diff options
| author | Aaron M. Ucko <ucko@debian.org> | 2005-03-24 18:46:06 +0000 |
|---|---|---|
| committer | Aaron M. Ucko <ucko@debian.org> | 2005-03-24 18:46:06 +0000 |
| commit | 63b21a5f6060202b6d5c888d203e78ba871abcc2 (patch) | |
| tree | 03fb3548fb6902e89097d17630f910e220b420a8 /algo/blast/api/blast_input.h | |
| parent | d5cd243f986e2366bd1dfe5f923d2ce7e1002f93 (diff) | |
Load ncbi (6.1.20041020) into ncbi-tools6/branches/upstream/current.
Diffstat (limited to 'algo/blast/api/blast_input.h')
| -rw-r--r-- | algo/blast/api/blast_input.h | 19 |
1 files changed, 11 insertions, 8 deletions
diff --git a/algo/blast/api/blast_input.h b/algo/blast/api/blast_input.h index 2db0736d..5025ee76 100644 --- a/algo/blast/api/blast_input.h +++ b/algo/blast/api/blast_input.h @@ -1,4 +1,4 @@ -/* $Id: blast_input.h,v 1.10 2003/12/03 17:30:25 dondosha Exp $ +/* $Id: blast_input.h,v 1.13 2004/07/14 13:17:38 madden Exp $ * =========================================================================== * * PUBLIC DOMAIN NOTICE @@ -31,7 +31,7 @@ Author: Ilya Dondoshansky Contents: Reading FASTA sequences for BLAST -$Revision: 1.10 $ +$Revision: 1.13 $ ******************************************************************************/ @@ -54,19 +54,22 @@ extern "C" { * @param query_is_na Are sequences nucleotide (or protein)? [in] * @param strand Which strands should SeqLocs contain (0 for protein, * 1 for plus, 2 for minus, 3 for both)? [in] + * @param max_total_length length of query sequences to be returned [in] * @param from Starting offset in query location [in] * @param to Ending offset in query location (-1 for end of sequence) [in] * @param lcase_mask The lower case masking locations (no lower case masking * if NULL [out] * @param query_slp List of query SeqLocs [out] - * @param ctr_start Number from which to start counting local ids [in] + * @param ctr Number from which to start counting local ids, will be + * incremented by number of queries read in [in|out] * @param num_queries Number of sequences read [out] - * @return Have all sequences been read? + * @param believe_query parse FASTA seqid if TRUE [in] + * @return number of letters read, negative number on error. */ -Boolean -BLAST_GetQuerySeqLoc(FILE *infp, Boolean query_is_na, Uint1 strand, - Int4 from, Int4 to, BlastMaskLoc** lcase_mask, SeqLocPtr* query_slp, Int4 ctr_start, - Int4* num_queries); +Int4 +BLAST_GetQuerySeqLoc(FILE *infp, Boolean query_is_na, Uint1 strand, Int4 max_total_length, + Int4 from, Int4 to, BlastMaskLoc** lcase_mask, SeqLocPtr* query_slp, Int2Ptr ctr, + Int4* num_queries, Boolean believe_query); /** Given a file containing sequence(s) in fasta format, * read a sequence and fill out a BLAST_SequenceBlk structure. |