diff options
Diffstat (limited to 'api/sqnutils.h')
| -rw-r--r-- | api/sqnutils.h | 26 |
1 files changed, 24 insertions, 2 deletions
diff --git a/api/sqnutils.h b/api/sqnutils.h index 20b6e762..e3a061e3 100644 --- a/api/sqnutils.h +++ b/api/sqnutils.h @@ -29,7 +29,7 @@ * * Version Creation Date: 9/2/97 * -* $Revision: 6.87 $ +* $Revision: 6.92 $ * * File Description: * @@ -47,6 +47,7 @@ #include <ncbi.h> #include <sequtil.h> +#include <objpubme.h> #undef NLM_EXTERN #ifdef NLM_IMPORT @@ -195,10 +196,15 @@ NLM_EXTERN void ResynchCodingRegionPartials (SeqEntryPtr sep); NLM_EXTERN void ResynchMessengerRNAPartials (SeqEntryPtr sep); +/* resynchronizes protein feature with product peptide bioseq */ + +NLM_EXTERN void ResynchProteinPartials (SeqEntryPtr sep); + /* individual feature callbacks for above functions */ NLM_EXTERN void ResynchMRNAPartials (SeqFeatPtr sfp, Pointer userdata); NLM_EXTERN void ResynchCDSPartials (SeqFeatPtr sfp, Pointer userdata); +NLM_EXTERN void ResynchPeptidePartials (SeqFeatPtr sfp, Pointer userdata); /* functions to parse [org=Drosophila melanogaster] and [gene=lacZ] from titles */ /* for example, passing "gene" to SqnTagFind returns "lacZ" */ @@ -493,11 +499,16 @@ NLM_EXTERN Int4 VisitSetsInSet (BioseqSetPtr bssp, Pointer userdata, VisitSetsFu typedef void (*VisitElementsFunc) (SeqEntryPtr sep, Pointer userdata); NLM_EXTERN Int4 VisitElementsInSep (SeqEntryPtr sep, Pointer userdata, VisitElementsFunc callback); -/* visits all SeqIds within a SeqLoc */ +/* visits all SeqIds within a SeqLoc, or within features, alignments, graphs, or annots */ typedef void (*VisitSeqIdFunc) (SeqIdPtr sip, Pointer userdata); NLM_EXTERN Int4 VisitSeqIdsInSeqLoc (SeqLocPtr slp, Pointer userdata, VisitSeqIdFunc callback); +NLM_EXTERN Int4 VisitSeqIdsInSeqFeat (SeqFeatPtr sfp, Pointer userdata, VisitSeqIdFunc callback); +NLM_EXTERN Int4 VisitSeqIdsInSeqAlign (SeqAlignPtr sap, Pointer userdata, VisitSeqIdFunc callback); +NLM_EXTERN Int4 VisitSeqIdsInSeqGraph (SeqGraphPtr sgp, Pointer userdata, VisitSeqIdFunc callback); +NLM_EXTERN Int4 VisitSeqIdsInSeqAnnot (SeqAnnotPtr annot, Pointer userdata, VisitSeqIdFunc callback); + /* visits all sub UserFields - if the data type is 11, VisitUserFieldsInUfp recurses */ typedef void (*VisitUserFieldsFunc) (UserFieldPtr ufp, Pointer userdata); @@ -538,6 +549,17 @@ NLM_EXTERN Int4 VisitBioSourcesInSep (SeqEntryPtr sep, Pointer userdata, VisitBi typedef void (*ScanBioseqSetFunc) (SeqEntryPtr sep, Pointer userdata); NLM_EXTERN Int4 ScanBioseqSetRelease (CharPtr inputFile, Boolean binary, Boolean compressed, Pointer userdata, ScanBioseqSetFunc callback); +/* PubMed registered fetch functionality */ + +NLM_EXTERN PubmedEntryPtr LIBCALL GetPubMedForUid (Int4 uid); + +/* internal support type, registration function */ + +typedef PubmedEntryPtr (LIBCALLBACK * PubMedFetchFunc) (Int4 uid); + +NLM_EXTERN void LIBCALL PubMedSetFetchFunc (PubMedFetchFunc func); + + #ifdef __cplusplus } |