/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | blast_seg.c | 1637 s_DecrementSV(Int4* sv, Int4 class) in s_DecrementSV() 1640 Int4 svi; in s_DecrementSV() 1655 s_IncrementSV(Int4* sv, Int4 class) in s_IncrementSV() 1813 static Int4 s_FindLow(Int4 i, Int4 limit, double hicut, double* H) in s_FindLow() 1816 Int4 j; in s_FindLow() 1836 static Int4 s_FindHigh(Int4 i, Int4 limit, double hicut, double* H) in s_FindHigh() 1839 Int4 j; in s_FindHigh() 1868 s_LnPerm(const Int4* sv, Int4 window_length) in s_LnPerm() 1872 Int4 i; in s_LnPerm() 1893 s_LnAss(const Int4* sv, Int4 alphasize) in s_LnAss() [all …]
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H A D | phi_lookup.c | 56 s_FindPrefixAndSuffixPos(Int4* S, Int4 mask, Int4 mask2, Uint4* prefixPos, in s_FindPrefixAndSuffixPos() 140 static Int4 142 Int4 length, Int4 maxLength) in s_ExpandPattern() 146 Int4 k, t; /*loop indices*/ in s_ExpandPattern() 210 static Int4 213 Int4 i; /*loop index*/ in s_PackPattern() 268 Int4 s_NumOfOne(Int4 a) in s_NumOfOne() 270 Int4 returnValue; in s_NumOfOne() 286 s_PackVeryLongPattern(Int4 *inputPatternMasked, Int4 numPlacesInPattern, in s_PackVeryLongPattern() 728 Int4 array_size) in PHIBlastScanSubject() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | blast_seg.c | 1637 s_DecrementSV(Int4* sv, Int4 class) in s_DecrementSV() 1640 Int4 svi; in s_DecrementSV() 1655 s_IncrementSV(Int4* sv, Int4 class) in s_IncrementSV() 1813 static Int4 s_FindLow(Int4 i, Int4 limit, double hicut, double* H) in s_FindLow() 1816 Int4 j; in s_FindLow() 1836 static Int4 s_FindHigh(Int4 i, Int4 limit, double hicut, double* H) in s_FindHigh() 1839 Int4 j; in s_FindHigh() 1868 s_LnPerm(const Int4* sv, Int4 window_length) in s_LnPerm() 1872 Int4 i; in s_LnPerm() 1893 s_LnAss(const Int4* sv, Int4 alphasize) in s_LnAss() [all …]
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H A D | phi_lookup.c | 56 s_FindPrefixAndSuffixPos(Int4* S, Int4 mask, Int4 mask2, Uint4* prefixPos, in s_FindPrefixAndSuffixPos() 140 static Int4 142 Int4 length, Int4 maxLength) in s_ExpandPattern() 146 Int4 k, t; /*loop indices*/ in s_ExpandPattern() 210 static Int4 213 Int4 i; /*loop index*/ in s_PackPattern() 268 Int4 s_NumOfOne(Int4 a) in s_NumOfOne() 270 Int4 returnValue; in s_NumOfOne() 286 s_PackVeryLongPattern(Int4 *inputPatternMasked, Int4 numPlacesInPattern, in s_PackVeryLongPattern() 728 Int4 array_size) in PHIBlastScanSubject() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/gumbel_params/ |
H A D | njn_localmaxstatutil.hpp | 72 const Int4 *score_, // scores in increasing order 77 const Int4 *score_, // scores in increasing order 83 const Int4 *score_, // scores in increasing order 89 const Int4 *score_, // scores in increasing order 92 Int4 power_ = 1); // power 96 const Int4 *score_, // scores in increasing order 103 const Int4 *score_, // scores in increasing order 118 const Int4 *score_); // scores 123 const Int4 *score_); // scores 127 const Int4 *score_, // values [all …]
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H A D | sls_alp_regression.hpp | 81 Int4 n_partition_, 98 Int4 min_length_, 109 Int4 &k1_opt_, 110 Int4 &k2_opt_, 117 Int4 k_start_, 137 Int4 &k1_opt_, 138 Int4 &k2_opt_, 145 Int4 k_start_, 195 Int4 dim_, 200 Int4 dim, [all …]
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | mblast.h | 219 *callback)PROTO((Int4 done, 220 Int4 227 (LIBCALLBACK *callback)PROTO((Int4 done, Int4 230 Int4 gi_list_total, 236 int (LIBCALLBACK *callback)(Int4 done, Int4 positives), 250 int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), 262 Int4 264 Int4 q_start, Int4 s_start, Int4 length, 273 Int4 BinarySearchInt4 PROTO((Int4 n, Int4Ptr A, Int4 size)); 279 Int4 LIBCALL [all …]
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H A D | csim.c | 133 …qLocPtr loc2, CharPtr A, CharPtr B, Int4 M, Int4 N, Int4 K, Int4 nseq, FloatHi cut_off, Int2Ptr PN… 135 static void diff(CharPtr A, CharPtr B, Int4 M, Int4 N, Int4 tb, Int4 te, matrix value, scriptr s_pt… 136 static Int4 diff1(CharPtr A, CharPtr B, Int4 M, Int4 N, Int4 tb, Int4 te, Int4Ptr CC, Int4Ptr DD, I… 139 static Int4 addnode(Int4 c, Int4 ci, Int4 cj, Int4 i, Int4 j, Int4 K, listptr plist) ; 142 static void display(CharPtr A, CharPtr B, Int4 M, Int4 N, Int4Ptr S, Int4 AP, Int4 BP, Int4Ptr rec_… 463 …qLocPtr loc2, CharPtr A, CharPtr B, Int4 M, Int4 N, Int4 K, Int4 nseq, FloatHi cut_off, Int2Ptr PN… in SIM() 482 Int4 q; in SIM() 746 static void diff(CharPtr A, CharPtr B, Int4 M, Int4 N, Int4 tb, Int4 te, matrix value, scriptr s_pt… in diff() 764 static Int4 diff1(CharPtr A, CharPtr B, Int4 M, Int4 N, Int4 tb, Int4 te, Int4Ptr CC, Int4Ptr DD, I… in diff1() 775 Int4 t; in diff1() [all …]
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H A D | salign.h | 22 Int4 gap_open; 23 Int4 gap_extend; 24 Int4 wordsize; 25 Int4 filter; 33 Int4 lg1_ext; 34 Int4 rg1_ext; 35 Int4 lg2_ext; 36 Int4 rg2_ext; 37 Int4 lg1_open; 38 Int4 lg2_open; [all …]
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H A D | blast_dust.h | 49 Int4 from, to; 53 Int4 DustSegs (Uint1* sequence, Int4 length, Int4 start, 55 Int4 level, Int4 windowsize, Int4 linker); 57 SeqLocPtr BioseqDustEx (BioseqPtr bsp, Int4 level, Int4 windowsize, Int4 linker); 58 SeqLocPtr SeqLocDustEx (SeqLocPtr this_slp, Int4 level, Int4 window, Int4 linker);
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H A D | falign.c | 221 void found(Int4, Int4); 222 void rfscan(Int4, Int4, Int4, Int4); 226 void ffound(Int4, Int4); 254 Int4 enterS(fragment PNTR, Int4, Int4); 278 Int4 pt_lscore(fragment PNTR, Int4, Int4); 279 Int4 rcpt_lscore(fragment PNTR, Int4, Int4); 281 Int4 gap_cost(Int4); 287 Int4 power(Int4, Int4); 850 void rfscan(Int4 t, Int4 b, Int4 l, Int4 r) in rfscan() 1890 Int4 enterS(fragment PNTR f, Int4 w, Int4 l) in enterS() [all …]
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/dports/biology/ncbi-toolkit/ncbi/desktop/ |
H A D | gphdraw.h | 66 Int4 min; 67 Int4 max; 68 Int4 axis; 69 Int4 bottom; 77 SegmenT pict, Int4 scaleX, 78 Int4 top, Int2 start, 82 Int4 xlen, Int4 top, Int2 start, 83 Int4 leftend, Int4 rightend, 86 extern void DrawGraphToPanel (SeqGraphPtr sgp, Int4 Xscale, 87 Int4 Yscale, Int4 Ylength, RecT PNTR rp, [all …]
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H A D | layout.h | 24 Int4 LayoutNodeFlat PROTO((ValNodePtr PNTR head, Int4 maxScale, Int4 top, Uint1 label_type, Boolean… 26 Int4 LayoutAlignFlat PROTO((ValNodePtr head, Int4 maxScale, Int4 top)); 42 Int4 LayoutFeatNode PROTO((ValNodePtr head, Int4 top, Int4 maxScale, Int4 next_sp, Boolean show_lab… 59 Int4 LayoutAlignNode PROTO((ValNodePtr head, Int4 top, Int4 maxScale, Int4 height)); 63 void modify_insert_fnode PROTO((ValNodePtr fnode, Int4 offset));
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_itree.c | 57 static Int4 64 Int4 midpt; in s_IntervalNodeInit() 123 static Int4 146 Blast_IntervalTreeInit(Int4 q_start, Int4 q_end, in Blast_IntervalTreeInit() 147 Int4 s_start, Int4 s_end) in Blast_IntervalTreeInit() 211 static Int4 329 Int4 midpt; in s_MidpointTreeHasHSPEndpoint() 1009 static Int4 1053 static Int4 1106 Int4 [all …]
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H A D | phi_lookup.c | 56 s_FindPrefixAndSuffixPos(Int4* S, Int4 mask, Int4 mask2, Uint4* prefixPos, in s_FindPrefixAndSuffixPos() 140 static Int4 142 Int4 length, Int4 maxLength) in s_ExpandPattern() 146 Int4 k, t; /*loop indices*/ in s_ExpandPattern() 210 static Int4 213 Int4 i; /*loop index*/ in s_PackPattern() 268 Int4 s_NumOfOne(Int4 a) in s_NumOfOne() 270 Int4 returnValue; in s_NumOfOne() 286 s_PackVeryLongPattern(Int4 *inputPatternMasked, Int4 numPlacesInPattern, in s_PackVeryLongPattern() 728 Int4 array_size) in PHIBlastScanSubject() [all …]
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H A D | pattern.h | 95 Int4 match_mask;/**< Bit mask representation of input pattern 108 Int4 numPlacesInWord[PHI_MAX_WORDS_IN_PATTERN]; 110 Int4 spacing[PHI_MAX_WORDS_IN_PATTERN]; 111 Int4 highestPlace; /**< Number of places in pattern representation 113 Int4 whichMostSpecific; /**< Which word in an extra long pattern 132 Int4 numWords; /**< Number of words need to hold bit representation 137 Int4 bitPatternByLetter[PHI_ASCII_SIZE][PHI_MAX_WORD_SIZE]; 142 Int4 SLL[PHI_MAX_WORDS_IN_PATTERN][PHI_ASCII_SIZE]; 168 Int4 num_patterns_db; /**< Number of patterns actually found during the 185 Int4 FindPatternHits(Int4 * hitArray, const Uint1 * seq, Int4 len, [all …]
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H A D | blast_nalookup.c | 201 Int4 i; in s_BlastSmallNaLookupFinalize() 445 Int4 i; in s_BlastNaLookupFinalize() 669 Int4 index; in s_FillDiscMBTable() 727 Int4 to; in s_FillDiscMBTable() 1114 Int4 i; in s_MBCountWordsInSubject_16_1() 1377 Int4 i; in FNV_hash() 1506 Int4 i; in BlastSparseUint1ArrayNew() 1539 static Int4 1601 Int4 i; in s_NaHashLookupCountWordsInSubject_16_1() 1720 Int4 i; in NaHashLookupThreadDataNew() [all …]
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/dports/biology/ncbi-toolkit/ncbi/vibrant/ |
H A D | ppict3d.h | 90 Int4 width; 91 Int4 height; 92 Int4 widthCur; 93 Int4 heightCur; 94 Int4 xmin, ymin; /* Intrested area */ 95 Int4 xmax, ymax; 96 Int4 zmax; 99 Int4 scale; 103 Int4 perspect; /* 1-10 */ 142 Int4 version; [all …]
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/dports/biology/ncbi-toolkit/ncbi/biostruc/ |
H A D | objmmdb3.h | 36 Int4 id; 221 Int4 id; 255 Int4 id; 327 Int4 r; 330 Int4 g; 333 Int4 b; 352 Int4 x; 353 Int4 y; 665 Int4 x; 666 Int4 y; [all …]
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/dports/biology/ncbi-toolkit/ncbi/gif/ |
H A D | ncbigif.h | 72 SegmenT picture, Int4 pntX, Int4 pntY, 73 Int2 align, Int4 scaleX, Int4 scaleY, 78 Int4 pntX, Int4 pntY, Int2 align, Int4 scaleX, Int4 scaleY); 82 Int2 gifHeight, Int4 pntX, Int4 pntY, 83 Int2 align, Int4 scaleX, Int4 scaleY, 89 Int2 gifHeight, Int4 pntX, Int4 pntY, 90 Int2 align, Int4 scaleX, Int4 scaleY,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
H A D | pattern.h | 95 Int4 match_mask;/**< Bit mask representation of input pattern 108 Int4 numPlacesInWord[PHI_MAX_WORDS_IN_PATTERN]; 110 Int4 spacing[PHI_MAX_WORDS_IN_PATTERN]; 111 Int4 highestPlace; /**< Number of places in pattern representation 113 Int4 whichMostSpecific; /**< Which word in an extra long pattern 132 Int4 numWords; /**< Number of words need to hold bit representation 137 Int4 bitPatternByLetter[PHI_ASCII_SIZE][PHI_MAX_WORD_SIZE]; 142 Int4 SLL[PHI_MAX_WORDS_IN_PATTERN][PHI_ASCII_SIZE]; 168 Int4 num_patterns_db; /**< Number of patterns actually found during the 185 Int4 FindPatternHits(Int4 * hitArray, const Uint1 * seq, Int4 len, [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/ |
H A D | pattern.h | 95 Int4 match_mask;/**< Bit mask representation of input pattern 108 Int4 numPlacesInWord[PHI_MAX_WORDS_IN_PATTERN]; 110 Int4 spacing[PHI_MAX_WORDS_IN_PATTERN]; 111 Int4 highestPlace; /**< Number of places in pattern representation 113 Int4 whichMostSpecific; /**< Which word in an extra long pattern 132 Int4 numWords; /**< Number of words need to hold bit representation 137 Int4 bitPatternByLetter[PHI_ASCII_SIZE][PHI_MAX_WORD_SIZE]; 142 Int4 SLL[PHI_MAX_WORDS_IN_PATTERN][PHI_ASCII_SIZE]; 168 Int4 num_patterns_db; /**< Number of patterns actually found during the 185 Int4 FindPatternHits(Int4 * hitArray, const Uint1 * seq, Int4 len, [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/gumbel_params/ |
H A D | gumbel_params.hpp | 162 const Int4** GetScoreMatrix(void) const in GetScoreMatrix() 270 Int4 x_GetScore(Uint4 i, Uint4 j) const in x_GetScore() 281 Int4 m_GapOpening; 284 Int4 m_GapExtension; 309 Int4 m_NumResidues; 376 Int4 G; 579 vector<Int4>& SetPrelimReNumbers(void) in SetPrelimReNumbers() 630 vector<Int4> m_PrelimReNumbers; 633 vector<Int4> m_PrelimReNumbersKilling; 636 Int4 m_TotalReNumber; [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | aalookup_unit_test.cpp | 228 Int4 i; in BOOST_AUTO_TEST_CASE() 254 Int4 index; in BOOST_AUTO_TEST_CASE() 259 Int4 score; in BOOST_AUTO_TEST_CASE() 260 Int4 count = 0; in BOOST_AUTO_TEST_CASE() 290 Int4 offset = ((Int4 *)(lookup->overflow))[num_used-1]; in BOOST_AUTO_TEST_CASE() 296 Int4 len = 65533; in BOOST_AUTO_TEST_CASE() 355 pssm_sbp->posMatrix = (Int4 **) calloc(len, sizeof(Int4 *)); 359 pssm_sbp->posMatrix[i] = (Int4 *) calloc(BLASTAA_SIZE, sizeof(Int4)); 391 Int4 index; 397 Int4 score; [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | aalookup_unit_test.cpp | 228 Int4 i; in BOOST_AUTO_TEST_CASE() 254 Int4 index; in BOOST_AUTO_TEST_CASE() 259 Int4 score; in BOOST_AUTO_TEST_CASE() 260 Int4 count = 0; in BOOST_AUTO_TEST_CASE() 290 Int4 offset = ((Int4 *)(lookup->overflow))[num_used-1]; in BOOST_AUTO_TEST_CASE() 296 Int4 len = 65533; in BOOST_AUTO_TEST_CASE() 355 pssm_sbp->posMatrix = (Int4 **) calloc(len, sizeof(Int4 *)); 359 pssm_sbp->posMatrix[i] = (Int4 *) calloc(BLASTAA_SIZE, sizeof(Int4)); 391 Int4 index; 397 Int4 score; [all …]
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