diff options
Diffstat (limited to 'network/id1arch/idfetch.c')
| -rw-r--r-- | network/id1arch/idfetch.c | 18 |
1 files changed, 13 insertions, 5 deletions
diff --git a/network/id1arch/idfetch.c b/network/id1arch/idfetch.c index ce439e7a..5d9afa05 100644 --- a/network/id1arch/idfetch.c +++ b/network/id1arch/idfetch.c @@ -25,6 +25,12 @@ * Author Karl Sirotkin * $Log: idfetch.c,v $ + Revision 1.29 2003/12/17 20:35:38 kans + initialize status, send NORMAL_STYLE to SeqEntrytoGnbk instead of 0 (also fixed in asn2gnbk), pass lookup flags + + Revision 1.28 2003/11/19 16:35:19 yaschenk + relaxing ranges for -g and -c + Revision 1.27 2003/03/28 18:48:39 yaschenk tuning ObjMgr, adding STREAM_SEQ_PORT_FIRST to SeqEntryToGnbk @@ -190,14 +196,14 @@ Args myargs[] = { 2 - get SeqIds\n\t\t\t\ 3 - get gi historyn (sequence change only)\n\t\t\t\ 4 - get gi revision history (any change to asn.1)\n", "0","0","4",TRUE,'i',ARG_INT,0.0,0,NULL}, - {"GI id for single Entity to dump" ,"0","0","99999999",TRUE,'g',ARG_INT,0.0,0,NULL}, + {"GI id for single Entity to dump" ,"0","0","999999999",TRUE,'g',ARG_INT,0.0,0,NULL}, {"File with list of gi's, accessions, accession.version's, fasta seqid's to dump",NULL,NULL,NULL,TRUE,'G',ARG_FILE_IN,0.0,0,NULL}, {"Max complexity:\t\ 0 - get the whole blob\n\t\t\t\ 1 - get the bioseq of interest\n\t\t\t\ 2 - get the minimal bioseq-set containing the bioseq of interest\n\t\t\t\ 3 - get the minimal nuc-prot containing the bioseq of interest\n\t\t\t\ -4 - get the minimal pub-set containing the bioseq of interest\n" ,"0","0","4",TRUE,'c',ARG_INT,0.0,0,NULL}, +4 - get the minimal pub-set containing the bioseq of interest\n" ,"0",NULL,NULL,TRUE,'c',ARG_INT,0.0,0,NULL}, {"flaTtened SeqId, format: \n \'type(name,accession,release,version)\'\n as \'5(HUMHBB)\' or \n type=accession, or \n type:number ", NULL,NULL,NULL,TRUE,'f',ARG_STRING,0.0,0,NULL}, {"Fasta style SeqId ENCLOSED IN QUOTES:\n\t\t\t\ @@ -857,7 +863,7 @@ static Boolean ProcessOneDocSum (Int4 num, Int4Ptr uids) static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex) { SeqEntryPtr sep=NULL; - Int4 status,gi_state; + Int4 status = 0,gi_state; SeqIdPtr sip_ret=NULL; SeqId si={SEQID_GI,0,0}; ID1SeqHistPtr ishp=NULL; @@ -991,7 +997,8 @@ static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex) if(!SeqEntryToFlat(sep, fp, GENBANK_FMT, RELEASE_MODE)){ #else AssignIDsInEntity(0,OBJ_SEQENTRY,sep); - if(!SeqEntryToGnbk(sep,NULL,GENBANK_FMT,ENTREZ_MODE,0,SHOW_CONTIG_FEATURES|ONLY_NEAR_FEATURES,STREAM_SEQ_PORT_FIRST,0,NULL,fp)){ + if(!SeqEntryToGnbk(sep,NULL,GENBANK_FMT,ENTREZ_MODE,0,SHOW_CONTIG_FEATURES|ONLY_NEAR_FEATURES, + LOOKUP_FAR_COMPONENTS|LOOKUP_FAR_LOCATIONS|LOOKUP_FAR_PRODUCTS|LOOKUP_FAR_HISTORY|STREAM_SEQ_PORT_FIRST,0,NULL,fp)){ #endif ErrPostEx(SEV_WARNING,0,0, "GenBank Format does not exist for this sequence "); @@ -1004,7 +1011,8 @@ static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex) if(!SeqEntryToFlat(sep, fp, GENPEPT_FMT, RELEASE_MODE)) #else AssignIDsInEntity(0,OBJ_SEQENTRY,sep); - if(!SeqEntryToGnbk(sep,NULL,GENPEPT_FMT,ENTREZ_MODE,0,SHOW_CONTIG_FEATURES|ONLY_NEAR_FEATURES,STREAM_SEQ_PORT_FIRST,0,NULL,fp)) + if(!SeqEntryToGnbk(sep,NULL,GENPEPT_FMT,ENTREZ_MODE,0,SHOW_CONTIG_FEATURES|ONLY_NEAR_FEATURES, + LOOKUP_FAR_COMPONENTS|LOOKUP_FAR_LOCATIONS|LOOKUP_FAR_PRODUCTS|LOOKUP_FAR_HISTORY|STREAM_SEQ_PORT_FIRST,0,NULL,fp)) #endif { ErrPostEx(SEV_WARNING,0,0, |