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/dports/biology/ncbi-toolkit/ncbi/biostruc/
H A Dcorematx.h101 FloatHiPtrPtr LIBCALL FHMatrix (Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch);
102 FloatLoPtrPtr LIBCALL FLMatrix (Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch);
103 Int2PtrPtr LIBCALL I2Matrix (Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch);
104 Int4PtrPtr LIBCALL I4Matrix (Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch);
111 Int4 oldcl, Int4 oldch, Int4 newrl, Int4 newcl);
127 FloatLoPtrPtrPtr LIBCALL FL3Matrix (Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch, Int4 ndl,
139 FloatLoPtr *matrix (Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch);
140 FloatHiPtr *dmatrix (Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch);
141 Int4Ptr *imatrix (Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch);
155 Int4 oldcl, Int4 oldch, Int4 newrl, Int4 newcl);
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H A Dcorematx.c240 FloatLoPtrPtr LIBCALL FLMatrix(Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch) in FLMatrix()
269 FloatHiPtrPtr LIBCALL FHMatrix(Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch) in FHMatrix()
298 Int2PtrPtr LIBCALL I2Matrix(Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch) in I2Matrix()
326 Int4PtrPtr LIBCALL I4Matrix(Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch) in I4Matrix()
354 Int4 oldcl, Int4 oldch, Int4 newrl, Int4 newcl) in FLSubmatrix()
553 FloatLoPtrPtrPtr LIBCALL FL3Matrix(Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch, Int4 ndl, in FL3Matrix()
649 FloatLoPtr *matrix(Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch) in matrix()
654 FloatHiPtr *dmatrix(Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch) in dmatrix()
659 Int4Ptr *imatrix(Int4 nrl, Int4 nrh, Int4 ncl, Int4 nch) in imatrix()
716 Int4 oldcl, Int4 oldch, Int4 newrl, Int4 newcl) in submatrix()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/gumbel_params/
H A Dsls_alp.hpp84 Int4 d_M;
295 Int4 d_HS_ij_pred;
296 Int4 d_HI_ij_pred;
297 Int4 d_HD_ij_pred;
298 Int4 d_H_ij_pred;
300 Int4 d_HS_ij_next;
301 Int4 d_HI_ij_next;
303 Int4 d_H_ij_next;
309 Int4 d_M;
311 Int4 d_nalp;
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H A Dsls_alp_sim.hpp65 Int4 d_nalp;
72 Int4 d_alp_number;
97 Int4 ind1_,
98 Int4 ind2_,
111 Int4 ind1_,
112 Int4 ind2_,
123 Int4 nalp_,
126 Int4 ind1_,
127 Int4 ind2_,
236 Int4 &i_,
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/
H A Dblast_aalookup.h157 Int4 BlastAaLookupTableNew(const LookupTableOptions* opt,
181 Int4 ** matrix,
184 Int4 query_bias);
206 Int4 query_offsets[COMPRESSED_HITS_PER_OVERFLOW_CELL];
212 Int4 query_offsets[COMPRESSED_HITS_PER_BACKBONE_CELL-1];
250 Int4 curr_overflow_bank; /**< current bank to fill-up */
303 static NCBI_INLINE Int4 s_ComputeCompressedIndex(Int4 wordsize, in s_ComputeCompressedIndex()
306 Int4* skip, in s_ComputeCompressedIndex()
309 Int4 i; in s_ComputeCompressedIndex()
310 Int4 index = 0; in s_ComputeCompressedIndex()
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H A Dblast_nalookup.h56 Int4 approx_table_entries, Int4 query_length,
57 Int4 *lut_width);
93 Int4 BlastSmallNaLookupTableNew(BLAST_SequenceBlk* query,
98 Int4 lut_width);
169 Int4 BlastNaLookupTableNew(BLAST_SequenceBlk* query,
174 Int4 lut_width);
289 Int4 approx_table_entries,
290 Int4 lut_width,
543 Int4 index; in ComputeDiscontiguousIndex()
601 Int4* pv_counts, Int4 words_per_bit);
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H A Dblast_stat.h86 Int4 N;
398 Int4 gap_extend, Int4 reward, Int4 penalty,
497 double BLAST_SpougeStoE (Int4 S, Blast_KarlinBlk* kbp, Blast_GumbelBlk* gbp, Int4 qlen, Int4 slen);
507 Int4 BLAST_SpougeEtoS (double E, Blast_KarlinBlk* kbp, Blast_GumbelBlk* gbp, Int4 qlen, Int4 slen);
597 Int4 query_length, Int4 subject_length,
626 Int4 query_length, Int4 subject_length,
644 Int4 query_length, Int4 subject_length,
680 Boolean BLAST_CheckRewardPenaltyScores(Int4 reward, Int4 penalty);
712 Int2 Blast_GetNuclAlphaBeta(Int4 reward, Int4 penalty, Int4 gap_open,
779 Int4
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_aalookup.h157 Int4 BlastAaLookupTableNew(const LookupTableOptions* opt,
181 Int4 ** matrix,
184 Int4 query_bias);
206 Int4 query_offsets[COMPRESSED_HITS_PER_OVERFLOW_CELL];
212 Int4 query_offsets[COMPRESSED_HITS_PER_BACKBONE_CELL-1];
250 Int4 curr_overflow_bank; /**< current bank to fill-up */
303 static NCBI_INLINE Int4 s_ComputeCompressedIndex(Int4 wordsize, in s_ComputeCompressedIndex()
306 Int4* skip, in s_ComputeCompressedIndex()
309 Int4 i; in s_ComputeCompressedIndex()
310 Int4 index = 0; in s_ComputeCompressedIndex()
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H A Dblast_nalookup.h56 Int4 approx_table_entries, Int4 query_length,
57 Int4 *lut_width);
93 Int4 BlastSmallNaLookupTableNew(BLAST_SequenceBlk* query,
98 Int4 lut_width);
169 Int4 BlastNaLookupTableNew(BLAST_SequenceBlk* query,
174 Int4 lut_width);
289 Int4 approx_table_entries,
290 Int4 lut_width,
543 Int4 index; in ComputeDiscontiguousIndex()
601 Int4* pv_counts, Int4 words_per_bit);
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H A Dblast_stat.h86 Int4 N;
398 Int4 gap_extend, Int4 reward, Int4 penalty,
497 double BLAST_SpougeStoE (Int4 S, Blast_KarlinBlk* kbp, Blast_GumbelBlk* gbp, Int4 qlen, Int4 slen);
507 Int4 BLAST_SpougeEtoS (double E, Blast_KarlinBlk* kbp, Blast_GumbelBlk* gbp, Int4 qlen, Int4 slen);
597 Int4 query_length, Int4 subject_length,
626 Int4 query_length, Int4 subject_length,
644 Int4 query_length, Int4 subject_length,
680 Boolean BLAST_CheckRewardPenaltyScores(Int4 reward, Int4 penalty);
712 Int2 Blast_GetNuclAlphaBeta(Int4 reward, Int4 penalty, Int4 gap_open,
779 Int4
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H A Djumper.h63 Int4 num_ops;
96 Int4 num_edits;
123 Int4 gap_open, Int4 gap_extend,
138 Int4 query_length, Int4 subject_length,
139 Int4 query_start, Int4 subject_start,
154 Int4 width;
179 Int4 word;
180 Int4 from;
181 Int4 to;
184 Int4 num_words;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/
H A Dblast_aalookup.h157 Int4 BlastAaLookupTableNew(const LookupTableOptions* opt,
181 Int4 ** matrix,
184 Int4 query_bias);
206 Int4 query_offsets[COMPRESSED_HITS_PER_OVERFLOW_CELL];
212 Int4 query_offsets[COMPRESSED_HITS_PER_BACKBONE_CELL-1];
250 Int4 curr_overflow_bank; /**< current bank to fill-up */
303 static NCBI_INLINE Int4 s_ComputeCompressedIndex(Int4 wordsize, in s_ComputeCompressedIndex()
306 Int4* skip, in s_ComputeCompressedIndex()
309 Int4 i; in s_ComputeCompressedIndex()
310 Int4 index = 0; in s_ComputeCompressedIndex()
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H A Dblast_nalookup.h56 Int4 approx_table_entries, Int4 query_length,
57 Int4 *lut_width);
93 Int4 BlastSmallNaLookupTableNew(BLAST_SequenceBlk* query,
98 Int4 lut_width);
169 Int4 BlastNaLookupTableNew(BLAST_SequenceBlk* query,
174 Int4 lut_width);
289 Int4 approx_table_entries,
290 Int4 lut_width,
543 Int4 index; in ComputeDiscontiguousIndex()
601 Int4* pv_counts, Int4 words_per_bit);
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H A Dblast_stat.h86 Int4 N;
398 Int4 gap_extend, Int4 reward, Int4 penalty,
497 double BLAST_SpougeStoE (Int4 S, Blast_KarlinBlk* kbp, Blast_GumbelBlk* gbp, Int4 qlen, Int4 slen);
507 Int4 BLAST_SpougeEtoS (double E, Blast_KarlinBlk* kbp, Blast_GumbelBlk* gbp, Int4 qlen, Int4 slen);
597 Int4 query_length, Int4 subject_length,
626 Int4 query_length, Int4 subject_length,
644 Int4 query_length, Int4 subject_length,
680 Boolean BLAST_CheckRewardPenaltyScores(Int4 reward, Int4 penalty);
712 Int2 Blast_GetNuclAlphaBeta(Int4 reward, Int4 penalty, Int4 gap_open,
779 Int4
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/dports/biology/ncbi-toolkit/ncbi/api/
H A Dalignmgr2.h283 Int4 n1;
284 Int4 n2;
285 Int4 n3;
286 Int4 n4;
387 Int4 n;
710 NLM_EXTERN Int4 AlnMgr2MapBioseqToSeqAlign(SeqAlignPtr sap, Int4 pos, Int4 row);
721 NLM_EXTERN Int4 AlnMgr2MapSeqAlignToBioseq(SeqAlignPtr sap, Int4 pos, Int4 row);
732 NLM_EXTERN Int4 AlnMgr2MapRowToRow(SeqAlignPtr sap, Int4 pos, Int4 row1, Int4 row2);
849 NLM_EXTERN void AlnMgr2ExtendToCoords(SeqAlignPtr sap, Int4 from, Int4 to, Int4 row);
973 NLM_EXTERN Int4 AlnMgr2MapBioseqToSeqAlignStdSeg(SeqAlignPtr sap, Int4 n, Int4 pos);
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H A Dsamutil.h292 Int4 Row;
374 NLM_EXTERN Boolean DDE_Select(DDE_StackPtr pStack, Int4 Row, Int4 Left, Int4 Right, Boolean Save);
375 NLM_EXTERN Boolean DDE_DeSelect(DDE_StackPtr pStack, Int4 Row, Int4 Left, Int4 Right, Boolean Save);
387 NLM_EXTERN Int4 DDE_GetAlignStop(DDE_InfoPtr pEditInfo, Int4 BlockIndex);
394 Int4 PNTR pOffset, Int4 PNTR pWidth);
413 NLM_EXTERN Int4 DDE_GetStart(MsaParaGPopListPtr pPopList, Int4 BlockIndex, Int4 Row);
414 NLM_EXTERN Int4 DDE_GetLen(MsaParaGPopListPtr pPopList, Int4 BlockIndex);
428 NLM_EXTERN Int4 DDE_GetInsertRow(DDE_InfoPtr pEditInfo, Int4 Row);
694 (Int4 NumSeqs, Int4 NumSegs, Boolean Strands);
720 NLM_EXTERN Int4 SAM_InRange(Int4 Position, Int4 From, Int4 To);
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/dports/biology/ncbi-toolkit/ncbi/desktop/
H A Ddotviewer.h99 Int4 to1;
101 Int4 to2;
120 Int4 n1;
121 Int4 n2;
122 Int4 n3;
123 Int4 n4;
124 Int4 n5;
134 Int4 q_start;
135 Int4 q_stop;
137 Int4 s_stop;
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/dports/biology/ncbi-toolkit/ncbi/tools/
H A Ddotseq.h94 Int4 length;
95 Int4 score;
96 Int4 rdmKey;
151 Int4 xstart;
152 Int4 xstop;
153 Int4 ystart;
154 Int4 ystop;
155 Int4 index;
182 …r mip, BioseqPtr qbsp, BioseqPtr sbsp, Int4 q_start, Int4 q_stop, Int4 s_start, Int4 s_stop, Int4 …
193 …r mip, BioseqPtr qbsp, BioseqPtr sbsp, Int4 word_size, Int4 tree_limit, Int4 qstart, Int4 qstop, I…
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H A Durktree.h86 extern Int4 GetDeepestLevelBranch (TreeNodePtr ptrNode, Int4 level);
93 extern Int4 SetNumberNode (TreeNodePtr ptrNode, Int4 nodenumber);
96 extern Int4 CountNodes (TreeNodePtr ptrNode, Int4 nodenumber);
97 extern Int4 CountNodesOnLevel (TreeNodePtr ptrNode, Int4 level);
116 Int4 Xdelta, Int4 Ydelta);
118 Int4 xcoord, Int4 ycoord,
119 Int4 xdelta, Int4 ydelta,
120 Int4 xroot, Int4 xparent,
121 Int4 xoffset, Int4 xoffmax);
130 extern void ShiftTree (TreeNodePtr ptrNode, Int4 sx, Int4 sy);
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H A Durkgraph.h111 Int4 startplot, Int4 stopplot);
117 Int4 start, Int4 stop,
135 Int4 graphtype, Int4 startplot,
136 Int4 window, Int4 graphpixelheight,
137 Int4 horiz_offset, Int4 vert_offset,
144 Int4 scale, Int4 trans,
145 Int4 startplot, Int4 stopplot,
146 Int4 horiz_offset, Int4 vert_offset);
148 extern SegmenT YscaleX (SegmenT seg, Int4 scale, Int4 trans,
151 Int4 startplot, Int4 stopplot,
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H A Dblastdef.h1441 Int4 last_hit;
1528 Int4 changed;
1544 Int4 num;
1556 Int4 num_ref;
1557 Int4 linked_to;
1573 Int4 maxsum1;
1579 Int4 qoffset,
1585 Int4 q_off;
1586 Int4 s_off;
1658 Int4 num_ref;
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H A Dspidey.h306 Int4 start;
307 Int4 n;
313 Int4 group;
386 Int4 i;
446 Int4 n1;
447 Int4 n2;
448 Int4 n3;
449 Int4 n4;
450 Int4 n5;
451 Int4 n6;
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Djumper.h65 Int4 num_ops;
98 Int4 num_edits;
125 Int4 gap_open, Int4 gap_extend,
141 Int4 query_start, Int4 subject_start,
156 Int4 width;
181 Int4 word;
182 Int4 from;
183 Int4 to;
186 Int4 num_words;
202 Int4 from, Int4 to);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Djumper.h65 Int4 num_ops;
98 Int4 num_edits;
125 Int4 gap_open, Int4 gap_extend,
141 Int4 query_start, Int4 subject_start,
156 Int4 width;
181 Int4 word;
182 Int4 from;
183 Int4 to;
186 Int4 num_words;
202 Int4 from, Int4 to);
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/dports/biology/diamond/diamond-2.0.13/src/lib/blast/
H A Dblast_stat.h84 Int4 N;
372 Int4 gap_extend, Int4 reward, Int4 penalty,
468 double BLAST_SpougeStoE (Int4 S, Blast_KarlinBlk* kbp, Blast_GumbelBlk* gbp, Int4 qlen, Int4 slen);
478 Int4 BLAST_SpougeEtoS (double E, Blast_KarlinBlk* kbp, Blast_GumbelBlk* gbp, Int4 qlen, Int4 slen);
568 Int4 query_length, Int4 subject_length,
597 Int4 query_length, Int4 subject_length,
615 Int4 query_length, Int4 subject_length,
651 bool BLAST_CheckRewardPenaltyScores(Int4 reward, Int4 penalty);
683 Int2 Blast_GetNuclAlphaBeta(Int4 reward, Int4 penalty, Int4 gap_open,
750 Int4
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