StringSave (master->common); sdp = CreateNewDescriptor (sep, Seq_descr_source); if (sdp == NULL) return; sdp->data.ptrvalue = (Pointer) biop; } static void ReplicatePopPhyMutSetBioSource (SeqEntryPtr sep) { BioSourcePtr biop; BioseqSetPtr bssp; OrgRefPtr orp; ObjValNodePtr ovp; SeqDescrPtr sdp; if (sep == NULL) return; if (! IS_Bioseq_set (sep)) return; bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) return; if (bssp->_class == 7 || (bssp->_class >= 13 && bssp->_class <= 16)) { sdp = SeqEntryGetSeqDescr (sep, Seq_descr_source, NULL); if (sdp == NULL) return; biop = (BioSourcePtr) sdp->data.ptrvalue; if (biop == NULL) return; orp = biop->org; if (orp == NULL) return; VisitElementsInSep (sep, (Pointer) orp, MakeBioSourceCopy); if (sdp->extended != 0) { ovp = (ObjValNodePtr) sdp; ovp->idx.deleteme = TRUE; } } } typedef struct featcount { Boolean is_mRNA; BioseqPtr bsp; Int2 numRNAs; SeqFeatPtr gene; Int4 numGene; Int4 numCDS; } FeatCount, PNTR FeatCountPtr; static void CountGenesAndCDSs (SeqFeatPtr sfp, Pointer userdata) { FeatCountPtr fcp; fcp = (FeatCountPtr) userdata; if (sfp->data.choice == SEQFEAT_GENE) { (fcp->numGene)++; fcp->gene = sfp; } else if (sfp->data.choice == SEQFEAT_CDREGION) { (fcp->numCDS)++; } } static void LookForMrna (BioseqPtr bsp, Pointer userdata) { FeatCountPtr fcp; MolInfoPtr mip; SeqDescrPtr sdp; if (bsp == NULL || bsp->length == 0) return; if (! ISA_na (bsp->mol)) return; fcp = (FeatCountPtr) userdata; for (sdp = bsp->descr; sdp != NULL; sdp = sdp->next) { if (sdp->choice != Seq_descr_molinfo) continue; mip = (MolInfoPtr) sdp->data.ptrvalue; if (mip != NULL && mip->biomol == MOLECULE_TYPE_MRNA) { fcp->is_mRNA = TRUE; fcp->bsp = bsp; (fcp->numRNAs)++; return; } } } static void ExtendSingleGeneOnMRNA (SeqEntryPtr sep, Pointer userdata) { FeatCount fc; SeqIntPtr sintp; ValNodePtr vnp; fc.is_mRNA = FALSE; fc.bsp = NULL; fc.numRNAs = 0; VisitBioseqsInSep (sep, (Pointer) &fc, LookForMrna); if (! fc.is_mRNA) return; fc.gene = NULL; fc.numGene = 0; fc.numCDS = 0; VisitFeaturesInSep (sep, (Pointer) &fc, CountGenesAndCDSs); if (fc.numGene == 1 && fc.numCDS < 2 && fc.numRNAs == 1 && fc.bsp != NULL && fc.gene != NULL) { if (fc.bsp != BioseqFindFromSeqLoc (fc.gene->location)) return; for (vnp = fc.gene->location; vnp != NULL; vnp = vnp->next) { if (vnp->choice != SEQLOC_INT) continue; sintp = (SeqIntPtr) vnp->data.ptrvalue; if (sintp == NULL) continue; if (sintp->from != 0 || sintp->to != fc.bsp->length - 1) { sintp->from = 0; sintp->to = fc.bsp->length - 1; } } } } static SeqFeatPtr BestCDS (SeqLocPtr loc, ValNodePtr cdslist) { SeqFeatPtr best_cds = NULL; SeqFeatPtr cds; Int4 diff; Int4 min = INT4_MAX; ValNodePtr vnp; if (loc == NULL || cdslist == NULL) return NULL; for (vnp = cdslist; vnp != NULL; vnp = vnp->next) { cds = (SeqFeatPtr) vnp->data.ptrvalue; diff = SeqLocAinB (loc, cds->location); if (diff >= 0) { if (diff < min) { min = diff; best_cds = cds; } } } return best_cds; } #define num_bond 5 static CharPtr feat_bond [num_bond] = { NULL, "disulfide bond", "thiolester bond", "xlink bond", "thioether bond" }; #define num_site 26 static CharPtr feat_site [num_site] = { NULL, "active", "binding", "cleavage", "inhibit", "modifi", "glycosylation", "myristoylation", "mutagenized", "metal-binding", "phosphorylation", "acetylation", "amidation", "methylation", "hydroxylation", "sulfatation", "oxidative-deamination", "pyrrolidone-carboxylic-acid", "gamma-carboxyglutamic-acid", "blocked", "lipid-binding", "np-binding", "dna-binding", "signal-peptide", "transit-peptide", "transmembrane-region" }; static Int2 FindStr (CharPtr PNTR array, Int2 array_num, CharPtr str) { Int2 i; for (i = 0; i < array_num; i++) { if (array [i] == NULL) continue; if (StringNCmp (str, array [i], StringLen (array [i])) == 0) return i; } return -1; } static ValNodePtr remove_node (ValNodePtr head, ValNodePtr x) { ValNodePtr v, p; if (head == NULL) return NULL; if (x == head) { head = x->next; x->next = NULL; ValNodeFree (x); return head; } for (v = head; v != NULL && v != x; v = v->next) { p = v; } if (v != NULL) { p->next = x->next; x->next = NULL; ValNodeFree (x); } return head; } static SeqLocPtr fake_bond_loc (SeqLocPtr slp) { SeqLocPtr loc, l, lnext, ldata; if (slp == NULL) return NULL; loc = MemNew (sizeof (SeqLoc)); MemCopy (loc, slp, sizeof (SeqLoc)); ldata = (SeqLocPtr) loc->data.ptrvalue; if (slp->choice != SEQLOC_MIX) return loc; for (l = ldata; l != NULL; l = lnext) { lnext = l->next; if (l->choice == SEQLOC_NULL) { ldata = remove_node (ldata, l); } } return loc; } static void ConvertImpFeatToProt (SeqFeatPtr feat, Pointer userdata) { SeqFeatPtr best_cds = NULL; Int2 bond = 0; BioseqPtr bsp; ValNodePtr cdslist; Uint1 choice = 0; Int4 frame; ImpFeatPtr ifp; SeqLocPtr loc; Uint1 processed = 0; ProtRefPtr prp; SeqFeatPtr sfp; SeqIdPtr sip; Int2 site = 0; SeqLocPtr slp; Uint1 subtype = 0; if (feat == NULL || feat->data.choice != SEQFEAT_IMP) return; ifp = (ImpFeatPtr) feat->data.value.ptrvalue; if (ifp == NULL) return; cdslist = (ValNodePtr) userdata; if (StringCmp (ifp->key, "mat_peptide") == 0) { processed = 2; choice = SEQFEAT_PROT; subtype = FEATDEF_mat_peptide_aa; } else if (StringCmp (ifp->key, "sig_peptide") == 0) { processed = 3; choice = SEQFEAT_PROT; subtype = FEATDEF_sig_peptide_aa; } else if (StringCmp (ifp->key, "transit_peptide") == 0) { processed = 4; choice = SEQFEAT_PROT; subtype = FEATDEF_transit_peptide_aa; } else if (StringCmp (ifp->key, "misc_feature") == 0 && feat->comment != NULL) { site = FindStr (feat_site, num_site, feat->comment); if (site != -1) { choice = SEQFEAT_SITE; subtype = FEATDEF_SITE; } else { bond = FindStr (feat_bond, num_bond, feat->comment); if (bond != -1) { choice = SEQFEAT_BOND; subtype = FEATDEF_BOND; } } } if (choice == 0) return; if (processed != 0 || site != 0) { best_cds = BestCDS (feat->location, cdslist); } else if (bond != 0) { loc = fake_bond_loc (feat->location); best_cds = BestCDS (loc, cdslist); SeqLocFree (loc); } if (best_cds == NULL) return; slp = dnaLoc_to_aaLoc (best_cds, feat->location, TRUE, &frame, FALSE); if (slp == NULL) return; sip = SeqLocId (best_cds->product); if (sip == NULL) return; bsp = BioseqLockById (sip); if (bsp == NULL) return; sfp = CreateNewFeatureOnBioseq (bsp, choice, slp); BioseqUnlock (bsp); if (sfp == NULL) return; sfp->partial = feat->partial; sfp->excpt = feat->excpt; sfp->exp_ev = feat->exp_ev; sfp->pseudo = feat->pseudo; sfp->comment = feat->comment; feat->comment = NULL; sfp->qual = feat->qual; feat->qual = NULL; sfp->title = feat->title; feat->title = NULL; sfp->ext = feat->ext; feat->ext = NULL; sfp->cit = feat->cit; feat->cit = NULL; sfp->xref = feat->xref; feat->xref = NULL; sfp->dbxref = feat->dbxref; feat->dbxref = NULL; sfp->except_text = feat->except_text; feat->except_text = NULL; if (choice == SEQFEAT_PROT) { prp = ProtRefNew (); sfp->data.value.ptrvalue = (Pointer) prp; if (prp != NULL) { prp->processed = processed; } switch (processed) { } } else if (choice == SEQFEAT_SITE) { sfp->data.value.intvalue = site; } else if (choice == SEQFEAT_BOND) { sfp->data.value.intvalue = bond; } sfp->idx.subtype = subtype; feat->idx.deleteme = TRUE; } static void GetListOfCDSs (SeqFeatPtr sfp, Pointer userdata) { ValNodePtr PNTR head; if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return; head = (ValNodePtr PNTR) userdata; ValNodeAddPointer (head, 0, sfp->data.value.ptrvalue); } static void ChangeImpFeatToProt (SeqEntryPtr sep) { ValNodePtr cdslist = NULL; VisitFeaturesInSep (sep, (Pointer) &cdslist, GetListOfCDSs); VisitFeaturesInSep (sep, (Pointer) cdslist, ConvertImpFeatToProt); ValNodeFree (cdslist); } static void MergeAdjacentAnnotsCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; SeqAnnotPtr nextsap; SeqAnnotPtr sap; SeqFeatPtr sfp; if (sep == NULL || sep->data.ptrvalue == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sap = bsp->annot; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sap = bssp->annot; } else return; while (sap != NULL) { nextsap = sap->next; if (sap->type == 1 && nextsap != NULL && nextsap->type == 1) { if (sap->id == NULL && nextsap->id == NULL && sap->name == NULL && nextsap->name == NULL && sap->db == 0 && nextsap->db == 0 && sap->desc == NULL && nextsap->desc == NULL && sap->data != NULL && nextsap->data != NULL) { sfp = (SeqFeatPtr) sap->data; while (sfp->next != NULL) { sfp = sfp->next; } sfp->next = (SeqFeatPtr) nextsap->data; nextsap->data = NULL; sap->next = nextsap->next; SeqAnnotFree (nextsap); nextsap = sap->next; } } sap = nextsap; } } static Boolean empty_citgen (CitGenPtr cit) { if (cit == NULL) return TRUE; if (cit->cit) return FALSE; if (cit->authors) return FALSE; if (cit->muid > 0) return FALSE; if (cit->journal) return FALSE; if (cit->volume) return FALSE; if (cit->issue) return FALSE; if (cit->pages) return FALSE; if (cit->date) return FALSE; if (cit->serial_number > 0) return FALSE; if (cit->title) return FALSE; if (cit->pmid > 0) return FALSE; return TRUE; } static Boolean PubIsEffectivelyEmpty (PubdescPtr pdp) { ValNodePtr vnp; if (pdp == NULL) return FALSE; vnp = pdp->pub; if (vnp != NULL && vnp->next == NULL && vnp->choice == PUB_Gen) { if (empty_citgen ((CitGenPtr) vnp->data.ptrvalue)) { return TRUE; } } return FALSE; } static void MarkEmptyDescsForCleanup (SeqDescrPtr sdp, Pointer userdata) { GBBlockPtr gbp; ObjValNodePtr ovp; PubdescPtr pdp; CharPtr str; if (sdp == NULL || sdp->extended == 0) return; ovp = (ObjValNodePtr) sdp; if (sdp->choice == Seq_descr_title) { str = (CharPtr) sdp->data.ptrvalue; if (StringHasNoText (str)) { ovp->idx.deleteme = TRUE; } } else if (sdp->choice == Seq_descr_pub) { pdp = (PubdescPtr) sdp->data.ptrvalue; if (pdp == NULL) return; if (PubIsEffectivelyEmpty (pdp)) { ovp->idx.deleteme = TRUE; } } else if (sdp->choice == Seq_descr_genbank) { gbp = (GBBlockPtr) sdp->data.ptrvalue; if (gbp == NULL) return; /* gbp->source = MemFree (gbp->source); */ /* gbp->origin = MemFree (gbp->origin); */ gbp->taxonomy = MemFree (gbp->taxonomy); if (gbp->extra_accessions == NULL && gbp->source == NULL && gbp->keywords == NULL && gbp->origin == NULL && gbp->date == NULL && gbp->entry_date == NULL && gbp->div == NULL && gbp->taxonomy == NULL) { ovp->idx.deleteme = TRUE; } } } static void MarkEmptyFeatsForCleanup (SeqFeatPtr sfp, Pointer userdata) { GeneRefPtr grp; PubdescPtr pdp; ProtRefPtr prp; ValNodePtr vnp; if (sfp == NULL) return; if (sfp->data.choice == SEQFEAT_GENE && sfp->data.value.ptrvalue != NULL) { grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (EmptyOrNullString (grp->locus)) { grp->locus = MemFree (grp->locus); } if (EmptyOrNullString (grp->allele)) { grp->allele = MemFree (grp->allele); } if (EmptyOrNullString (grp->desc)) { grp->desc = MemFree (grp->desc); } if (EmptyOrNullString (grp->maploc)) { grp->maploc = MemFree (grp->maploc); } if (EmptyOrNullString (grp->locus) && EmptyOrNullString (grp->allele) && EmptyOrNullString (grp->desc) && EmptyOrNullString (grp->maploc) && grp->db == NULL && grp->syn == NULL) { sfp->idx.deleteme = TRUE; } } else if (sfp->data.choice == SEQFEAT_PROT && sfp->data.value.ptrvalue != NULL) { prp = (ProtRefPtr) sfp->data.value.ptrvalue; if (prp->processed != 3 && prp->processed != 4) { vnp = prp->name; if ((vnp == NULL || EmptyOrNullString ((CharPtr) vnp->data.ptrvalue)) && EmptyOrNullString (prp->desc) && prp->ec == NULL && prp->activity == NULL && prp->db == NULL) { sfp->idx.deleteme = TRUE; } } } else if (sfp->data.choice == SEQFEAT_PUB && sfp->data.value.ptrvalue != NULL) { pdp = (PubdescPtr) sfp->data.value.ptrvalue; if (PubIsEffectivelyEmpty (pdp)) { sfp->idx.deleteme = TRUE; } } else if (sfp->data.choice == SEQFEAT_COMMENT && EmptyOrNullString (sfp->comment)) { sfp->idx.deleteme = TRUE; } } static void ConvertPubFeatDescProc (SeqFeatPtr sfp, Pointer userdata) { BioseqPtr bsp; size_t len; ObjValNodePtr ovp; PubdescPtr pdp; SeqDescPtr sdp; SeqEntryPtr sep; SeqIdPtr sip; CharPtr str; ValNode vn; /* look for publication features */ if (sfp == NULL || sfp->data.choice != SEQFEAT_PUB) return; /* get bioseq by feature location */ sip = SeqLocId (sfp->location); bsp = BioseqFind (sip); if (bsp == NULL) return; sip = SeqIdFindBest(bsp->id, 0); if (sip == NULL) return; vn.choice = SEQLOC_WHOLE; vn.extended = 0; vn.data.ptrvalue = (Pointer) sip; vn.next = NULL; /* is feature full length? */ if (SeqLocCompare (sfp->location, &vn) != SLC_A_EQ_B) return; sep = SeqMgrGetSeqEntryForData (bsp); if (sep == NULL) return; sdp = CreateNewDescriptor (sep, Seq_descr_pub); if (sdp == NULL) return; /* move publication from feature to descriptor */ sdp->data.ptrvalue = sfp->data.value.ptrvalue; if (sdp->extended != 0) { ovp = (ObjValNodePtr) sdp; ovp->idx.subtype = Seq_descr_pub; } sfp->data.value.ptrvalue = NULL; /* flag old feature for removal */ sfp->idx.deleteme = TRUE; /* move comment to remark */ if (sfp->comment == NULL) return; pdp = (PubdescPtr) sdp->data.ptrvalue; if (pdp == NULL) return; if (pdp->comment == NULL) { pdp->comment = sfp->comment; sfp->comment = NULL; } else { len = StringLen (pdp->comment) + StringLen (sfp->comment) + 5; str = MemNew (sizeof (Char) * len); StringCpy (str, pdp->comment); StringCat (str, "; "); StringCat (str, sfp->comment); pdp->comment = MemFree (pdp->comment); pdp->comment = str; } } static void ConvertSourceFeatDescProc (SeqFeatPtr sfp, Pointer userdata) { BioSourcePtr biop; BioseqPtr bsp; SubSourcePtr lastssp; ObjValNodePtr ovp; SeqDescPtr sdp; SeqEntryPtr sep; SeqIdPtr sip; SubSourcePtr ssp; ValNode vn; /* look for biosource features */ if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC) return; /* get bioseq by feature location */ sip = SeqLocId (sfp->location); bsp = BioseqFind (sip); if (bsp == NULL) return; sip = SeqIdFindBest(bsp->id, 0); if (sip == NULL) return; vn.choice = SEQLOC_WHOLE; vn.extended = 0; vn.data.ptrvalue = (Pointer) sip; vn.next = NULL; /* is feature full length? */ if (SeqLocCompare (sfp->location, &vn) != SLC_A_EQ_B) return; sep = SeqMgrGetSeqEntryForData (bsp); if (sep == NULL) return; sdp = CreateNewDescriptor (sep, Seq_descr_source); if (sdp == NULL) return; /* move biosource from feature to descriptor */ sdp->data.ptrvalue = sfp->data.value.ptrvalue; if (sdp->extended != 0) { ovp = (ObjValNodePtr) sdp; ovp->idx.subtype = Seq_descr_source; } sfp->data.value.ptrvalue = NULL; /* flag old feature for removal */ sfp->idx.deleteme = TRUE; /* move comment to subsource note */ if (sfp->comment == NULL) return; biop = (BioSourcePtr) sdp->data.ptrvalue; if (biop == NULL) return; ssp = SubSourceNew (); if (ssp == NULL) return; ssp->subtype = SUBSRC_other; ssp->name = sfp->comment; sfp->comment = NULL; /* link in at end, since BasicSeqEntry will have sorted this list */ if (biop->subtype == NULL) { biop->subtype = ssp; } else { lastssp = biop->subtype; while (lastssp->next != NULL) { lastssp = lastssp->next; } lastssp->next = ssp; } } static void PromoteOrgRefDescToBioSource (SeqDescrPtr sdp, Pointer userdata) { BioSourcePtr biop; OrgRefPtr orp; ObjValNodePtr ovp; if (sdp->choice != Seq_descr_org) return; orp = (OrgRefPtr) sdp->data.ptrvalue; if (orp == NULL) return; biop = BioSourceNew (); if (biop == NULL) return; biop->org = orp; sdp->choice = Seq_descr_source; sdp->data.ptrvalue = (Pointer) biop; if (sdp->extended != 0) { ovp = (ObjValNodePtr) sdp; ovp->idx.subtype = Seq_descr_source; } } static void PromoteOrgRefFeatToBioSource (SeqFeatPtr sfp, Pointer userdata) { BioSourcePtr biop; OrgRefPtr orp; if (sfp->data.choice != SEQFEAT_ORG) return; orp = (OrgRefPtr) sfp->data.value.ptrvalue; if (orp == NULL) return; biop = BioSourceNew (); if (biop == NULL) return; biop->org = orp; sfp->data.choice = SEQFEAT_BIOSRC; sfp->data.value.ptrvalue = (Pointer) biop; sfp->idx.subtype = FEATDEF_BIOSRC; } static void DeleteBadMarkedGeneXrefs (SeqFeatPtr sfp, Pointer userdata) { SeqFeatXrefPtr nextxref; SeqFeatXrefPtr PNTR prevxref; Boolean unlink; SeqFeatXrefPtr xref; if (sfp == NULL) return; xref = sfp->xref; prevxref = (SeqFeatXrefPtr PNTR) &(sfp->xref); while (xref != NULL) { nextxref = xref->next; unlink = FALSE; if (xref->specialCleanupFlag && xref->data.choice == SEQFEAT_GENE) { if (SeqMgrGetOverlappingGene (sfp->location, NULL) != NULL) { unlink = TRUE; } } xref->specialCleanupFlag = FALSE; if (unlink) { *(prevxref) = xref->next; xref->next = NULL; SeqFeatXrefFree (xref); } else { prevxref = (SeqFeatXrefPtr PNTR) &(xref->next); } xref = nextxref; } } static void LookForMarkedGeneXrefs (SeqFeatPtr sfp, Pointer userdata) { BoolPtr hasMarkedGenes; SeqFeatXrefPtr xref; if (sfp == NULL || sfp->xref == NULL) return; for (xref = sfp->xref; xref != NULL; xref = xref->next) { if (xref->specialCleanupFlag) { hasMarkedGenes = (BoolPtr) userdata; *hasMarkedGenes = TRUE; return; } } } NLM_EXTERN void CautiousSeqEntryCleanup (SeqEntryPtr sep, SeqEntryFunc taxfun, SeqEntryFunc taxmerge) { Boolean correct = FALSE; Uint2 entityID; Boolean hasMarkedGenes; ErrSev lsev; ErrSev msev; SeqEntryPtr oldscope; Boolean strip = TRUE; Boolean taxserver; if (sep == NULL) return; msev = ErrSetMessageLevel (SEV_MAX); lsev = ErrSetLogLevel (SEV_MAX); entityID = SeqMgrGetEntityIDForSeqEntry (sep); BasicSeqEntryCleanup (sep); VisitFeaturesInSep (sep, NULL, PromoteOrgRefFeatToBioSource); VisitDescriptorsInSep (sep, NULL, PromoteOrgRefDescToBioSource); oldscope = SeqEntrySetScope (sep); VisitFeaturesInSep (sep, NULL, ConvertSourceFeatDescProc); VisitFeaturesInSep (sep, NULL, ConvertPubFeatDescProc); SeqEntrySetScope (oldscope); VisitFeaturesInSep (sep, NULL, MarkEmptyFeatsForCleanup); VisitDescriptorsInSep (sep, NULL, MarkEmptyDescsForCleanup); DeleteMarkedObjects (0, OBJ_SEQENTRY, (Pointer) sep); SeqEntryExplore (sep, NULL, MergeAdjacentAnnotsCallback); ChangeImpFeatToProt (sep); DeleteMarkedObjects (0, OBJ_SEQENTRY, (Pointer) sep); VisitElementsInSep (sep, NULL, ExtendSingleGeneOnMRNA); ReplicatePopPhyMutSetBioSource (sep); SeqEntryExplore (sep, NULL, RemoveMultipleTitles); /* LoopSeqEntryToAsn3 section here */ taxserver = (Boolean) (taxfun != NULL || taxmerge != NULL); /* if (correct) { SeqEntryExplore(sep, (Pointer)(&porg), CorrectSourceFeat); } */ /* a few more things to do here */ hasMarkedGenes = FALSE; VisitFeaturesInSep (sep, (Pointer) &hasMarkedGenes, LookForMarkedGeneXrefs); if (hasMarkedGenes) { SeqMgrIndexFeatures (entityID, NULL); VisitFeaturesInSep (sep, NULL, DeleteBadMarkedGeneXrefs); SeqMgrClearFeatureIndexes (entityID, NULL); } BasicSeqEntryCleanup (sep); AssignIDsInEntity (entityID, 0, NULL); ErrSetMessageLevel (msev); ErrSetLogLevel (lsev); } /* static Int4 LoopSeqEntryToAsn3 (SeqEntryPtr sep, Boolean strip, Boolean correct, SeqEntryFunc taxfun, SeqEntryFunc taxmerge) { BioseqSetPtr bssp; SeqEntryPtr oldscope; Int4 rsult; Boolean taxserver; rsult = 0; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && (bssp->_class == 7 || bssp->_class == 13 || bssp->_class == 14 || bssp->_class == 15)) { for (sep = bssp->seq_set; sep != NULL; sep = sep->next) { rsult += LoopSeqEntryToAsn3 (sep, strip, correct, taxfun, taxmerge); } return rsult; } } oldscope = SeqEntrySetScope (sep); taxserver = (Boolean) (taxfun != NULL || taxmerge != NULL); rsult = SeqEntryToAsn3Ex (sep, strip, correct, taxserver, taxfun, taxmerge); SeqEntrySetScope (oldscope); return rsult; } LoopSeqEntryToAsn3 (sep, TRUE, FALSE, taxfun, taxmerge); */ typedef struct featdefNameStruct { Uint1 type; CharPtr name; } FeatdefNameData, PNTR FeatdefNamePtr; static FeatdefNameData featdefWithName [] = { { FEATDEF_10_signal , "-10_signal" }, { FEATDEF_35_signal , "-35_signal" }, { FEATDEF_3clip , "3'clip" }, { FEATDEF_3UTR , "3'UTR" }, { FEATDEF_5clip , "5'clip" }, { FEATDEF_5UTR , "5'UTR" }, { FEATDEF_attenuator , "attenuator" }, { FEATDEF_BOND , "Bond" }, { FEATDEF_CAAT_signal , "CAAT_signal" }, { FEATDEF_CDS , "CDS" }, { FEATDEF_PUB , "Cit" }, { FEATDEF_COMMENT , "Comment" }, { FEATDEF_conflict , "conflict" }, { FEATDEF_C_region , "C_region" }, { FEATDEF_D_loop , "D-loop" }, { FEATDEF_D_segment , "D_segment" }, { FEATDEF_enhancer , "enhancer" }, { FEATDEF_exon , "exon" }, { FEATDEF_GC_signal , "GC_signal" }, { FEATDEF_GENE , "Gene" }, { FEATDEF_HET , "Het" }, { FEATDEF_iDNA , "iDNA" }, { FEATDEF_IMP , "Imp" }, { FEATDEF_Imp_CDS , "Imp_CDS" }, { FEATDEF_intron , "intron" }, { FEATDEF_J_segment , "J_segment" }, { FEATDEF_LTR , "LTR" }, { FEATDEF_mat_peptide_aa , "mat_peptide" }, { FEATDEF_mat_peptide , "mat_peptide_nt" }, { FEATDEF_misc_binding , "misc_binding" }, { FEATDEF_misc_difference , "misc_difference" }, { FEATDEF_misc_feature , "misc_feature" }, { FEATDEF_misc_recomb , "misc_recomb" }, { FEATDEF_otherRNA , "misc_RNA" }, { FEATDEF_misc_signal , "misc_signal" }, { FEATDEF_misc_structure , "misc_structure" }, { FEATDEF_modified_base , "modified_base" }, { FEATDEF_mRNA , "mRNA" }, { FEATDEF_NON_STD_RESIDUE , "NonStdRes" }, { FEATDEF_NUM , "Num" }, { FEATDEF_N_region , "N_region" }, { FEATDEF_old_sequence , "old_sequence" }, { FEATDEF_polyA_signal , "polyA_signal" }, { FEATDEF_polyA_site , "polyA_site" }, { FEATDEF_preRNA , "precursor_RNA" }, { FEATDEF_preprotein , "preprotein" }, { FEATDEF_primer_bind , "primer_bind" }, { FEATDEF_prim_transcript , "prim_transcript" }, { FEATDEF_promoter , "promoter" }, { FEATDEF_PROT , "Protein" }, { FEATDEF_protein_bind , "protein_bind" }, { FEATDEF_RBS , "RBS" }, { FEATDEF_REGION , "Region" }, { FEATDEF_repeat_region , "repeat_region" }, { FEATDEF_repeat_unit , "repeat_unit" }, { FEATDEF_rep_origin , "rep_origin" }, { FEATDEF_rRNA , "rRNA" }, { FEATDEF_RSITE , "Rsite" }, { FEATDEF_satellite , "satellite" }, { FEATDEF_scRNA , "scRNA" }, { FEATDEF_PSEC_STR , "SecStr" }, { FEATDEF_sig_peptide_aa , "sig_peptide" }, { FEATDEF_sig_peptide , "sig_peptide_nt" }, { FEATDEF_SITE , "Site" }, { FEATDEF_site_ref , "Site-ref" }, { FEATDEF_snoRNA , "snoRNA" }, { FEATDEF_snRNA , "snRNA" }, { FEATDEF_source , "source" }, { FEATDEF_BIOSRC , "Src" }, { FEATDEF_stem_loop , "stem_loop" }, { FEATDEF_STS , "STS" }, { FEATDEF_S_region , "S_region" }, { FEATDEF_TATA_signal , "TATA_signal" }, { FEATDEF_terminator , "terminator" }, { FEATDEF_transit_peptide_aa , "transit_peptide" }, { FEATDEF_transit_peptide , "transit_peptide_nt" }, { FEATDEF_tRNA , "tRNA" }, { FEATDEF_TXINIT , "TxInit" }, { FEATDEF_unsure , "unsure" }, { FEATDEF_USER , "User" }, { FEATDEF_variation , "variation" }, { FEATDEF_virion , "virion" }, { FEATDEF_V_region , "V_region" }, { FEATDEF_V_segment , "V_segment" }, { FEATDEF_SEQ , "Xref" } }; NLM_EXTERN Uint1 FindFeatDefTypeFromKey (CharPtr key) { Int2 L, R, mid; if (key == NULL || *key == '\0') return FEATDEF_BAD; L = 0; R = (sizeof (featdefWithName) / sizeof (FeatdefNameData)) - 1; while (L < R) { mid = (L + R) / 2; if (StringICmp (featdefWithName [mid].name, key) < 0) { L = mid + 1; } else { R = mid; } } if (StringICmp (featdefWithName [R].name, key) == 0) { return featdefWithName [R].type; } return FEATDEF_BAD; } static CharPtr featurekeys [] = { "???" , "Gene" , "Org" , "CDS" , "Protein" , "precursor_RNA" , "mRNA" , "tRNA" , "rRNA" , "snRNA" , "scRNA" , "misc_RNA" , "Cit" , "Xref" , "Imp" , "allele" , "attenuator" , "C_region" , "CAAT_signal" , "CDS" , "conflict" , "D-loop" , "D_segment" , "enhancer" , "exon" , "GC_signal" , "iDNA" , "intron" , "J_segment" , "LTR" , "mat_peptide" , "misc_binding" , "misc_difference" , "misc_feature" , "misc_recomb" , "misc_RNA" , "misc_signal" , "misc_structure" , "modified_base" , "mutation" , "N_region" , "old_sequence" , "polyA_signal" , "polyA_site" , "precursor_RNA" , "prim_transcript" , "primer_bind" , "promoter" , "protein_bind" , "RBS" , "repeat_region" , "repeat_unit" , "rep_origin" , "S_region" , "satellite" , "sig_peptide" , "source" , "stem_loop" , "STS" , "TATA_signal" , "terminator" , "transit_peptide" , "unsure" , "V_region" , "V_segment" , "variation" , "virion" , "3'clip" , "3'UTR" , "5'clip" , "5'UTR" , "-10_signal" , "-35_signal" , "Site-ref" , "Region" , "Comment" , "Bond" , "Site" , "Rsite" , "User" , "TxInit" , "Num" , "SecStr" , "NonStdRes" , "Het" , "Src" , "Protein" , "mat_peptide" , "sig_peptide" , "transit_peptide", "snoRNA" }; NLM_EXTERN CharPtr FindKeyFromFeatDefType (Uint1 type, Boolean forGBFF) { CharPtr key; if (type < FEATDEF_GENE || type >= FEATDEF_MAX) { type = FEATDEF_BAD; } key = featurekeys [type]; if (forGBFF) { if (type == FEATDEF_GENE) { key = "gene"; } else if (type == FEATDEF_REGION || type == FEATDEF_COMMENT || type == FEATDEF_SITE) { key = "misc_feature"; } } return key; } /* tRNA codon index to codon string lookup table functions */ typedef struct gcCodonStruct { Uint1 index; CharPtr codon; } GcCodonData, PNTR GcCodonPtr; static CharPtr gcCodonStrings = NULL; static GcCodonPtr codonGcIndex = NULL; /* mapping from NCBI2na to codon codes */ static Uint1 codon_xref [4] = { 2, /* A */ 1, /* C */ 3, /* G */ 0 /* T */ }; static int LIBCALLBACK SortCodonByString ( VoidPtr vp1, VoidPtr vp2 ) { int compare; GcCodonPtr gcp1 = vp1; GcCodonPtr gcp2 = vp2; if (gcp1 == NULL || gcp2 == NULL) return 0; compare = StringICmp (gcp1->codon, gcp2->codon); if (compare > 0) { return 1; } else if (compare < 0) { return -1; } return 0; } static void InitGcCodons (void) { Uint1 codon [4], index; GcCodonPtr codonGcIdx; CharPtr gcCodonStr; Int2 i, j, k; int idx, offset; CharPtr ptr; Uint1 residue; SeqMapTablePtr smtp; if (codonGcIndex != NULL && gcCodonStrings != NULL) return; gcCodonStr = (CharPtr) MemNew (sizeof (Char) * 256); if (gcCodonStr == NULL) return; codonGcIdx = (GcCodonPtr) MemNew (sizeof (GcCodonData) * 64); if (codonGcIdx == NULL) return; smtp = SeqMapTableFind (Seq_code_iupacna, Seq_code_ncbi2na); if (smtp == NULL) return; for (idx = 0; idx < 64; idx++) { index = (Uint1) idx; for (i = 0, j = 16; i < 3; i++, j /= 4) { residue = (Uint1) ((Int2) index / j); index -= (Uint1) (residue * j); for (k = 0; k < 4; k++) { if (codon_xref [k] == residue) { residue = (Uint1) k; break; } } residue = SeqMapTableConvert (smtp, residue); codon [i] = residue; } codon [3] = 0; offset = 4 * idx; ptr = gcCodonStr + offset; StringCpy (ptr, (CharPtr) codon); codonGcIdx [idx].index = (Uint1) idx; codonGcIdx [idx].codon = ptr; } HeapSort (codonGcIdx, (size_t) 64, sizeof (GcCodonData), SortCodonByString); gcCodonStrings = gcCodonStr; codonGcIndex = codonGcIdx; } NLM_EXTERN Uint1 CodonToGcIndex (CharPtr codon) { Char ch; Int2 i, L, R, mid; Char tmp [4]; if (codonGcIndex == NULL) { InitGcCodons (); } if (codonGcIndex == NULL) return 255; if (StringLen (codon) != 3) return 255; StringNCpy_0 (tmp, codon, sizeof (tmp)); for (i = 0; i < 3; i++) { ch = tmp [i]; ch = TO_UPPER (ch); if (ch == 'U') { ch = 'T'; } tmp [i] = ch; } L = 0; R = 63; while (L < R) { mid = (L + R) / 2; if (StringICmp (codonGcIndex [mid].codon, tmp) < 0) { L = mid + 1; } else { R = mid; } } if (StringICmp (codonGcIndex [R].codon, tmp) == 0) { return codonGcIndex [R].index; } return 255; } NLM_EXTERN CharPtr GcIndextoCodon (Uint1 index) { int offset; CharPtr ptr; if (gcCodonStrings == NULL) { InitGcCodons (); } if (gcCodonStrings == NULL) return NULL; if (index > 63) return NULL; offset = 4 * index; ptr = gcCodonStrings + offset; return ptr; }