/* objfdef.c * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * 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 have not placed any restriction on its use or reproduction. * * 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. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * File Name: objfdef.c * * Author: James Ostell * * Version Creation Date: 9/94 * * $Revision: 6.21 $ * * File Description: Object manager for feature definitions * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * $Log: objfdef.c,v * Revision 4.4 1995/09/21 02:26:14 ostel * changed label for RNA to keep typelabel in most case * * Revision 4.3 1995/09/06 22:48:12 kans * improved tRNA label function (JO) * * Revision 4.2 1995/09/06 22:08:56 ostell * revision to tRNA label function * * Revision 4.1 1995/08/30 19:13:28 ostell * change LabelContent so Imp-feat get ifp->key even if ONLY_CONTENT * * Revision 4.0 1995/07/26 13:48:06 ostell * force revision to 4.0 * * Revision 1.11 1995/07/20 14:29:51 kans * FEATDEF_otherRNA corrected from 7 to 255 * * Revision 1.10 1995/05/15 21:22:00 ostell * added Log line * * * * ========================================================================== */ #include /* the features interface */ #include /* the AsnTool header */ #include #include /* new public location of SeqMgrGetBestProteinFeature */ static Boolean loaded = FALSE; /***************************************************************************** * * FeatDefAsnLoad() * requires SeqAsnLoad() to be called first * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL FeatDefAsnLoad (void) { if (loaded) return TRUE; loaded = TRUE; if ( ! AsnLoad()) { loaded = FALSE; return FALSE; } return TRUE; } /***************************************************************************** * * FeatDef Routines * *****************************************************************************/ /***************************************************************************** * * FeatDefNew() * *****************************************************************************/ NLM_EXTERN FeatDefPtr LIBCALL FeatDefNew (void) { return (FeatDefPtr)MemNew(sizeof(FeatDef)); } /***************************************************************************** * * FeatDefFree(fdp) * Frees one FeatDef and associated data * *****************************************************************************/ NLM_EXTERN FeatDefPtr LIBCALL FeatDefFree (FeatDefPtr fdp) { if (fdp == NULL) return (FeatDefPtr)NULL; MemFree(fdp->typelabel); MemFree(fdp->menulabel); return (FeatDefPtr)MemFree(fdp); } /***************************************************************************** * * FeatDefAsnWrite(fdp, aip, atp) * atp is the current type (if identifier of a parent struct) * if atp == NULL, then assumes it stands alone (FeatDef ::=) * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL FeatDefAsnWrite (FeatDefPtr fdp, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! FeatDefAsnLoad()) return FALSE; } if (aip == NULL) return FALSE; atp = AsnLinkType(orig, FEATDEF); /* link local tree */ if (atp == NULL) return FALSE; if (fdp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer)fdp)) goto erret; av.ptrvalue = fdp->typelabel; if (! AsnWrite(aip, FEATDEF_typelabel, &av)) goto erret; av.ptrvalue = fdp->menulabel; if (! AsnWrite(aip, FEATDEF_menulabel, &av)) goto erret; av.intvalue = (Int4)(fdp->featdef_key); if (! AsnWrite(aip, FEATDEF_featdef_key, &av)) goto erret; av.intvalue = (Int4)(fdp->seqfeat_key); if (! AsnWrite(aip, FEATDEF_seqfeat_key, &av)) goto erret; av.intvalue = (Int4)(fdp->entrygroup); if (! AsnWrite(aip, FEATDEF_entrygroup, &av)) goto erret; av.intvalue = (Int4)(fdp->displaygroup); if (! AsnWrite(aip, FEATDEF_displaygroup, &av)) goto erret; av.intvalue = (Int4)(fdp->molgroup); if (! AsnWrite(aip, FEATDEF_molgroup, &av)) goto erret; if (! AsnCloseStruct(aip, atp, (Pointer)fdp)) goto erret; retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /***************************************************************************** * * FeatDefAsnRead(aip, atp) * atp is the current type (if identifier of a parent struct) * assumption is readIdent has occured * if atp == NULL, then assumes it stands alone and read ident * has not occured. * *****************************************************************************/ NLM_EXTERN FeatDefPtr LIBCALL FeatDefAsnRead (AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp, oldtype; FeatDefPtr fdp; if (! loaded) { if (! FeatDefAsnLoad()) return (FeatDefPtr)NULL; } if (aip == NULL) return (FeatDefPtr)NULL; if (orig == NULL) /* FeatDef ::= (self contained) */ atp = AsnReadId(aip, amp, FEATDEF); else atp = AsnLinkType(orig, FEATDEF); /* link in local tree */ oldtype = atp; if (atp == NULL) return (FeatDefPtr)NULL; fdp = FeatDefNew(); if (fdp == NULL) goto erret; if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ while ((atp = AsnReadId(aip, amp, atp)) != oldtype) { if (atp == NULL) goto erret; if (AsnReadVal(aip, atp, &av) <= 0) goto erret; if (atp == FEATDEF_typelabel) fdp->typelabel = (CharPtr)av.ptrvalue; else if (atp == FEATDEF_menulabel) fdp->menulabel = (CharPtr)av.ptrvalue; else if (atp == FEATDEF_featdef_key) fdp->featdef_key = (Uint1)(av.intvalue); else if (atp == FEATDEF_seqfeat_key) fdp->seqfeat_key = (Uint1)(av.intvalue); else if (atp == FEATDEF_entrygroup) fdp->entrygroup = (Uint1)(av.intvalue); else if (atp == FEATDEF_displaygroup) fdp->displaygroup = (Uint1)(av.intvalue); else if (atp == FEATDEF_molgroup) fdp->molgroup = (Uint1)(av.intvalue); } if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return fdp; erret: fdp = FeatDefFree(fdp); goto ret; } /***************************************************************************** * * FeatDefSetFree(fdp) * Frees set of FeatDef * *****************************************************************************/ NLM_EXTERN FeatDefPtr LIBCALL FeatDefSetFree (FeatDefPtr fdp) { FeatDefPtr next; while (fdp != NULL) { next = fdp->next; FeatDefFree(fdp); fdp = next; } return (FeatDefPtr)NULL; } /***************************************************************************** * * FeatDefSetAsnWrite(fdp, aip, atp) * atp is the current type (if identifier of a parent struct) * if atp == NULL, then assumes it stands alone (FeatDef ::=) * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL FeatDefSetAsnWrite (FeatDefPtr fdp, AsnIoPtr aip, AsnTypePtr orig) { AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! FeatDefAsnLoad()) return FALSE; } if (aip == NULL) return FALSE; atp = AsnLinkType(orig, FEATDEFSET); /* link local tree */ if (atp == NULL) return FALSE; if (fdp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer)fdp)) goto erret; while (fdp != NULL) { if (! FeatDefAsnWrite(fdp, aip, FEATDEFSET_E)) goto erret; fdp = fdp->next; } if (! AsnCloseStruct(aip, atp, (Pointer)fdp)) goto erret; retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /***************************************************************************** * * FeatDefSetAsnRead(aip, atp) * atp is the current type (if identifier of a parent struct) * assumption is readIdent has occured * if atp == NULL, then assumes it stands alone and read ident * has not occured. * *****************************************************************************/ NLM_EXTERN FeatDefPtr LIBCALL FeatDefSetAsnRead (AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp, oldtype; FeatDefPtr fdp, first=NULL, last=NULL; if (! loaded) { if (! FeatDefAsnLoad()) return (FeatDefPtr)NULL; } if (aip == NULL) return (FeatDefPtr)NULL; if (orig == NULL) /* FeatDef ::= (self contained) */ atp = AsnReadId(aip, amp, FEATDEFSET); else atp = AsnLinkType(orig, FEATDEFSET); /* link in local tree */ oldtype = atp; if (atp == NULL) return (FeatDefPtr)NULL; if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ while ((atp = AsnReadId(aip, amp, atp)) != oldtype) { if (atp == NULL) goto erret; fdp = FeatDefAsnRead(aip, atp); if (fdp == NULL) goto erret; if (first == NULL) first = fdp; if (last != NULL) last->next = fdp; last = fdp; } if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return first; erret: first = FeatDefSetFree(first); goto ret; } /***************************************************************************** * * FeatDispGroup Routines * *****************************************************************************/ /***************************************************************************** * * FeatDispGroupNew() * *****************************************************************************/ NLM_EXTERN FeatDispGroupPtr LIBCALL FeatDispGroupNew (void) { return (FeatDispGroupPtr)MemNew(sizeof(FeatDispGroup)); } /***************************************************************************** * * FeatDispGroupFree(fdp) * Frees one FeatDispGroup and associated data * *****************************************************************************/ NLM_EXTERN FeatDispGroupPtr LIBCALL FeatDispGroupFree (FeatDispGroupPtr fdp) { if (fdp == NULL) return (FeatDispGroupPtr)NULL; MemFree(fdp->groupname); return (FeatDispGroupPtr)MemFree(fdp); } /***************************************************************************** * * FeatDispGroupAsnWrite(fdp, aip, atp) * atp is the current type (if identifier of a parent struct) * if atp == NULL, then assumes it stands alone (FeatDispGroup ::=) * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL FeatDispGroupAsnWrite (FeatDispGroupPtr fdp, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! FeatDefAsnLoad()) return FALSE; } if (aip == NULL) return FALSE; atp = AsnLinkType(orig, FEATDISPGROUP); /* link local tree */ if (atp == NULL) return FALSE; if (fdp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer)fdp)) goto erret; av.intvalue = (Int4)(fdp->groupkey); if (! AsnWrite(aip, FEATDISPGROUP_groupkey, &av)) goto erret; av.ptrvalue = fdp->groupname; if (! AsnWrite(aip, FEATDISPGROUP_groupname, &av)) goto erret; if (! AsnCloseStruct(aip, atp, (Pointer)fdp)) goto erret; retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /***************************************************************************** * * FeatDispGroupAsnRead(aip, atp) * atp is the current type (if identifier of a parent struct) * assumption is readIdent has occured * if atp == NULL, then assumes it stands alone and read ident * has not occured. * *****************************************************************************/ NLM_EXTERN FeatDispGroupPtr LIBCALL FeatDispGroupAsnRead (AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp, oldtype; FeatDispGroupPtr fdp; if (! loaded) { if (! FeatDefAsnLoad()) return (FeatDispGroupPtr)NULL; } if (aip == NULL) return (FeatDispGroupPtr)NULL; if (orig == NULL) /* FeatDispGroup ::= (self contained) */ atp = AsnReadId(aip, amp, FEATDISPGROUP); else atp = AsnLinkType(orig, FEATDISPGROUP); /* link in local tree */ oldtype = atp; if (atp == NULL) return (FeatDispGroupPtr)NULL; fdp = FeatDispGroupNew(); if (fdp == NULL) goto erret; if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ while ((atp = AsnReadId(aip, amp, atp)) != oldtype) { if (atp == NULL) goto erret; if (AsnReadVal(aip, atp, &av) <= 0) goto erret; if (atp == FEATDISPGROUP_groupname) fdp->groupname = (CharPtr)av.ptrvalue; else if (atp == FEATDISPGROUP_groupkey) fdp->groupkey = (Uint1)(av.intvalue); } if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return fdp; erret: fdp = FeatDispGroupFree(fdp); goto ret; } /***************************************************************************** * * FeatDispGroupSetFree(fdp) * Frees set of FeatDispGroup * *****************************************************************************/ NLM_EXTERN FeatDispGroupPtr LIBCALL FeatDispGroupSetFree (FeatDispGroupPtr fdp) { FeatDispGroupPtr next; while (fdp != NULL) { next = fdp->next; FeatDispGroupFree(fdp); fdp = next; } return (FeatDispGroupPtr)NULL; } /***************************************************************************** * * FeatDispGroupSetAsnWrite(fdp, aip, atp) * atp is the current type (if identifier of a parent struct) * if atp == NULL, then assumes it stands alone (FeatDispGroup ::=) * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL FeatDispGroupSetAsnWrite (FeatDispGroupPtr fdp, AsnIoPtr aip, AsnTypePtr orig) { AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! FeatDefAsnLoad()) return FALSE; } if (aip == NULL) return FALSE; atp = AsnLinkType(orig, FEATDISPGROUPSET); /* link local tree */ if (atp == NULL) return FALSE; if (fdp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer)fdp)) goto erret; while (fdp != NULL) { if (! FeatDispGroupAsnWrite(fdp, aip, FEATDISPGROUPSET_E)) goto erret; fdp = fdp->next; } if (! AsnCloseStruct(aip, atp, (Pointer)fdp)) goto erret; retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /***************************************************************************** * * FeatDispGroupSetAsnRead(aip, atp) * atp is the current type (if identifier of a parent struct) * assumption is readIdent has occured * if atp == NULL, then assumes it stands alone and read ident * has not occured. * *****************************************************************************/ NLM_EXTERN FeatDispGroupPtr LIBCALL FeatDispGroupSetAsnRead (AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp, oldtype; FeatDispGroupPtr fdp, first=NULL, last=NULL; if (! loaded) { if (! FeatDefAsnLoad()) return (FeatDispGroupPtr)NULL; } if (aip == NULL) return (FeatDispGroupPtr)NULL; if (orig == NULL) /* FeatDispGroup ::= (self contained) */ atp = AsnReadId(aip, amp, FEATDISPGROUPSET); else atp = AsnLinkType(orig, FEATDISPGROUPSET); /* link in local tree */ oldtype = atp; if (atp == NULL) return (FeatDispGroupPtr)NULL; if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ while ((atp = AsnReadId(aip, amp, atp)) != oldtype) { if (atp == NULL) goto erret; fdp = FeatDispGroupAsnRead(aip, atp); if (fdp == NULL) goto erret; if (first == NULL) first = fdp; if (last != NULL) last->next = fdp; last = fdp; } if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return first; erret: first = FeatDispGroupSetFree(first); goto ret; } static FeatDefPtr featdefp = NULL; static FeatDefPtr PNTR featdeflookup; /* kludge which assumes featdef_key in order */ static Int2 numfdef, numfdispg; static FeatDispGroupPtr featdgp; /***************************************************************************** * * featDefSetMemStr as last resort embedded version of featdef.prt * *****************************************************************************/ #ifndef WIN16 static CharPtr featDefSetMemStr = "FeatDefGroupSet ::= {\n" \ "groups {\n" \ "{ groupkey 0 , groupname \"Unrecognized Features\" } ,\n" \ "{ groupkey 1 , groupname \"Genes and Named Regions\" } ,\n" \ "{ groupkey 2 , groupname \"Coding Regions and Transcripts\" } ,\n" \ "{ groupkey 3 , groupname \"Structural RNAs\" } ,\n" \ "{ groupkey 4 , groupname \"Bibliographic and Comments\" } ,\n" \ "{ groupkey 5 , groupname \"Sites and Bonds\" } } ,\n" \ "defs {\n" \ "{ typelabel \"???\" , menulabel \"Unsupported feature\" , featdef-key 0 , seqfeat-key 0 , entrygroup 0 , displaygroup 0 , molgroup both } ,\n" \ "{ typelabel \"Gene\" , menulabel \"Gene\" , featdef-key 1 , seqfeat-key 1 , entrygroup 1 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"Org\" , menulabel \"Organism\" , featdef-key 2 , seqfeat-key 2 , entrygroup 4 , displaygroup 4 , molgroup both } ,\n" \ "{ typelabel \"CDS\" , menulabel \"Coding Region\" , featdef-key 3 , seqfeat-key 3 , entrygroup 2 , displaygroup 2 , molgroup na } ,\n" \ "{ typelabel \"Prot\" , menulabel \"Protein Names\" , featdef-key 4 , seqfeat-key 4 , entrygroup 1 , displaygroup 1 , molgroup aa } ,\n" \ "{ typelabel \"preRNA\" , menulabel \"Precursor RNA\" , featdef-key 5 , seqfeat-key 5 , entrygroup 2 , displaygroup 2 , molgroup na } ,\n" \ "{ typelabel \"mRNA\" , menulabel \"Mature Messenger RNA\" , featdef-key 6 , seqfeat-key 5 , entrygroup 2 , displaygroup 2 , molgroup na } ,\n" \ "{ typelabel \"tRNA\" , menulabel \"Transfer RNA\" , featdef-key 7 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \ "{ typelabel \"rRNA\" , menulabel \"Ribosomal RNA\" , featdef-key 8 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \ "{ typelabel \"snRNA\" , menulabel \"Small Nuclear RNA\" , featdef-key 9 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \ "{ typelabel \"scRNA\" , menulabel \"Small Cytoplasmic RNA\" , featdef-key 10 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \ "{ typelabel \"RNA\" , menulabel \"Other Types of RNA\" , featdef-key 11 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \ "{ typelabel \"Cit\" , menulabel \"Bibliographic Citations\" , featdef-key 12 , seqfeat-key 6 , entrygroup 4 , displaygroup 4 , molgroup both } ,\n" \ "{ typelabel \"Xref\" , menulabel \"Reference to Another Sequence\" , featdef-key 13 , seqfeat-key 7 , entrygroup 4 , displaygroup 4 , molgroup both } ,\n" \ "{ typelabel \"Imp\" , menulabel \"Unclassified ImpFeat\" , featdef-key 14 , seqfeat-key 8 , entrygroup 0 , displaygroup 0 , molgroup na } ,\n" \ "{ typelabel \"allele\" , menulabel \"Allelic Varient\" , featdef-key 15 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"attenuator\" , menulabel \"Attenuator\" , featdef-key 16 , seqfeat-key 8 , entrygroup 0 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"C_region\" , menulabel \"Immunoglobin/T-cell receptor constant region\" , featdef-key 17 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"CAAT_signal\" , menulabel \"CAAT box\" , featdef-key 18 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"CDS\" , menulabel \"Untranslatable coding region\" , featdef-key 19 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \ "{ typelabel \"conflict\" , menulabel \"Sequence determinations differ\" , featdef-key 20 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \ "{ typelabel \"D-loop\" , menulabel \"Displacement Loop\" , featdef-key 21 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"D_segment\" , menulabel \"Diversity Segment of Immunoglobin\" , featdef-key 22 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"enhancer\" , menulabel \"Enhancer\" , featdef-key 23 , seqfeat-key 8 , entrygroup 0 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"exon\" , menulabel \"Exon\" , featdef-key 24 , seqfeat-key 8 , entrygroup 2 , displaygroup 2 , molgroup na } ,\n" \ "{ typelabel \"GC_signal\" , menulabel \"GC box\" , featdef-key 25 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"iDNA\" , menulabel \"intervening DNA\" , featdef-key 26 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"intron\" , menulabel \"Intron\" , featdef-key 27 , seqfeat-key 8 , entrygroup 2 , displaygroup 2 , molgroup na } ,\n" \ "{ typelabel \"J_segment\" , menulabel \"IG joining segment\" , featdef-key 28 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"LTR\" , menulabel \"Long Terminal Repeat\" , featdef-key 29 , seqfeat-key 8 , entrygroup 1 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"mat_peptide\" , menulabel \"Mature Peptide labeled on Nuc Acid\" , featdef-key 30 , seqfeat-key 8 , entrygroup 0 , displaygroup 2 , molgroup na } ,\n" \ "{ typelabel \"misc_binding\" , menulabel \"Miscellaneaous binding site\" , featdef-key 31 , seqfeat-key 8 , entrygroup 0 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"misc_difference\" , menulabel \"Miscellaneous sequence difference\" , featdef-key 32 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \ "{ typelabel \"misc_feature\" , menulabel \"Miscellaneaous feature\" , featdef-key 33 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \ "{ typelabel \"misc_recomb\" , menulabel \"Miscellaneous recombination\" , featdef-key 34 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"misc_RNA\" , menulabel \"Miscellaneous RNA\" , featdef-key 35 , seqfeat-key 8 , entrygroup 0 , displaygroup 3 , molgroup na } ,\n" \ "{ typelabel \"misc_signal\" , menulabel \"Miscellaneous signal sequence\" , featdef-key 36 , seqfeat-key 8 , entrygroup 0 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"misc_structure\" , menulabel \"Miscellaneous secondary structure\" , featdef-key 37 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"modified_base\" , menulabel \"Modified base\" , featdef-key 38 , seqfeat-key 8 , entrygroup 0 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"mutation\" , menulabel \"site of mutation in related strain\" , featdef-key 39 , seqfeat-key 8 , entrygroup 0 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"N_region\" , menulabel \"Extra na in rearranged IG\" , featdef-key 40 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"old_sequence\" , menulabel \"Location of sequence revision\" , featdef-key 41 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \ "{ typelabel \"polyA_signal\" , menulabel \"PolyA addition recognition signal\" , featdef-key 42 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"polyA_site\" , menulabel \"Point where polyA tail begins\" , featdef-key 43 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"precursor_RNA\" , menulabel \"RNA which is a post-transcriptional intermediate\" , featdef-key 44 , seqfeat-key 8 , entrygroup 0 , displaygroup 2 , molgroup na } ,\n" \ "{ typelabel \"prim_transcript\" , menulabel \"Primary transcript\" , featdef-key 45 , seqfeat-key 8 , entrygroup 0 , displaygroup 2 , molgroup na } ,\n" \ "{ typelabel \"primer_bind\" , menulabel \"Primer binding site\" , featdef-key 46 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"promoter\" , menulabel \"Promoter\" , featdef-key 47 , seqfeat-key 8 , entrygroup 0 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"protein_bind\" , menulabel \"Protein binding site\" , featdef-key 48 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"RBS\" , menulabel \"Ribosome binding site\" , featdef-key 49 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"repeat_region\" , menulabel \"Region containing repeats\" , featdef-key 50 , seqfeat-key 8 , entrygroup 1 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"repeat_unit\" , menulabel \"Single repeat unit\" , featdef-key 51 , seqfeat-key 8 , entrygroup 1 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"rep_origin\" , menulabel \"Origin of replication\" , featdef-key 52 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"S_region\" , menulabel \"IG switch region\" , featdef-key 53 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"satellite\" , menulabel \"satellite repeat region\" , featdef-key 54 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"sig_peptide\" , menulabel \"Signal Peptide annotated on Nuc Acid\" , featdef-key 55 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"source\" , menulabel \"Source of Nuc Acid\" , featdef-key 56 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \ "{ typelabel \"stem_loop\" , menulabel \"Stem loop structure\" , featdef-key 57 , seqfeat-key 8 , entrygroup 1 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"STS\" , menulabel \"Sequence tagged site\" , featdef-key 58 , seqfeat-key 8 , entrygroup 1 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"TATA_signal\" , menulabel \"TATA box\" , featdef-key 59 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"terminator\" , menulabel \"Transcription terminator\" , featdef-key 60 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"transit_peptide\" , menulabel \"Transit peptide annotated on Nuc Acid\" , featdef-key 61 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"unsure\" , menulabel \"Unsure of exact sequence\" , featdef-key 62 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \ "{ typelabel \"V_region\" , menulabel \"IG variable region\" , featdef-key 63 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"V_segment\" , menulabel \"IG variable segment\" , featdef-key 64 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"variation\" , menulabel \"Strain differences\" , featdef-key 65 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \ "{ typelabel \"virion\" , menulabel \"Viral genome\" , featdef-key 66 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \ "{ typelabel \"3'clip\" , menulabel \"3' region of transcript clipped off in processing\" , featdef-key 67 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"3'UTR\" , menulabel \"3' untranslated region\" , featdef-key 68 , seqfeat-key 8 , entrygroup 2 , displaygroup 2 , molgroup na } ,\n" \ "{ typelabel \"5'clip\" , menulabel \"5' region of transcript clipped off in processing\" , featdef-key 69 , seqfeat-key 8 , entrygroup 0 , displaygroup 1 , molgroup na } ,\n" \ "{ typelabel \"5'UTR\" , menulabel \"5' untranslated region\" , featdef-key 70 , seqfeat-key 8 , entrygroup 2 , displaygroup 2 , molgroup na } ,\n" \ "{ typelabel \"-10_signal\" , menulabel \"Pribnow box\" , featdef-key 71 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"-35_signal\" , menulabel \"-35 region of transcription start\" , featdef-key 72 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"Site-ref\" , menulabel \"SITES type reference\" , featdef-key 73 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \ "{ typelabel \"Region\" , menulabel \"Named region of sequence\" , featdef-key 74 , seqfeat-key 9 , entrygroup 1 , displaygroup 1 , molgroup both } ,\n" \ "{ typelabel \"Comment\" , menulabel \"Comment associated with sequence\" , featdef-key 75 , seqfeat-key 10 , entrygroup 4 , displaygroup 4 , molgroup both } ,\n" \ "{ typelabel \"Bond\" , menulabel \"Chemical bonds\" , featdef-key 76 , seqfeat-key 11 , entrygroup 5 , displaygroup 5 , molgroup aa } ,\n" \ "{ typelabel \"Site\" , menulabel \"Binding/Active Sites\" , featdef-key 77 , seqfeat-key 12 , entrygroup 5 , displaygroup 5 , molgroup both } ,\n" \ "{ typelabel \"Rsite\" , menulabel \"Restriction Sites\" , featdef-key 78 , seqfeat-key 13 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"User\" , menulabel \"User Defined feature\" , featdef-key 79 , seqfeat-key 14 , entrygroup 0 , displaygroup 4 , molgroup both } ,\n" \ "{ typelabel \"TxInit\" , menulabel \"Transcription Initiation Site\" , featdef-key 80 , seqfeat-key 15 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \ "{ typelabel \"Num\" , menulabel \"Numbering System for Sequence\" , featdef-key 81 , seqfeat-key 16 , entrygroup 4 , displaygroup 4 , molgroup both } ,\n" \ "{ typelabel \"SecStr\" , menulabel \"Protein Secondary Structure\" , featdef-key 82 , seqfeat-key 17 , entrygroup 1 , displaygroup 1 , molgroup aa } ,\n" \ "{ typelabel \"NonStdRes\" , menulabel \"Non-standard Residue\" , featdef-key 83 , seqfeat-key 18 , entrygroup 5 , displaygroup 5 , molgroup aa } ,\n" \ "{ typelabel \"Het\" , menulabel \"Heterogen\" , featdef-key 84 , seqfeat-key 19 , entrygroup 5 , displaygroup 5 , molgroup aa } ,\n" \ "{ typelabel \"Src\" , menulabel \"Biological Source\" , featdef-key 85 , seqfeat-key 20 , entrygroup 4 , displaygroup 4 , molgroup both } ,\n" \ "{ typelabel \"proprotein\" , menulabel \"Proprotein\" , featdef-key 86 , seqfeat-key 4 , entrygroup 1 , displaygroup 1 , molgroup aa } ,\n" \ "{ typelabel \"mat_peptide\" , menulabel \"Mature Peptide\" , featdef-key 87 , seqfeat-key 4 , entrygroup 1 , displaygroup 1 , molgroup aa } ,\n" \ "{ typelabel \"sig_peptide\" , menulabel \"Signal Peptide\" , featdef-key 88 , seqfeat-key 4 , entrygroup 1 , displaygroup 1 , molgroup aa } ,\n" \ "{ typelabel \"transit_peptide\" , menulabel \"Transit Peptide\" , featdef-key 89 , seqfeat-key 4 , entrygroup 1 , displaygroup 1 , molgroup aa } ,\n" \ "{ typelabel \"snoRNA\" , menulabel \"Small Nucleolar RNA\" , featdef-key 90 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } } };\n"; #endif /***************************************************************************** * * FeatDefPtr FeatDefSetLoad() * loads all current feature defintions * looks for "featdef.val" in the "data" directory * *****************************************************************************/ static FeatDefPtr LIBCALL FeatDefGroupSetAsnRead (AsnIoPtr aip, AsnTypePtr orig) { FeatDefPtr fdp; FeatDispGroupPtr fdgp; Int2 i; DataVal av; AsnTypePtr atp, oldtype; if (! loaded) { if (! FeatDefAsnLoad()) return (FeatDefPtr)NULL; } if (aip == NULL) return (FeatDefPtr)NULL; if (orig == NULL) /* FeatDefGroupSet ::= (self contained) */ atp = AsnReadId(aip, amp, FEATDEFGROUPSET); else atp = AsnLinkType(orig, FEATDEFGROUPSET); /* link in local tree */ oldtype = atp; if (atp == NULL) return (FeatDefPtr)NULL; if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ while ((atp = AsnReadId(aip, amp, atp)) != oldtype) { if (atp == NULL) goto erret; if (atp == FEATDEFGROUPSET_groups) { featdgp = FeatDispGroupSetAsnRead(aip, atp); if (featdgp == NULL) goto erret; } else if (atp == FEATDEFGROUPSET_defs) { featdefp = FeatDefSetAsnRead(aip, atp); if (featdefp == NULL) goto erret; } } if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* end struct */ for (numfdef = 0, fdp = featdefp; fdp != NULL; fdp = fdp->next) numfdef++; featdeflookup = MemNew((size_t)(sizeof(FeatDefPtr) * numfdef)); for (i = 0, fdp = featdefp; i < numfdef; fdp = fdp->next, i++) featdeflookup[i] = fdp; for (numfdispg = 0, fdgp = featdgp; fdgp != NULL; fdgp = fdgp->next) numfdispg++; ret: AsnUnlinkType(orig); /* unlink local tree */ return featdefp; erret: featdgp = FeatDispGroupSetFree(featdgp); featdefp = FeatDefSetFree(featdefp); goto ret; } static Boolean LoadFeatDefFromLocalString (void) { #ifndef WIN16 AsnIoMemPtr aimp; aimp = AsnIoMemOpen ("r", (BytePtr) featDefSetMemStr, (Int4) StringLen (featDefSetMemStr)); if (aimp == NULL || aimp->aip == NULL) return FALSE; FeatDefGroupSetAsnRead (aimp->aip, NULL); AsnIoMemClose (aimp); #endif return (Boolean) (featdefp != NULL); } NLM_EXTERN FeatDefPtr LIBCALL FeatDefSetLoad (void) { Char buf[256]; AsnIoPtr aip; if (featdefp != NULL) return featdefp; if (! loaded) { if (! FeatDefAsnLoad()) return (FeatDefPtr)NULL; } if (! FindPath("ncbi", "ncbi", "data", buf, sizeof (buf))) { if (LoadFeatDefFromLocalString ()) { return featdefp; } ErrPost(CTX_NCBIOBJ, 1, "FindPath failed in FeatDefSetTableLoad - ncbi configuration file missing or incorrect"); return featdefp; } StringCat(buf, "featdef.val"); if ((aip = AsnIoOpen(buf, "rb")) == NULL) { if (LoadFeatDefFromLocalString ()) { return featdefp; } ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s]", buf); return featdefp; } FeatDefGroupSetAsnRead (aip, NULL); AsnIoClose(aip); return featdefp; } /***************************************************************************** * * FindImpFeatType(sfp) * returns the featdef_key by matching the key of an Imp-feat * returns FEATDEF_BAD if can't match it * *****************************************************************************/ static Uint1 FindImpFeatType (SeqFeatPtr sfp) { FeatDefPtr PNTR fdpp; FeatDefPtr fdp; ImpFeatPtr ifp; CharPtr tmp; Int2 i; if (sfp == NULL) return FEATDEF_BAD; if (sfp->data.choice != SEQFEAT_IMP) return FEATDEF_BAD; ifp = (ImpFeatPtr)(sfp->data.value.ptrvalue); tmp = ifp->key; if (FeatDefSetLoad() == NULL) return FEATDEF_BAD; fdpp = featdeflookup; for (i = 0; i < numfdef; i++, fdpp++) { fdp = *fdpp; if (fdp->seqfeat_key == SEQFEAT_IMP) { if (! StringCmp(fdp->typelabel, tmp)) return fdp->featdef_key; } } return FEATDEF_BAD; } /***************************************************************************** * * FindFeatDefType(sfp) * Finds the featdef_type for a SeqFeat * returns FEATDEF_BAD if can't find it * *****************************************************************************/ NLM_EXTERN Uint1 LIBCALL FindFeatDefType(SeqFeatPtr sfp) { RnaRefPtr rrp; ProtRefPtr prp; if (sfp == NULL) return FEATDEF_BAD; switch (sfp->data.choice) { case SEQFEAT_GENE: return FEATDEF_GENE; case SEQFEAT_ORG: return FEATDEF_ORG; case SEQFEAT_CDREGION: return FEATDEF_CDS; case SEQFEAT_PROT: prp = (ProtRefPtr)(sfp->data.value.ptrvalue); switch (prp->processed) { case 0: return FEATDEF_PROT; case 1: return FEATDEF_preprotein; case 2: return FEATDEF_mat_peptide_aa; case 3: return FEATDEF_sig_peptide_aa; case 4: return FEATDEF_transit_peptide_aa; } return FEATDEF_BAD; case SEQFEAT_RNA: rrp = (RnaRefPtr)(sfp->data.value.ptrvalue); switch (rrp->type) { case 0: return FEATDEF_otherRNA; /* unknownRNA mapped to otherRNA */ case 1: return FEATDEF_preRNA; case 2: return FEATDEF_mRNA; case 3: return FEATDEF_tRNA; case 4: return FEATDEF_rRNA; case 5: return FEATDEF_snRNA; case 6: return FEATDEF_scRNA; case 7: return FEATDEF_snoRNA; case 255: return FEATDEF_otherRNA; } return FEATDEF_BAD; case SEQFEAT_PUB: return FEATDEF_PUB; case SEQFEAT_SEQ: return FEATDEF_SEQ; case SEQFEAT_IMP: return FindImpFeatType(sfp); case SEQFEAT_REGION: return FEATDEF_REGION; case SEQFEAT_COMMENT: return FEATDEF_COMMENT; case SEQFEAT_BOND: return FEATDEF_BOND; case SEQFEAT_SITE: return FEATDEF_SITE; case SEQFEAT_RSITE: return FEATDEF_RSITE; case SEQFEAT_USER: return FEATDEF_USER; case SEQFEAT_TXINIT: return FEATDEF_TXINIT; case SEQFEAT_NUM: return FEATDEF_NUM; case SEQFEAT_PSEC_STR: return FEATDEF_PSEC_STR; case SEQFEAT_NON_STD_RESIDUE: return FEATDEF_NON_STD_RESIDUE; case SEQFEAT_HET: return FEATDEF_HET; case SEQFEAT_BIOSRC: return FEATDEF_BIOSRC; } return FEATDEF_BAD; } /***************************************************************************** * * FeatDefTypeLabel(sfp) * returns the type label for the feature * returns NULL if can't find one * *****************************************************************************/ NLM_EXTERN const char * LIBCALL FeatDefTypeLabel(SeqFeatPtr sfp) { Int2 i; if (sfp == NULL) return (const char *)NULL; if (FeatDefSetLoad() == NULL) return (const char *)NULL; i = (Int2) FindFeatDefType(sfp); if (i == FEATDEF_BAD) return NULL; return (const char *)(featdeflookup[i]->typelabel); } static Int2 NEAR FeatDefLabelContent (SeqFeatPtr sfp, CharPtr buf, Int2 buflen, Uint1 labeltype, CharPtr typelabel) { GeneRefPtr grp=NULL; OrgRefPtr orp=NULL; ProtRefPtr prp=NULL; SeqFeatXrefPtr sfxrp; SeqIdPtr sip; BioseqPtr bsp; BioseqContextPtr bcp; SeqFeatPtr sfp2; RsiteRefPtr rrp; UserObjectPtr uop; BioSourcePtr bsrcp; CharPtr label = NULL; RnaRefPtr trrp; tRNAPtr trp; Char tbuf[40], snpbuf [64]; Int2 len = buflen, diff; GBQualPtr gbp; CharPtr prefix=NULL, suffix=NULL, ptr; PubdescPtr pdp; ValNodePtr vnp; ImpFeatPtr ifp; Boolean first; ValNode vn; static CharPtr slash = " /"; SeqMapTablePtr smtp; SeqCodeTablePtr sctp; Uint1 aacode; DbtagPtr dbt; ObjectIdPtr oip; if (sfp == NULL) return 0; switch (sfp->data.choice) { case SEQFEAT_GENE: grp = (GeneRefPtr)(sfp->data.value.ptrvalue); generef: if (grp->locus != NULL) label = (grp->locus); else if (grp->desc != NULL) label = (grp->desc); else if (grp->syn != NULL) label = (CharPtr)(grp->syn->data.ptrvalue); else if (grp->db != NULL) return DbtagLabel((DbtagPtr)(grp->db->data.ptrvalue), buf, buflen); else if (grp->maploc != NULL) label = (grp->maploc); break; case SEQFEAT_ORG: orp = (OrgRefPtr)(sfp->data.value.ptrvalue); orgref: if (orp->taxname != NULL) label = (orp->taxname); else if (orp->common != NULL) label = (orp->common); else if (orp->db != NULL) return DbtagLabel((DbtagPtr)(orp->db->data.ptrvalue), buf, buflen); break; case SEQFEAT_CDREGION: for (sfxrp = sfp->xref; sfxrp != NULL; sfxrp = sfxrp->next) { switch (sfxrp->data.choice) { case SEQFEAT_PROT: prp = (ProtRefPtr)(sfxrp->data.value.ptrvalue); break; case SEQFEAT_GENE: grp = (GeneRefPtr)(sfxrp->data.value.ptrvalue); break; } } if (prp != NULL) goto protref; if (sfp->product != NULL) { sip = SeqLocId(sfp->product); bsp = BioseqFind(sip); if (bsp != NULL) { /* first see if preindexed in object manager */ sfp2 = SeqMgrGetBestProteinFeature (bsp, NULL); if (sfp2 != NULL) { prp = (ProtRefPtr)(sfp2->data.value.ptrvalue); if (prp != NULL) { goto protref; } } /* if not preindexed, find with bioseq context */ bcp = BioseqContextNew(bsp); sfp2 = BioseqContextGetSeqFeat(bcp, SEQFEAT_PROT, NULL, NULL, 0); BioseqContextFree(bcp); if (sfp2 != NULL) { prp = (ProtRefPtr)(sfp2->data.value.ptrvalue); goto protref; } } } if (grp != NULL && ((grp->locus != NULL && grp->locus [0] != '\0') || grp->allele != NULL || grp->desc != NULL || grp->maploc != NULL || grp->pseudo || grp->db != NULL || grp->syn != NULL)) goto generef; break; case SEQFEAT_PROT: prp = (ProtRefPtr)(sfp->data.value.ptrvalue); protref: if (prp->name != NULL) label = (prp->name->data.ptrvalue); else if (prp->desc != NULL) label = (prp->desc); else if (prp->db != NULL) return DbtagLabel((DbtagPtr)(prp->db->data.ptrvalue), buf, buflen); break; case SEQFEAT_RNA: trrp = (RnaRefPtr)(sfp->data.value.ptrvalue); if (labeltype == OM_LABEL_CONTENT) { prefix = StringMove(tbuf, typelabel); StringMove(prefix, "-"); prefix = tbuf; } switch (trrp->ext.choice) { case 0: label = sfp->comment; if (label != NULL) { /* if RNA already in comment, skip it */ if (StringStr(label, typelabel) != NULL) prefix = NULL; } else { prefix = NULL; label = typelabel; } break; case 1: label = (CharPtr)(trrp->ext.value.ptrvalue); if (label != NULL) { if (StringStr(label, typelabel) != NULL) prefix = NULL; } else { prefix = NULL; label = typelabel; } break; case 2: trp = (tRNAPtr)(trrp->ext.value.ptrvalue); switch (trp->aatype) { case 1: aacode = Seq_code_iupacaa; break; case 2: aacode = Seq_code_ncbieaa; break; case 3: aacode = Seq_code_ncbi8aa; break; case 4: aacode = Seq_code_ncbistdaa; break; default: aacode = 0; break; } if (! aacode) break; sctp = SeqCodeTableFind(Seq_code_iupacaa3); if (sctp == NULL) { label = prefix; prefix = NULL; break; } if (aacode != Seq_code_ncbistdaa) { smtp = SeqMapTableFind(Seq_code_ncbistdaa, aacode); if (smtp == NULL) { label = prefix; prefix = NULL; break; } aacode = SeqMapTableConvert(smtp, trp->aa); } else { aacode = trp->aa; } if (aacode == 255) { label = prefix; prefix = NULL; break; } label = sctp->symbols[aacode - sctp->start_at]; break; default: break; } break; /* just return the type label for now */ case SEQFEAT_PUB: pdp = (PubdescPtr)(sfp->data.value.ptrvalue); vn.choice = PUB_Equiv; vn.data.ptrvalue = pdp->pub; vn.next = NULL; return PubLabel(&vn, buf, buflen, OM_LABEL_CONTENT); case SEQFEAT_SEQ: break; case SEQFEAT_IMP: ifp = (ImpFeatPtr)(sfp->data.value.ptrvalue); if (! StringICmp("Site-ref", ifp->key)) { if (sfp->cit != NULL) { first = TRUE; for (vnp = (ValNodePtr)(sfp->cit->data.ptrvalue); vnp != NULL; vnp = vnp->next) { if (! first) { diff = LabelCopy(buf, ",", buflen); buflen -= diff; buf += diff; } else first = FALSE; diff = PubLabel(vnp, buf, buflen, OM_LABEL_CONTENT); buflen -= diff; buf += diff; first = FALSE; } return (len - buflen); } } else if (labeltype == OM_LABEL_CONTENT) /* show key */ { if (! StringICmp("CDS", ifp->key)) label = "[CDS]"; else if ((! StringICmp("repeat_unit", ifp->key)) || (! StringICmp("repeat_region", ifp->key))) { for (gbp = sfp->qual; ((label == NULL) && (gbp != NULL)); gbp = gbp->next) { if (! StringICmp("rpt_family", gbp->qual)) label = gbp->val; } if (label == NULL) label = typelabel; } else if (! StringICmp("STS", ifp->key)) { for (gbp = sfp->qual; ((label == NULL) && (gbp != NULL)); gbp = gbp->next) { if (! StringICmp("standard_name", gbp->qual)) label = gbp->val; } if (label == NULL && (! StringHasNoText (sfp->comment))) { StringNCpy_0 (snpbuf, sfp->comment, sizeof (snpbuf)); ptr = StringChr (snpbuf, ';'); if (ptr != NULL) { *ptr = '\0'; } label = snpbuf; } if (label == NULL) label = typelabel; } else if (StringICmp("misc_feature", ifp->key)) { for (gbp = sfp->qual; label == NULL && gbp != NULL; gbp = gbp->next) { if (StringICmp ("standard_name", gbp->qual) == 0) { label = gbp->val; } } for (gbp = sfp->qual; label == NULL && gbp != NULL; gbp = gbp->next) { if (StringICmp ("function", gbp->qual) == 0) { label = gbp->val; } } for (gbp = sfp->qual; label == NULL && gbp != NULL; gbp = gbp->next) { if (StringICmp ("number", gbp->qual) == 0) { label = gbp->val; } } for (gbp = sfp->qual; label == NULL && gbp != NULL; gbp = gbp->next) { label = gbp->val; } if (label == NULL) label = typelabel; } } break; case SEQFEAT_REGION: label = (sfp->data.value.ptrvalue); if (StringICmp (label, "Domain") == 0 && sfp->comment != NULL) { label = sfp->comment; } break; case SEQFEAT_COMMENT: label = sfp->comment; break; case SEQFEAT_BOND: label = AsnEnumStr("SeqFeatData.bond", (Int2)(sfp->data.value.intvalue)); break; case SEQFEAT_SITE: label = AsnEnumStr("SeqFeatData.site", (Int2)(sfp->data.value.intvalue)); break; case SEQFEAT_RSITE: rrp = (RsiteRefPtr)(sfp->data.value.ptrvalue); if (rrp->choice == 1) label = (rrp->data.ptrvalue); else if (rrp->choice == 2) { /* return DbtagLabel((DbtagPtr)(rrp->data.ptrvalue), buf, buflen); */ label = "?"; dbt = (DbtagPtr) rrp->data.ptrvalue; if (dbt != NULL) { oip = dbt->tag; if (oip != NULL) { label = oip->str; } } } break; case SEQFEAT_USER: uop = (UserObjectPtr)(sfp->data.value.ptrvalue); label = (uop->_class); if (label == NULL) { oip = uop->type; if (oip != NULL) { label = oip->str; } } break; case SEQFEAT_TXINIT: break; case SEQFEAT_NUM: break; case SEQFEAT_PSEC_STR: label = AsnEnumStr("SeqFeatData.psec-str", (Int2)(sfp->data.value.intvalue)); break; case SEQFEAT_NON_STD_RESIDUE: label = (sfp->data.value.ptrvalue); break; case SEQFEAT_HET: label = (sfp->data.value.ptrvalue); break; case SEQFEAT_BIOSRC: bsrcp = (BioSourcePtr)(sfp->data.value.ptrvalue); orp = bsrcp->org; goto orgref; default: break; } if (label != NULL) return LabelCopyExtra (buf, label, buflen, prefix, suffix); first = TRUE; diff = 1; /* just to make the first pass through loop work */ for (gbp=sfp->qual; ((gbp != NULL) && (diff)); gbp = gbp->next) { if (first) prefix = (slash + 1); else prefix = slash; first = FALSE; diff = LabelCopyExtra (buf, gbp->qual, buflen, prefix, NULL); buflen -= diff; buf += diff; if (gbp->val != NULL) { prefix = "="; diff = LabelCopyExtra(buf, gbp->val, buflen, prefix, NULL); buflen -= diff; buf += diff; } } if (sfp->comment != NULL) { if (! first) prefix = "; "; else prefix = NULL; diff = LabelCopyExtra(buf, sfp->comment, buflen, prefix, NULL); buflen -= diff; } return (len - buflen); } /***************************************************************************** * * FeatDefLabel(sfp, buf, buflen, type) * fills in buf with a content based label * if longer than buflen, makes the last visible char > * guarantees a '\0' at the end of the string * * NOTE: buf MUST be (buflen+1) long * * This function makes nicer labels since it can combine elements * returns length of string or 0 on failure * * type is OM_LABEL_TYPE_ defined in objmgr.h * *****************************************************************************/ NLM_EXTERN Int2 LIBCALL FeatDefLabel (SeqFeatPtr sfp, CharPtr buf, Int2 buflen, Uint1 labeltype) { Int2 len, i, diff; CharPtr curr, typelabel, tmp; Uint1 extras = 0; Char tbuf[40]; ImpFeatPtr ifp; CharPtr suffix = NULL; if ((sfp == NULL) || (buf == NULL) || (! buflen)) return 0; buf[0] = '\0'; curr = buf; len = buflen; if (FeatDefSetLoad() == NULL) return 0; i = (Int2) FindFeatDefType(sfp); if (i != FEATDEF_BAD) { typelabel = featdeflookup[i]->typelabel; if ((sfp->data.choice == SEQFEAT_IMP) && (! StringCmp("CDS", typelabel))) { tmp = StringMove(tbuf, "["); tmp = StringMove(tmp, typelabel); tmp = StringMove(tmp, "]"); typelabel = tbuf; } else if (sfp->data.choice == SEQFEAT_REGION && StringICmp ((CharPtr) sfp->data.value.ptrvalue, "Domain") == 0 && sfp->comment != NULL) { StringCpy (tbuf, "Domain"); typelabel = tbuf; } } else { typelabel = tbuf; switch (sfp->data.choice) { case SEQFEAT_IMP: ifp = (ImpFeatPtr)(sfp->data.value.ptrvalue); tmp = StringMove(tbuf, "["); tmp = StringMove(tmp, ifp->key); tmp = StringMove(tmp, "]"); break; default: sprintf(tbuf, "[Unknown=%d]", (int)(sfp->data.choice)); break; } } if ((labeltype == OM_LABEL_TYPE) || (labeltype == OM_LABEL_BOTH)) { if (labeltype == OM_LABEL_BOTH) suffix = ": "; else suffix = NULL; diff = LabelCopyExtra(curr, typelabel, buflen, NULL, suffix); curr += diff; buflen -= diff; } if ((labeltype == OM_LABEL_TYPE) || (! buflen)) return (len - buflen); diff = FeatDefLabelContent (sfp, curr, buflen, labeltype, typelabel); buflen -= diff; if ((! diff) && (labeltype == OM_LABEL_CONTENT)) { buflen -= LabelCopy(curr, typelabel, buflen); } return (len - buflen); } /***************************************************************************** * * DispGroupNum() * returns number of display groups * returns 0 on failure * loads featdef.val if not already loaded * *****************************************************************************/ NLM_EXTERN Int2 LIBCALL DispGroupNum(void) { FeatDefSetLoad(); return numfdispg; } /***************************************************************************** * * DispGroupFindNext(curr, groupptr, groupname) * returns display groups in order * start with curr=NULL, then return current in curr until function * returns NULL * loads featdef.val if necessary * groupptr is filled in with the key for the group, used * in FeatDefFindNext() below. * groupname points to the string naming the group * *****************************************************************************/ NLM_EXTERN FeatDispGroupPtr LIBCALL DispGroupFindNext(FeatDispGroupPtr curr, Uint1Ptr groupptr, CharPtr PNTR groupname) { FeatDefSetLoad(); if (curr == NULL) curr = featdgp; else curr = curr->next; if (curr != NULL) { *groupptr = curr->groupkey; *groupname = curr->groupname; } return curr; } /***************************************************************************** * * FeatDefNum() * returns total number of FeatDef * loads featdef.val if necessary * *****************************************************************************/ NLM_EXTERN Int2 LIBCALL FeatDefNum(void) { FeatDefSetLoad(); return numfdef; } /***************************************************************************** * * FeatDefFindNext(curr, keyptr, menulabel, group, for_display) * returns next FeatDef within display group * if group == FEATDEF_ANY returns all * start with curr = NULL and return current in curr until function * returns NULL * keyptr is filled in with featdef-key * menulabel is filled in with menulabel * if for_display == TRUE then group must match display group * else group must match entrygroup * loads featdef.val if necessary * *****************************************************************************/ NLM_EXTERN FeatDefPtr LIBCALL FeatDefFindNext (FeatDefPtr curr, Uint1Ptr keyptr, CharPtr PNTR menulabel, Uint1 group, Boolean for_display) { FeatDefSetLoad(); if (curr == NULL) curr = featdefp; else curr = curr->next; if ((group == FEATDEF_ANY) && (curr != NULL)) { *keyptr = curr->featdef_key; *menulabel = curr->menulabel; return curr; } while (curr != NULL) { if (for_display) { if (group == curr->displaygroup) { *keyptr = curr->featdef_key; *menulabel = curr->menulabel; return curr; } } else { if (group == curr->entrygroup) { *keyptr = curr->featdef_key; *menulabel = curr->menulabel; return curr; } } curr = curr->next; } return curr; }