diff options
Diffstat (limited to 'algo/blast/core/blast_setup.c')
| -rw-r--r-- | algo/blast/core/blast_setup.c | 29 |
1 files changed, 17 insertions, 12 deletions
diff --git a/algo/blast/core/blast_setup.c b/algo/blast/core/blast_setup.c index 6cda6a1e..3e478246 100644 --- a/algo/blast/core/blast_setup.c +++ b/algo/blast/core/blast_setup.c @@ -1,5 +1,5 @@ static char const rcsid[] = - "$Id: blast_setup.c,v 1.62 2003/10/27 23:02:11 dondosha Exp $"; + "$Id: blast_setup.c,v 1.65 2004/01/07 21:44:36 dondosha Exp $"; /* =========================================================================== * * PUBLIC DOMAIN NOTICE @@ -32,7 +32,7 @@ Author: Tom Madden Contents: Utilities initialize/setup BLAST. -$Revision: 1.62 $ +$Revision: 1.65 $ ******************************************************************************/ @@ -394,7 +394,7 @@ Int2 BLAST_MainSetUp(Uint1 program_number, const BlastHitSavingOptions * hit_options, BLAST_SequenceBlk * query_blk, BlastQueryInfo * query_info, - BlastSeqLoc ** lookup_segments, BlastMask * *filter_out, + BlastSeqLoc ** lookup_segments, BlastMaskLoc * *filter_out, BlastScoreBlk * *sbpp, Blast_Message * *blast_message) { BlastScoreBlk *sbp; @@ -407,10 +407,10 @@ Int2 BLAST_MainSetUp(Uint1 program_number, BlastSeqLoc *filter_slp = NULL; /* SeqLocPtr computed for filtering. */ BlastSeqLoc *filter_slp_combined; /* Used to hold combined SeqLoc's */ BlastSeqLoc *loc; /* Iterator variable */ - BlastMask *last_filter_out = NULL; + BlastMaskLoc *last_filter_out = NULL; Uint1 *buffer; /* holds sequence for plus strand or protein. */ Boolean reverse; /* Indicates the strand when masking filtered locations */ - BlastMask *mask_slp, *next_mask_slp; /* Auxiliary locations for lower + BlastMaskLoc *mask_slp, *next_mask_slp; /* Auxiliary locations for lower case masks */ Int4 context_offset; Boolean no_forward_strand; @@ -502,15 +502,20 @@ Int2 BLAST_MainSetUp(Uint1 program_number, /* Attach the lower case mask locations to the filter locations and combine them */ - if (filter_slp && mask_slp) { - for (loc = filter_slp; loc->next; loc = loc->next) ; - loc->next = mask_slp->loc_list; + if (mask_slp) { + if (filter_slp) { + for (loc = filter_slp; loc->next; loc = loc->next); + loc->next = mask_slp->loc_list; + } else { + filter_slp = mask_slp->loc_list; + } /* Set location list to NULL, to allow safe memory deallocation */ mask_slp->loc_list = NULL; } filter_slp_combined = NULL; - CombineMaskLocations(filter_slp, &filter_slp_combined); + CombineMaskLocations(filter_slp, &filter_slp_combined, 0); + filter_slp = BlastSeqLocFree(filter_slp); /* NB: for translated searches filter locations are returned in @@ -520,10 +525,10 @@ Int2 BLAST_MainSetUp(Uint1 program_number, if (filter_slp_combined) { if (!last_filter_out) { last_filter_out = *filter_out = - (BlastMask *) calloc(1, sizeof(BlastMask)); + (BlastMaskLoc *) calloc(1, sizeof(BlastMaskLoc)); } else { last_filter_out->next = - (BlastMask *) calloc(1, sizeof(BlastMask)); + (BlastMaskLoc *) calloc(1, sizeof(BlastMaskLoc)); last_filter_out = last_filter_out->next; } last_filter_out->index = index; @@ -561,7 +566,7 @@ Int2 BLAST_MainSetUp(Uint1 program_number, /* Free the filtering locations if masking done for lookup table only */ if (mask_at_hash) { - *filter_out = BlastMaskFree(*filter_out); + *filter_out = BlastMaskLocFree(*filter_out); } /* Get "ideal" values if the calculated Karlin-Altschul params bad. */ |