/dports/biology/ncbi-toolkit/ncbi/algo/blast/composition_adjustment/ |
H A D | redo_alignment.c | 96 int hspcnt; /**< number of alignment in member 218 s_DistinctAlignmentsSort(BlastCompo_Alignment ** plist, int hspcnt) in s_DistinctAlignmentsSort() 646 int hspcnt, int border, int sequence_length, in s_WindowsFromTranslatedAligns() 874 BlastCompo_QueryInfo * query_info, int hspcnt, in s_WindowsFromAligns() 1103 BlastCompo_Alignment * incoming_aligns, int hspcnt, in Blast_RedoOneMatch() 1313 int hspcnt, in Blast_RedoOneMatchSmithWaterman()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/composition_adjustment/ |
H A D | redo_alignment.c | 96 int hspcnt; /**< number of alignment in member 218 s_DistinctAlignmentsSort(BlastCompo_Alignment ** plist, int hspcnt) in s_DistinctAlignmentsSort() 646 int hspcnt, int border, int sequence_length, in s_WindowsFromTranslatedAligns() 874 BlastCompo_QueryInfo * query_info, int hspcnt, in s_WindowsFromAligns() 1103 BlastCompo_Alignment * incoming_aligns, int hspcnt, in Blast_RedoOneMatch() 1313 int hspcnt, in Blast_RedoOneMatchSmithWaterman()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/composition_adjustment/ |
H A D | redo_alignment.c | 96 int hspcnt; /**< number of alignment in member 218 s_DistinctAlignmentsSort(BlastCompo_Alignment ** plist, int hspcnt) in s_DistinctAlignmentsSort() 646 int hspcnt, int border, int sequence_length, in s_WindowsFromTranslatedAligns() 874 BlastCompo_QueryInfo * query_info, int hspcnt, in s_WindowsFromAligns() 1103 BlastCompo_Alignment * incoming_aligns, int hspcnt, in Blast_RedoOneMatch() 1313 int hspcnt, in Blast_RedoOneMatchSmithWaterman()
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | hspfilter_collector.c | 241 Int4 hspcnt; in s_BlastHSPCollectorRun_RPS() local
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H A D | link_hsps.c | 1508 s_LinkedHSPSetArraySetUp(BlastHSP** hsp_array, Int4 hspcnt, in s_LinkedHSPSetArraySetUp() 1543 s_LinkedHSPSetArrayCleanUp(BlastLinkedHSPSet** link_hsp_array, Int4 hspcnt) in s_LinkedHSPSetArrayCleanUp() 1567 s_LinkedHSPSetArrayIndexQueryEnds(BlastLinkedHSPSet** hsp_array, Int4 hspcnt, in s_LinkedHSPSetArrayIndexQueryEnds() 1624 Int4 hspcnt, index, index1; in s_BlastUnevenGapLinkHSPs() local
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H A D | blast_hits.h | 158 Int4 hspcnt; /**< Number of HSPs saved */ member
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H A D | blast_hits.c | 1732 Int4 hspcnt; in Blast_HSPListSaveHSP() local 2186 Int4 hspcnt; /* total number of HSP's to iterate over. */ in Blast_HSPListPurgeNullHSPs() local 2504 Int4 index, context, hspcnt; in Blast_HSPListReevaluateUngapped() local 3716 int hspcnt; in s_TrimResultsByTotalHSPLimitEx() local
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H A D | blast_kappa.c | 216 s_HitlistReapContained(BlastHSP * hsp_array[], Int4 * hspcnt) in s_HitlistReapContained() 760 BlastHSP * hsp_array[], Int4 hspcnt, in s_ResultHspToDistinctAlign()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | hspfilter_collector.c | 241 Int4 hspcnt; in s_BlastHSPCollectorRun_RPS() local
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H A D | link_hsps.c | 1508 s_LinkedHSPSetArraySetUp(BlastHSP** hsp_array, Int4 hspcnt, in s_LinkedHSPSetArraySetUp() 1543 s_LinkedHSPSetArrayCleanUp(BlastLinkedHSPSet** link_hsp_array, Int4 hspcnt) in s_LinkedHSPSetArrayCleanUp() 1567 s_LinkedHSPSetArrayIndexQueryEnds(BlastLinkedHSPSet** hsp_array, Int4 hspcnt, in s_LinkedHSPSetArrayIndexQueryEnds() 1624 Int4 hspcnt, index, index1; in s_BlastUnevenGapLinkHSPs() local
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H A D | blast_hits.c | 1757 Int4 hspcnt; in Blast_HSPListSaveHSP() local 2223 Int4 hspcnt; /* total number of HSP's to iterate over. */ in Blast_HSPListPurgeNullHSPs() local 2612 Int4 index, context, hspcnt; in Blast_HSPListReevaluateUngapped() local 3823 int hspcnt; in s_TrimResultsByTotalHSPLimitEx() local
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H A D | blast_kappa.c | 224 s_HitlistReapContained(BlastHSP * hsp_array[], Int4 * hspcnt) in s_HitlistReapContained() 770 BlastHSP * hsp_array[], Int4 hspcnt, in s_ResultHspToDistinctAlign()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | hspfilter_collector.c | 241 Int4 hspcnt; in s_BlastHSPCollectorRun_RPS() local
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H A D | link_hsps.c | 1508 s_LinkedHSPSetArraySetUp(BlastHSP** hsp_array, Int4 hspcnt, in s_LinkedHSPSetArraySetUp() 1543 s_LinkedHSPSetArrayCleanUp(BlastLinkedHSPSet** link_hsp_array, Int4 hspcnt) in s_LinkedHSPSetArrayCleanUp() 1567 s_LinkedHSPSetArrayIndexQueryEnds(BlastLinkedHSPSet** hsp_array, Int4 hspcnt, in s_LinkedHSPSetArrayIndexQueryEnds() 1624 Int4 hspcnt, index, index1; in s_BlastUnevenGapLinkHSPs() local
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H A D | blast_hits.c | 1757 Int4 hspcnt; in Blast_HSPListSaveHSP() local 2223 Int4 hspcnt; /* total number of HSP's to iterate over. */ in Blast_HSPListPurgeNullHSPs() local 2612 Int4 index, context, hspcnt; in Blast_HSPListReevaluateUngapped() local 3823 int hspcnt; in s_TrimResultsByTotalHSPLimitEx() local
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H A D | blast_kappa.c | 224 s_HitlistReapContained(BlastHSP * hsp_array[], Int4 * hspcnt) in s_HitlistReapContained() 770 BlastHSP * hsp_array[], Int4 hspcnt, in s_ResultHspToDistinctAlign()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/ |
H A D | blast_hits.h | 158 Int4 hspcnt; /**< Number of HSPs saved */ member
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
H A D | blast_hits.h | 158 Int4 hspcnt; /**< Number of HSPs saved */ member
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | blastutl.c | 4569 Int4 hspcnt, index, index1, index2; in BioseqBlastEngineCore() local 7831 BLASTResultHitlistNew(Int4 hspcnt) in BLASTResultHitlistNew() 8717 …4 subject_length, GapAlignBlkPtr gap_align, BLAST_HSPPtr *hsp_array, Int4Ptr hspcnt, Int4Ptr hspcn… in BlastNtGappedScoreInternal() 8875 BlastHitRangeLoad (BlastSearchBlkPtr search, BLAST_HSPPtr *hsp_array, Int4 hspcnt, BlastHitRangePtr… in BlastHitRangeLoad() 8938 void BLASTCheckHSPInclusion(BLAST_HSPPtr *hsp_array, Int4 hspcnt, in BLASTCheckHSPInclusion() 9578 Int4 hspcnt=0, new_hspcnt=0, hspset_cnt_old; in SumBlastGetGappedAlignmentEx() local 9728 Int4 hspcnt=0, new_hspcnt=0; in BlastGetGapAlgnTbck() local 10422 HspArrayPurge (BLAST_HSPPtr PNTR hsp_array, Int4 hspcnt, Boolean clear_num) in HspArrayPurge() 10482 Int4 hspcnt, hspmax, high_index, low_index; in BlastSaveCurrentHsp() local 10615 Int4 hspcnt, hspmax, index, new_index, high_index, old_index, low_index; in BlastNtSaveCurrentHspGapped() local [all …]
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H A D | blastool.c | 3575 Int4 begin, end, hspcnt, query_length; in BlastInsertList2Heap() local 3670 Int4 begin, end, i, hspcnt, query_length; in BlastFreeHeap() local 4588 Int4 hspcnt, number, numseg; in BlastPrintAlignInfo() local 5464 Int4 index, hspcnt, index1, q_overlap; in BlastClusterHitsFromSeqAlign() local 5667 Int4 length,hitlist_count,sequence_length,index,index1,total_num_hsp=0,hspcnt; in BLASTPostSearchLogic() local
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H A D | rpsutil.c | 881 Int4 hspcnt, index; in RPSUpdateCoordinates() local 981 Int4 i, index, hspcnt, seq_no; in RPSExtractNewResult() local 1182 Int4 hspcnt, index /* , index1 */ ; in RPSCalcEValue() local
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H A D | blast.c | 2949 Int4 context, hspcnt, hspcnt_max, index, index1, status; in BlastReevaluateWithAmbiguities() local 6466 Int4 index, hspcnt; in BlastReapPartialHitlistByEvalue() local 9781 Int4 hspcnt, index, index1, new_index, old_index, low_index, high_index; in BlastSaveCurrentHitlist() local 10776 BLAST_HSPArrayIndexQueryEnds(BLAST_HSPPtr* hsp_array, Int4 hspcnt, in BLAST_HSPArrayIndexQueryEnds() 10993 BLAST_HSPArraySwapSequences(BLAST_HSPPtr PNTR hsp_array, Int4 hspcnt) in BLAST_HSPArraySwapSequences() 11017 BLAST_HSPPtr PNTR hsp_array, Int4 hspcnt) in new_link_hsps_setup() 11071 Int4 hspcnt, index, index1; in new_link_hsps() local
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H A D | mblast.c | 2829 Int4 index, i, hspcnt, buf_len=0; in MegaBlastGappedAlign() local 3760 Int4 index, context, hspcnt, buf_len=0; in MegaBlastReevaluateWithAmbiguities() local 4019 Int4 hspcnt, index, index1, new_index, old_index, low_index, high_index; in MegaBlastSaveCurrentHitlist() local
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H A D | xmlblast.c | 1444 Int4 hspcnt = 0, last_seg, i; in GetHspFromSeqAlign() local
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/dports/biology/ncbi-toolkit/ncbi/demo/ |
H A D | blastclust.c | 664 Int4 id1, id2, root1, root2, hspcnt; in PrintNeighbors() local
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