New upstream version 6.1.20160908

1 files changed, 5 insertions, 594 deletions

diff --git a/api/asn2ff3.c b/api/asn2ff3.c
index f8eca746..bb9ee7eb 100644
--- a/api/asn2ff3.c
+++ b/api/asn2ff3.c
@@ -34,595 +34,6 @@
 *
 * Modifications:  
 * --------------------------------------------------------------------------
-* $Log: asn2ff3.c,v $
-* Revision 6.120  2011/12/19 18:33:53  gouriano
-* Corrected printf formatting. NOJIRA
-*
-* Revision 6.119  2006/07/13 17:06:38  bollin
-* use Uint4 instead of Uint2 for itemID values
-* removed unused variables
-* resolved compiler warnings
-*
-* Revision 6.118  2003/07/22 16:18:27  kans
-* added ZFIN as legal db_xref
-*
-* Revision 6.117  2003/06/10 18:44:10  kans
-* added GeneDB to list of legal db_xrefs
-*
-* Revision 6.116  2003/05/29 20:25:19  kans
-* added Interpro to list of legal dbxrefs
-*
-* Revision 6.115  2002/11/30 20:18:27  kans
-* added GOA to list of legal db_xrefs
-*
-* Revision 6.114  2002/11/27 22:25:17  kans
-* added AceView/WormGenes, NextDB, and WorfDB to legal db_xrefs
-*
-* Revision 6.113  2002/07/12 17:34:35  kans
-* WormBase is now legal dbxref for all records, not just RefSeq
-*
-* Revision 6.112  2002/06/21 15:31:11  kans
-* added GABI db_xref
-*
-* Revision 6.111  2002/06/18 20:59:59  kans
-* added ISFinder as legal db_xref with hotlink
-*
-* Revision 6.110  2002/05/06 22:15:12  kans
-* added IFO and JCM db_xrefs
-*
-* Revision 6.109  2002/02/27 13:47:11  kans
-* fixed model evidence printing
-*
-* Revision 6.108  2002/02/20 21:59:04  tatiana
-* IMGT/LIGM dbxref added
-*
-* Revision 6.107  2002/01/31 22:31:31  tatiana
-* allow trascript_id in NC records
-*
-* Revision 6.106  2002/01/18 19:53:24  kans
-* if RefSeq, allow WormBase dbxref
-*
-* Revision 6.105  2001/12/28 21:37:10  kans
-* allow sfp->product to be SEQLOC_EQUIV
-*
-* Revision 6.104  2001/11/29 18:29:38  kans
-* added FANTOM_DB to list of legal db_xrefs, incremented DBNUM
-*
-* Revision 6.103  2001/11/12 19:32:38  kans
-* updated mRNAEvidenceComment
-*
-* Revision 6.102  2001/10/25 12:45:45  kans
-* Get3LetterSymbol was using table->num instead of table_3aa->num
-*
-* Revision 6.101  2001/10/15 17:08:44  kans
-* updated legal db_xref list to collaboration + RefSeq
-*
-* Revision 6.100  2001/10/15 13:57:22  kans
-* added BDGP_INS and SoyBase as legal db_xrefs
-*
-* Revision 6.99  2001/10/02 17:39:50  yaschenk
-* Removing memory leaks
-*
-* Revision 6.98  2001/09/06 20:31:24  yaschenk
-* removing memory leak - seqid returned by GetSeqIdForGI() needs to be freed
-*
-* Revision 6.97  2001/09/05 23:37:42  tatiana
-* ribosomal slippage added to /note
-*
-* Revision 6.96  2001/09/05 23:32:39  tatiana
-* supressed comparison of note to gene->synonym
-*
-* Revision 6.95  2001/08/22 22:35:07  kans
-* added ProductIsLocal for /translation
-*
-* Revision 6.94  2001/08/07 16:49:41  kans
-* use NUM_SEQID, added third party annotation SeqIDs to one more place
-*
-* Revision 6.93  2001/08/03 20:36:16  kans
-* implemented ASN2GNBK_PRINT_UNKNOWN_ORG test to suppress unwanted mode diffs for asn2gnbk QA
-*
-* Revision 6.92  2001/07/12 17:12:49  kans
-* biop->genome range checks in AddBioSourceToGBQual to prevent crashes
-*
-* Revision 6.91  2001/07/08 21:18:50  kans
-* if ssp->subtype is 0, use ? as tag in note
-*
-* Revision 6.90  2001/06/26 19:50:07  kans
-* call AddPID with is_NC as an option for showing /protein_id with the gi
-*
-* Revision 6.89  2001/06/25 22:22:17  kans
-* ProteinFromCdRegion and GetProductFromCDS only if sfp->product and ! ajp->genome_view, should eliminate unwanted fetches to get far delta components
-*
-* Revision 6.88  2001/05/31 17:42:18  kans
-* NC and NG RefSeq records allow remote fetching for /protein_id and /transcript_id, show gi if fetching not enabled
-*
-* Revision 6.87  2001/03/17 00:51:30  tatiana
-* GeneID added to dbxref array
-*
-* Revision 6.86  2001/02/13 23:31:58  kans
-* allow trans splicing exception, do not change sfp_in->excpt
-*
-* Revision 6.85  2001/01/30 16:25:54  kans
-* precursor_RNA now has /product as legal qualifier
-*
-* Revision 6.84  2001/01/26 19:26:36  kans
-* added niaEST, increased DBNUM
-*
-* Revision 6.83  2001/01/26 19:21:45  kans
-* extrachromosomal into source note, removed macronuclear, extrachrom, plasmid from organism line
-*
-* Revision 6.82  2001/01/18 23:57:01  kans
-* add GO (gene ontology) to list of legal dbxrefs
-*
-* Revision 6.81  2001/01/02 19:56:48  kans
-* Get3LetterSymbol protects against empty string
-*
-* Revision 6.80  2000/12/07 19:03:53  tatiana
-* transcript_id shows for NT only
-*
-* Revision 6.79  2000/12/06 22:00:46  tatiana
-* ifdef removed
-*
-* Revision 6.78  2000/12/06 20:56:24  tatiana
-* AceView link added
-*
-* Revision 6.76  2000/12/04 22:23:47  tatiana
-* contig comments added
-*
-* Revision 6.75  2000/11/22 16:48:18  tatiana
-* remove debugging error printing
-*
-* Revision 6.74  2000/11/10 00:37:13  tatiana
-* changes in AddPID
-*
-* Revision 6.73  2000/10/25 15:57:57  kans
-* sfp_in->excpt set to FALSE, not NULL, UNIX compiler does not know the difference, but Mac and PC compilers do
-*
-* Revision 6.72  2000/10/24 20:35:35  tatiana
-* CDS without protein sequence is accepted for  not forgbrel mode
-*
-* Revision 6.70  2000/10/19 18:52:32  kans
-* added another NULL entry to organelleQual for endogenous virus to suppress as organelle qualifier
-*
-* Revision 6.69  2000/10/16 19:10:17  kans
-* added UniSTS and InterimID to legal dbxrefs
-*
-* Revision 6.68  2000/10/10 15:06:02  kans
-* added SUBSRC_endogenous_virus_name
-*
-* Revision 6.67  2000/08/28 22:17:18  kans
-* added CDD to list of legal dbxrefs
-*
-* Revision 6.66  2000/07/14 20:24:26  kans
-* added RGD as dbxref with web link
-*
-* Revision 6.65  2000/07/12 22:45:15  kans
-* added ORGMOD_old_lineage
-*
-* Revision 6.64  2000/06/20 17:31:34  kans
-* added authority through breed as orgmod.subtypes
-*
-* Revision 6.63  2000/06/15 16:45:40  kans
-* added segment to biosource note print
-*
-* Revision 6.62  2000/06/05 17:52:11  tatiana
-* increase size of feature arrays to Int4
-*
-* Revision 6.61  2000/05/15 15:52:50  bazhin
-* Removed memory leak in "PrintSourceFeat()".
-*
-* Revision 6.60  2000/03/30 20:37:29  kans
-* added tilde to newline code in PrintImpFeatEx (thanks to Sergei B)
-*
-* Revision 6.59  2000/03/01 19:09:53  tatiana
-* for SYN records with multiple source features there is no subtraction
-*
-* Revision 6.58  2000/02/17 21:59:18  kans
-* /organelle not under ajp->forgbrel for this release now
-*
-* Revision 6.57  2000/02/15 22:53:56  kans
-* added dbSNP and RATMAP as legal dbxrefs, put /organelle under ajp->forgrel control
-*
-* Revision 6.56  2000/02/09 01:12:51  tatiana
-* remove space in organelle qualifier
-*
-* Revision 6.55  2000/01/21 20:48:45  kans
-* changes to merge several source qualifiers under new organelle qualifier
-*
-* Revision 6.54  2000/01/11 22:49:37  tatiana
-* protein accession is not required in DUMP_MODE
-*
-* Revision 6.53  2000/01/03 23:16:17  kans
-* CDS note components from GetProtRefComment are separated by semicolons - to be consistent with upcoming asn2gnbk style
-*
-* Revision 6.52  1999/10/18 20:13:34  kans
-* removed erroneous cast in sprintf
-*
-* Revision 6.51  1999/10/06 22:18:29  kans
-* calls ComposeCodonsRecognizedString
-*
-* Revision 6.50  1999/10/06 20:23:48  bazhin
-* Removed memory leaks.
-*
-* Revision 6.49  1999/08/03 20:48:23  tatiana
-* UMR error fixed in PrintImpFeat
-*
-* Revision 6.47  1999/04/26 18:53:00  tatiana
-*  added pseuod from sfp in ConvertToNAImpFeat()
-*
-* Revision 6.46  1999/04/06 22:37:45  tatiana
-* protein_id hot link added
-*
-* Revision 6.45  1999/04/06 15:00:16  tatiana
-* www_featkey is not called for slp view
-*
-* Revision 6.44  1999/03/30 22:23:33  kans
-* pseudo can be on grp or sfp
-*
-* Revision 6.43  1999/03/30 19:18:19  tatiana
-* changes for SEQID_OTHER
-*
-* Revision 6.42  1999/03/22 23:09:26  tatiana
-* AddPID() changes
-*
-* Revision 6.41  1998/10/19 15:57:35  tatiana
-* UniGene added to dbtag array
-*
-* Revision 6.40  1998/09/24 17:45:57  kans
-* fixed GetDBXrefFromGene problem (TT)
-*
-* Revision 6.39  1998/09/01 19:25:21  kans
-* context parameter in get best protein, get cds/rna given product
-*
-* Revision 6.38  1998/08/19 18:40:38  tatiana
-* RiceGenes added to dbtag array
-*
-* Revision 6.37  1998/07/21 15:14:50  kans
-* GetProtRefComments modified for indexes because continue statement avoided get next feature, got stuck
-*
-* Revision 6.36  1998/07/15 22:07:19  kans
-* implemented sequence manager indexes for non-segmented nucleotides
-*
-* Revision 6.35  1998/07/13 14:52:24  tatiana
-* subtypes added to source feature /note
-*
-* Revision 6.34  1998/06/15 14:57:22  tatiana
-* UNIX compiler warnings  and extra HTML characters in notes fixed
-*
-* Revision 6.33  1998/05/20 20:05:40  tatiana
-* SEQFEAT_REGION added to get_prot_feats()
-*
-* Revision 6.32  1998/05/18 14:41:53  tatiana
-* GI added to dbtag array
-*
-* Revision 6.31  1998/05/08 21:56:56  tatiana
-* added new PARTIAL_MODE
-*
-* Revision 6.30  1998/04/30 21:42:36  tatiana
-* *** empty log message ***
-*
-* Revision 6.29  1998/04/27 18:31:51  tatiana
-* added /focus in PrintSourceFeat()
-*
-* Revision 6.28  1998/04/24 15:10:08  tatiana
-* GetProtRefComment() fixed: only main Prot-Ref feature adds comment to CDS
-*
-* Revision 6.27  1998/04/15 21:38:32  kans
-* rearrange dbtag array so PID set is at start, allow unknown database on all but release_mode (Tatiana)
-*
-* Revision 6.24  1998/04/06 14:59:08  tatiana
-* PutTranslationLast has been moved
-*
-* Revision 6.23  1998/04/03 22:38:36  tatiana
-* selenocysteine added tp /note in ComposeCodeBreakQuals()
-*
-* Revision 6.22  1998/04/02 21:42:53  tatiana
-* ignore old_name in OrgMod
-*
-* Revision 6.21  1998/04/02 17:21:23  tatiana
-* a bug fixed in AddBioSourceToGBQual()
-*
-* Revision 6.20  1998/03/30 20:38:56  tatiana
-* nat_host changed to specific_host
-*
-* Revision 6.19  1998/03/27 23:01:54  tatiana
-* AddBioSourceToGBQual: added all OrgMod.subtypes as /notes on the source feature
-*
-* Revision 6.18  1998/03/24 19:47:45  tatiana
-* added check for sfp->except_text
-*
-* Revision 6.17  1998/03/04 18:38:48  tatiana
-*  illegal feature will be dropped in ConvertToAAImpFeat
-*
-* Revision 6.16  1998/02/19 21:28:52  tatiana
-* dbtags array updated
-*
-* Revision 6.15  1998/01/26 21:16:16  tatiana
-* biovar and country added to source feature /note
-*
-* Revision 6.14  1998/01/20 22:45:11  tatiana
-* show both product and descr in Genpept
-*
-* Revision 6.13  1998/01/13 16:27:38  tatiana
-* fixed a bug in dbtag check in PrintSourceFeat
-*
-* Revision 6.12  1997/12/23 21:57:16  tatiana
-* focus and specimen_voucher
-*
-* Revision 6.11  1997/12/15 15:48:33  tatiana
-* features processing has been changed
-*
-* Revision 6.10  1997/12/02 18:15:02  tatiana
-* fix use of printf
-*
-* Revision 6.9  1997/10/23 16:57:42  tatiana
-* *** empty log message ***
-*
-* Revision 6.6  1997/09/16 15:48:07  kans
-* removed automatically generated diff lines
-*
-* Revision 6.5  1997/09/16 15:42:52  kans
-* show non-gbff source qualifiers in note with labels (TT)
-*
-* Revision 6.4  1997/09/12 20:20:18  tatiana
-* fixed typo
-*
-* Revision 6.3  1997/09/12 20:03:53  tatiana
-* added source feature in genome_view
-*
-* Revision 6.2  1997/09/04 01:16:48  kans
-* fixed typo
-*
-* Revision 6.1  1997/09/03 21:49:37  tatiana
-* GatherItemWithLock() added for ProtRef features
-*
-* Revision 6.0  1997/08/25 18:04:51  madden
-* Revision changed to 6.0
-*
-* Revision 5.59  1997/08/21 19:03:17  tatiana
-* map, syn, description eliminated from features other than gene
-*
-* Revision 5.58  1997/08/05 20:09:08  kans
-* added check for po->sfp null in PrintSourceFeat
-*
-* Revision 5.57  1997/07/29 14:55:51  kans
-* make sure features on protein are SEQFEAT_PROT
-*
-* Revision 5.56  1997/07/16 21:08:28  tatiana
-* Use gene synonym for /gene qualifier
-*
-* Revision 5.55  1997/06/19 18:37:02  vakatov
-* [WIN32,MSVC++]  Adopted for the "NCBIOBJ.LIB" DLL'ization
-*
-* Revision 5.54  1997/06/12 16:56:37  kans
-* fixed typo that resulted in lost note (TT)
-*
-* Revision 5.53  1997/06/10 15:27:12  tatiana
-* fix a typo in COnvertToNa... that leaded to the lost /note
-*
- * Revision 5.47  1997/03/14  21:21:33  tatiana
- * exp_evidence fix
- *
- * Revision 5.46  1997/03/05  22:12:33  tatiana
- * print 'pseudo' in /note for orphan genes
- *
- * Revision 5.45  1997/03/04  23:45:14  tatiana
- * check for 'pseudo' gene added in ConvertToNAImpFeat()
- *
- * Revision 5.44  1997/02/25  23:47:21  tatiana
- * new error message added for dropped feature
- *
- * Revision 5.42  1997/01/29  15:49:11  tatiana
- * fix the entityID in GatherProductGeneInfo()
- *
- * Revision 5.40  1997/01/15  17:23:38  tatiana
- * a bug fixed (purify reported) in PrintNAFeatByNumber()
- *
- * Revision 5.39  1997/01/07  23:27:13  tatiana
- * check for NULLs added in CompareTranslation
- *
- * Revision 5.38  1997/01/07  22:32:41  tatiana
- * added SEQFEAT_SITE to get_prot_feats callback
- *
- * Revision 5.37  1997/01/02  22:49:55  tatiana
- * gather SEQFEAT_BOND
- *
- * Revision 5.36  1996/12/10  17:45:41  tatiana
- * a bug fixed in ComposeNoteFromNoteStruct()
- *
- * Revision 5.35  1996/12/09  19:12:33  tatiana
- * SPTREMBL added to legal db_xref database names
- *
- * Revision 5.34  1996/12/04  16:52:16  tatiana
- * a typo fixed in Add_dbxref
- *
- * Revision 5.33  1996/12/03  15:49:57  tatiana
- * 'CK' added to array of legal databases in db_xref
- *
- * Revision 5.32  1996/10/30  16:52:36  tatiana
- * SeqIdFindBest added in PrintSourceFeat
- *
- * Revision 5.31  1996/10/25  22:11:19  tatiana
- * NoteCmp changed
- *
- * Revision 5.30  1996/10/24  20:40:12  tatiana
- * a bug fixed in AddDBXref()
- *
- * Revision 5.29  1996/10/18  21:37:22  tatiana
- * a bug fixed in NoteCmp
- *
- * Revision 5.28  1996/10/09  15:15:00  tatiana
- * Take the main protein ONLY (not sig_peptide mat_peptide)
- * to make CDS comments
- *
- * Revision 5.27  1996/09/25  18:05:45  tatiana
- * SEQFEAT_COMMENT becomes misc_feature
- *
- * Revision 5.26  1996/09/18  20:41:26  kans
- * changed uninitialized variable names to correct names, removed unused
- * variable
- *
- * Revision 5.25  1996/09/18  20:21:27  tatiana
- * NoteCmp added to ComposeNoteFromNoteStruct to check for identical notes
- *
- * Revision 5.24  1996/09/17  14:59:04  tatiana
- * virion and transl_except added
- *
- * Revision 5.23  1996/09/12  17:52:28  tatiana
- * a bug fixed in PrintSourceFeat
- *
- * Revision 5.22  1996/09/06  14:58:00  tatiana
- * clean sfp_out at the end of PrintSourceFeat and PrintNAFeatByNumber
- *
- * Revision 5.21  1996/09/04  13:40:17  tatiana
- * a  bug fixed in GetDotTRNA
- *
- * Revision 5.19  1996/09/03  19:51:30  tatiana
- * extra_loc added
- *
- * Revision 5.18  1996/08/16  20:32:23  tatiana
- * for ifp->key StringSave is used not StringCpy
- *
- * Revision 5.17  1996/08/12  16:36:40  tatiana
- * ErrPostEx changed to ErrPostStr
- *
- * Revision 5.16  1996/08/06  20:30:46  kans
- * SeqIdFindBest called to handle local IDs and genbank IDs coexisting
- *
- * Revision 5.15  1996/08/02  21:41:23  tatiana
- * turned off metho conceptual transl by author
- *
- * Revision 5.14  1996/07/30  17:28:07  kans
- * ParFlat_... arrays now external in header file
- *
- * Revision 5.13  1996/07/30  16:34:09  tatiana
- * minor change in PrintSourcefeat
- *
- * Revision 5.12  1996/07/29  19:46:14  tatiana
- * GBQual_names changed to use a structureGBQual_names changed to use a structure
- *
- * Revision 5.11  1996/07/23  22:33:40  tatiana
- * prot feats in genpept (piptides)
- *
- * Revision 5.10  1996/07/22  22:07:21  tatiana
- * a bug fixed in DoTRNAQual
- *
- * Revision 5.9  1996/07/15  18:07:10  tatiana
- * minor changes in PrintSourceFeat to show 'unknown' in debug mode
- *
- * Revision 5.8  1996/07/12  20:38:22  tatiana
- * concept_transl_a supressed
- *
- * Revision 5.7  1996/07/12  20:11:49  tatiana
- * DotRNAQuals() changed
- *
- * Revision 5.6  1996/07/11  14:58:27  tatiana
- * product in tRNA
- *
- * Revision 5.5  1996/07/09  16:31:34  tatiana
- * a bug fixed in PrintNAFeatByNumber
- *
- * Revision 5.4  1996/07/02  18:09:17  tatiana
- * don't print duplicated features (PrintNAFeatByNumber)
- *
- * Revision 5.3  1996/06/14  18:03:56  tatiana
- * GetNAFeatKey change
- *
- * Revision 5.2  1996/06/11  15:35:04  tatiana
- * make GetGeneticCode static and get_prot_feats non-static
- *
- * Revision 5.1  1996/05/31  18:01:24  tatiana
- * check for /pseudo in CdRegion added
- *
- * Revision 4.35  1996/05/21  21:02:03  tatiana
- * a bug fixed in location[] size in PrintSourceFeat()
- *
- * Revision 4.34  1996/05/16  20:58:09  tatiana
- * GetCdregionGeneXrefInfo changed to Boolean
- *
- * Revision 4.33  1996/04/25  14:55:33  kans
- * protect against biosource subsource subtype of 255 (other) or bad values
- *
- * Revision 4.32  1996/04/15  14:36:49  tatiana
- * memory leaks cleaning
- *
- * Revision 4.31  1996/04/08  21:53:56  tatiana
- * change in www_featloc
- *
- * Revision 4.30  1996/04/05  17:43:36  ostell
- * added quickie patch for overrun of buf[30] when called by
- * www_featloc()
- *
- * Revision 4.29  1996/03/25  15:20:19  tatiana
- * add html symbols
- *
- * Revision 4.28  1996/03/19  23:58:27  tatiana
- * print activity in CDS
- *
- * Revision 4.27  1996/03/12  21:36:32  tatiana
- * 'serotype' added to orgmod_subtype array
- *
- * Revision 4.26  1996/02/28  04:53:06  ostell
- * changes to support segmented master seeuquences
- *
- * Revision 4.25  1996/02/26  00:46:18  ostell
- * removed unused local variables and integer size mismatch fusses
- *
- * Revision 4.24  1996/02/18  21:16:48  tatiana
- * memory leaks cleaned up
- *
- * Revision 4.23  1996/02/16  16:22:32  tatiana
- * a bug fixed in ConvertToNAImpFeat
- *
- * Revision 4.22  1996/02/15  15:52:18  tatiana
- * Gather for temp loaded items and sortin features within entity addded
- *
- * Revision 4.21  1996/01/29  22:34:42  tatiana
- * mainly PID changes
- *
- * Revision 4.20  1995/12/20  22:38:02  tatiana
- * gene xrefs to db_xref
- *
- * Revision 4.19  1995/12/15  02:47:01  ostell
- * added protection so that GatherProductGeneInfo does not gather if protein
- * bioseq not already in memory
- *
- * Revision 4.18  1995/12/13  16:31:36  tatiana
- * anticodon added to new tRNA slot
- *
- * Revision 4.17  1995/12/04  23:01:16  tatiana
- * take starin from OrgRef.mod in PrintSourceFeat()
- *
- * Revision 4.16  1995/11/28  15:19:46  tatiana
- * GetPID fixed
- *
- * Revision 4.15  1995/11/22  18:59:42  tatiana
- * a bug fixed in orphan genes printing
- *
- * Revision 4.14  1995/11/17  21:49:19  tatiana
- * hot link to genetic code added
- *
- * Revision 4.13  1995/11/17  21:28:35  kans
- * asn2ff now uses gather (Tatiana)
- *
- * Revision 4.4  1995/08/18  22:18:31  tatiana
- * a bug fix
- *
- * Revision 4.1  1995/08/01  14:51:29  tatiana
- * change SeqIdPrint to SeqIdWrite
- *
- * Revision 1.65  1995/07/17  19:33:20  kans
- * parameters combined into Asn2ffJobPtr structure
- *
- * Revision 1.61  1995/06/19  21:40:02  kans
- * Tatiana's first major reorganization, moving printing, adding HTML
- *
- * Revision 1.60  1995/05/19  21:25:06  kans
- * no longer fetches CDS protein product causing Entrez disc swap
- *
- * Revision 1.59  1995/05/15  21:46:05  ostell
- * added Log line
- *
 *
 **************************************/
 #include <asn2ffp.h>
@@ -3709,7 +3120,7 @@ NLM_EXTERN void Add_trid (Asn2ffJobPtr ajp, SeqFeatPtr sfp_out)
 
 {
 	ImpFeatPtr ifp;
-	Int4 gi = -1;
+	BIG_ID gi = -1;
 	SeqIdPtr sip, newid=NULL;
 	ValNodePtr product;
 	Char buf[MAX_ACCESSION_LEN+5];
@@ -3728,7 +3139,7 @@ NLM_EXTERN void Add_trid (Asn2ffJobPtr ajp, SeqFeatPtr sfp_out)
 		if ((newid = GetSeqIdForGI(sip->data.intvalue)) != NULL) {
 			SeqIdWrite(newid, buf, PRINTID_TEXTID_ACC_VER, MAX_ACCESSION_LEN+1);
 		} else {
-			sprintf(buf, "%d", sip->data.intvalue);
+			sprintf(buf, "%ld", sip->data.intvalue);
 		}
 	} else {	
 		SeqIdWrite(sip, buf, PRINTID_TEXTID_ACC_VER, MAX_ACCESSION_LEN+1);
@@ -3748,7 +3159,7 @@ NLM_EXTERN void AddPID (Asn2ffJobPtr ajp, SeqFeatPtr sfp_out, Boolean is_NTorNG)
 
 {
 	ImpFeatPtr ifp;
-	Int4 gi = -1;
+	BIG_ID gi = -1;
 	SeqIdPtr sip, new_id=NULL;
 	ValNodePtr product, vnp;
 	BioseqPtr p_bsp = NULL;
@@ -3771,7 +3182,7 @@ NLM_EXTERN void AddPID (Asn2ffJobPtr ajp, SeqFeatPtr sfp_out, Boolean is_NTorNG)
 				SeqIdWrite(new_id, buf, PRINTID_TEXTID_ACC_VER, MAX_ACCESSION_LEN+1);
 				SeqIdFree(new_id); /*** need to free it !!! (EY) ***/
 			} else {
-				sprintf(buf, "%d", sip->data.intvalue);
+				sprintf(buf, "%ld", sip->data.intvalue);
 			}
 			sfp_out->qual = AddGBQual(sfp_out->qual, "protein_id", buf);
 		} else if ((p_bsp = BioseqFind(sip)) != NULL) {
@@ -4630,7 +4041,7 @@ NLM_EXTERN GBQualPtr AddBioSourceToGBQual (Asn2ffJobPtr ajp, NoteStructPtr nsp,
 *	This code prints out an ImpFeat in GenBank and HTML format.
 *
 ****************************************************************************/
-NLM_EXTERN Int2 PrintImpFeatEx (Asn2ffJobPtr ajp, BioseqPtr bsp, SeqFeatPtr sfp, Int4 gi, Int2 entityID, Uint4 itemID)
+NLM_EXTERN Int2 PrintImpFeatEx (Asn2ffJobPtr ajp, BioseqPtr bsp, SeqFeatPtr sfp, BIG_ID gi, Int2 entityID, Uint4 itemID)
 {
 	CharPtr flatloc_ptr, key, loc;
 	GBQualPtr gbqp;