/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | dynprog_end.c | 372 *bestr = r = rlength; in find_best_endpoint_to_queryend_indels_8() 450 *bestr = r = rlength; in find_best_endpoint_to_queryend_indels_16() 527 *bestr = r = rlength; in find_best_endpoint_to_queryend_indels_std() 573 *bestr = rlength; in find_best_endpoint_to_queryend_nogaps() 574 *bestc = rlength; in find_best_endpoint_to_queryend_nogaps() 1320 if (rlength <= 0) { in Dynprog_end5_gap() 1351 …intf("At query offset %d-%d, %.*s\n",rev_roffset-rlength+1,rev_roffset,rlength,&(rev_rsequence[-rl… in Dynprog_end5_gap() 1670 if (rlength <= 0 || rlength > dynprog->max_rlength) { in Dynprog_end5_splicejunction() 1687 …intf("At query offset %d-%d, %.*s\n",rev_roffset-rlength+1,rev_roffset,rlength,&(rev_rsequence[-rl… in Dynprog_end5_splicejunction() 2248 if (rlength <= 0 || rlength > dynprog->max_rlength) { in Dynprog_end3_splicejunction() [all …]
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H A D | dynprog_single.c | 372 for (r = 1; r <= rlength; r++) { in single_gap_simple() 515 debug(printf("At query offset %d-%d, %.*s\n",roffset,roffset+rlength-1,rlength,rsequence)); in Dynprog_single_gap() 529 rlength_orig = rlength; in Dynprog_single_gap() 570 } else if (glength == rlength && in Dynprog_single_gap() 1014 i = rlength-1; in Dynprog_microexon_int() 1064 cL,rlength,mincR,maxcR)); in Dynprog_microexon_int() 1256 debug(printf(" Query sequence is %.*s\n",rlength,&(rev_rsequence[-rlength+1]))); 1259 if (glength < rlength) { 1283 endlength = rlength - c; 1374 if (glength < rlength) { [all …]
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H A D | dynprog_simd.c | 2467 rhigh = rlength; in Dynprog_simd_8_nonavx2() 2693 rhigh = rlength; in Dynprog_simd_8_nonavx2() 3177 rhigh = rlength; in Dynprog_simd_8() 3448 rhigh = rlength; in Dynprog_simd_8() 3930 rhigh = rlength; in Dynprog_simd_8_upper_nonavx2() 4054 rhigh = rlength; in Dynprog_simd_8_upper_nonavx2() 4394 rhigh = rlength; in Dynprog_simd_8_upper() 4556 rhigh = rlength; in Dynprog_simd_8_upper() 5964 rhigh = rlength; in Dynprog_simd_16_nonavx2() 6171 rhigh = rlength; in Dynprog_simd_16_nonavx2() [all …]
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H A D | dynprog.c | 218 if (glength <= 0 || rlength <= 0) { in Matrix32_alloc() 284 for (i = 0; i <= rlength; ++i) { in Dynprog_Matrix32_print() 380 for (i = 0; i <= rlength; ++i) { in Matrix3_print() 423 for (i = 0; i <= rlength; ++i) { in Matrix3_print() 466 for (i = 0; i <= rlength; ++i) { in Matrix3_print() 560 for (i = 0; i <= rlength; ++i) { in Dynprog_Directions32_print() 1198 int rlength, int glength, in Dynprog_standard() argument 1281 for ( ; r <= rlength; r++) { in Dynprog_standard() 1293 for ( ; r <= rlength; r++) { in Dynprog_standard() 1379 rhigh = rlength; in Dynprog_standard() [all …]
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H A D | dynprog_simd.h | 20 int rlength, int glength, 30 int rlength, int glength, 40 int rlength, int glength, 51 int rlength, int glength, 61 int rlength, int glength, 71 int rlength, int glength,
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H A D | dynprog_genome.c | 635 for (rL = 1, rR = rlength-1; rL < rlength; rL++, rR--) { in bridge_intron_gap_8_intron_level() 1065 for (rL = 1, rR = rlength-1; rL < rlength; rL++, rR--) { in bridge_intron_gap_8_site_level() 1508 for (rL = 1, rR = rlength-1; rL < rlength; rL++, rR--) { in bridge_intron_gap_16_intron_level() 1939 for (rL = 1, rR = rlength-1; rL < rlength; rL++, rR--) { in bridge_intron_gap_16_site_level() 2380 for (rL = 1, rR = rlength-1; rL < rlength; rL++, rR--) { in bridge_intron_gap_intron_level() 2660 for (rL = 1, rR = rlength-1; rL < rlength; rL++, rR--) { in bridge_intron_gap_site_level() 3052 for (rL = 1, rR = rlength-1; rL < rlength; rL++, rR--) { in genome_gap_simple() 3331 if (rlength <= 1) { in Dynprog_genome_gap() 3528 rlength,glengthR, in Dynprog_genome_gap() 3537 rlength,glengthR, in Dynprog_genome_gap() [all …]
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/dports/databases/hbase/hbase-1.2.1/hbase-common/src/main/java/org/apache/hadoop/hbase/ |
H A D | KeyValue.java | 620 row, roffset, rlength, in KeyValue() 703 public KeyValue(final int rlength, in KeyValue() argument 725 public KeyValue(final int rlength, in KeyValue() argument 828 if (rlength > Short.MAX_VALUE) { in createEmptyByteArray() 860 pos += rlength; in createEmptyByteArray() 887 if (rlength > Short.MAX_VALUE) { in checkParameters() 1396 private int getFamilyOffset(int rlength) { in getFamilyOffset() argument 1887 int rlength = r.getRowLength(); in compareRowKey() local 1951 rlength, rrowlength); in compareFlatKey() 2127 roffset, rlength, lrowlength); in compareIgnoringPrefix() [all …]
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/dports/biology/jalview/jalview/src/jalview/datamodel/ |
H A D | CigarBase.java | 82 int rlength = 0; in getSequenceAndDeletions() local 95 rlength = reference.length(); in getSequenceAndDeletions() 130 if (sbend > rlength) in getSequenceAndDeletions() 133 while (sbend-- >= rlength) in getSequenceAndDeletions() 448 if (rlength > remain) in deleteRange() 455 deleted += rlength; in deleteRange() 456 addDeleted(rlength); in deleteRange() 461 rlength = 0; in deleteRange() 466 if (remain - rlength > 0) in deleteRange() 470 rlength = 0; in deleteRange() [all …]
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/dports/converters/p5-Convert-BinHex/Convert-BinHex-1.125/bin/ |
H A D | binhex.pl | 104 my ($has, $dlength, $rlength, $finfo, $flags); 126 $rlength = $has->{ioFlRLgLen}; 137 $hqx->resource->length($rlength); 147 $rlength = (-s "$inpath.rsrc"); 151 $rlength = 0; 158 print " Resource size: $rlength\n" if defined($rlength);
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/dports/editors/led/led-2.0/src/ |
H A D | macro.c | 39 static int rlength; variable 83 if (rlength + 1 >= rsize) { in macro_recordkey() 87 record[rlength++] = keysym; in macro_recordkey() 107 if (rpos >= rlength) { in macro_getkey() 150 rlength = 0; in macro_record() 155 if (rlength) { in macro_playback()
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/dports/biology/vt/vt-0.57721/lib/pcre2/ |
H A D | pcre2_substitute.c | 78 pcre2_match_context *mcontext, PCRE2_SPTR replacement, PCRE2_SIZE rlength, in pcre2_substitute() argument 115 rc = PRIV(valid_utf)(replacement, rlength, &(match_data->rightchar)); in pcre2_substitute() 136 if (rlength == PCRE2_ZERO_TERMINATED) rlength = PRIV(strlen)(replacement); in pcre2_substitute() 202 for (i = 0; i < rlength; i++) in pcre2_substitute() 212 if (++i == rlength) goto BAD; in pcre2_substitute() 221 if (++i == rlength) goto BAD; in pcre2_substitute() 229 while (i < rlength - 1) in pcre2_substitute() 243 if (i == rlength) break; in pcre2_substitute() 252 if (i == rlength || next != CHAR_RIGHT_CURLY_BRACKET) goto BAD; in pcre2_substitute()
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/dports/graphics/xfractint/xfractint-20.04p16/common/ |
H A D | biginit.c | 96 rlength = bnlength + padding; in calc_lengths() 151 bntmp1 = bnroot+ptr; ptr += rlength; in init_bf_2() 152 bntmp2 = bnroot+ptr; ptr += rlength; in init_bf_2() 153 bntmp3 = bnroot+ptr; ptr += rlength; in init_bf_2() 154 bntmp4 = bnroot+ptr; ptr += rlength; in init_bf_2() 155 bntmp5 = bnroot+ptr; ptr += rlength; in init_bf_2() 156 bntmp6 = bnroot+ptr; ptr += rlength; in init_bf_2() 183 bnold.x = bnroot+ptr; ptr += rlength; in init_bf_2() 184 bnold.y = bnroot+ptr; ptr += rlength; in init_bf_2() 185 bnnew.x = bnroot+ptr; ptr += rlength; in init_bf_2() [all …]
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/dports/math/R-cran-zoo/zoo/R/ |
H A D | na.trim.R | 9 rlength <- function(x) if(all(!x)) length(x) else min(which(x)) - 1L function 13 idx0 | rlength(idx0) > maxgap 17 rev(idx0) | rlength(idx0) > maxgap 22 (idx0l | rlength(idx0l) > maxgap) & (rev(idx0r) | rlength(idx0r) > maxgap)
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/dports/net/openmpi3/openmpi-3.1.6/test/datatype/ |
H A D | to_self.c | 194 int myself, tag = 0, i, slength, rlength; in isend_recv() local 201 MPI_Type_size( rdt, &rlength ); in isend_recv() 202 rlength *= rcount; in isend_recv() 228 int myself, tag = 0, i, slength, rlength; in irecv_send() local 235 MPI_Type_size( rdt, &rlength ); in irecv_send() 236 rlength *= rcount; in irecv_send() 262 int myself, tag = 0, i, slength, rlength; in isend_irecv_wait() local 269 MPI_Type_size( rdt, &rlength ); in isend_irecv_wait() 270 rlength *= rcount; in isend_irecv_wait() 307 MPI_Type_size( rdt, &rlength ); in irecv_isend_wait() [all …]
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/dports/security/libksba/libksba-1.6.0/src/ |
H A D | oid.c | 183 ksba_oid_from_str (const char *string, unsigned char **rbuf, size_t *rlength) in ksba_oid_from_str() argument 191 if (!string || !rbuf || !rlength) in ksba_oid_from_str() 194 *rlength = 0; in ksba_oid_from_str() 258 *rlength = buflen; in ksba_oid_from_str() 270 unsigned char **rbuf, size_t *rlength) in _ksba_oid_from_buf() argument 279 *rlength = 0; in _ksba_oid_from_buf() 284 err = ksba_oid_from_str (string, rbuf, rlength); in _ksba_oid_from_buf()
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/dports/java/openjdk16/jdk16u-jdk-16.0.2-7-1/src/jdk.incubator.vector/share/classes/jdk/incubator/vector/ |
H A D | AbstractVector.java | 537 int rlength = dsp.laneCount; in defaultCast() local 545 byte[] a = new byte[rlength]; in defaultCast() 559 int[] a = new int[rlength]; in defaultCast() 566 long[] a = new long[rlength]; in defaultCast() 595 byte[] a = new byte[rlength]; in defaultCast() 609 int[] a = new int[rlength]; in defaultCast() 665 int rlength; in convert0() local 674 rlength = rsp.laneCount(); in convert0() 680 rvtype, rtype, rlength, in convert0() 685 rlength = rsp.laneCount(); in convert0() [all …]
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/dports/java/openjdk17/jdk17u-jdk-17.0.1-12-1/src/jdk.incubator.vector/share/classes/jdk/incubator/vector/ |
H A D | AbstractVector.java | 537 int rlength = dsp.laneCount; in defaultCast() local 545 byte[] a = new byte[rlength]; in defaultCast() 559 int[] a = new int[rlength]; in defaultCast() 566 long[] a = new long[rlength]; in defaultCast() 595 byte[] a = new byte[rlength]; in defaultCast() 609 int[] a = new int[rlength]; in defaultCast() 665 int rlength; in convert0() local 674 rlength = rsp.laneCount(); in convert0() 680 rvtype, rtype, rlength, in convert0() 685 rlength = rsp.laneCount(); in convert0() [all …]
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/dports/databases/hbase/hbase-1.2.1/hbase-server/src/main/java/org/apache/hadoop/hbase/mapreduce/ |
H A D | CellCreator.java | 68 public Cell create(byte[] row, int roffset, int rlength, byte[] family, int foffset, int flength, in create() argument 71 return create(row, roffset, rlength, family, foffset, flength, qualifier, qoffset, qlength, in create() 94 public Cell create(byte[] row, int roffset, int rlength, byte[] family, int foffset, int flength, in create() argument 101 return new KeyValue(row, roffset, rlength, family, foffset, flength, qualifier, qoffset, in create() 123 public Cell create(byte[] row, int roffset, int rlength, byte[] family, int foffset, int flength, in create() argument 126 return new KeyValue(row, roffset, rlength, family, foffset, flength, qualifier, qoffset, in create()
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/dports/net/openmpi/openmpi-4.1.1/test/datatype/ |
H A D | to_self.c | 345 MPI_Type_size( rdt, &rlength ); in isend_recv() 346 rlength *= rcount; in isend_recv() 359 print_result( rlength, trials, timers ); in isend_recv() 374 MPI_Type_size( rdt, &rlength ); in irecv_send() 375 rlength *= rcount; in irecv_send() 388 print_result( rlength, trials, timers ); in irecv_send() 403 MPI_Type_size( rdt, &rlength ); in isend_irecv_wait() 404 rlength *= rcount; in isend_irecv_wait() 432 MPI_Type_size( rdt, &rlength ); in irecv_isend_wait() 433 rlength *= rcount; in irecv_isend_wait() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/tools2/assemble-fragments/ |
H A D | fragment.hpp | 116 unsigned rlength() const ///< effects how many bases of the reference sequence in rlength() function 194 int rlength; ///< aligned length on reference member 200 …CIGAR(unsigned rlength, unsigned left_clip, unsigned qlength, unsigned right_clip, std::vector<CIG… in CIGAR() 202 , rlength(rlength) in CIGAR() 210 , rlength(0) in CIGAR() 216 , rlength(0) in CIGAR() 283 rlength += length; in CIGAR() 291 rlength += length; in CIGAR() 299 qclip = qfirst = qlength = rlength = 0; in CIGAR() 315 return CIGAR(rlength, qclip, qlength, qfirst, std::vector<CIGAR_OP>(rbegin(), rend())); in adjoint()
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/dports/devel/icu/icu/source/test/intltest/ |
H A D | colldata.cpp | 537 int32_t rlength = 0; in minLengthInChars() local 542 if (rlength <= 0) { in minLengthInChars() 551 if (shortestLength > slength + rlength) { in minLengthInChars() 552 shortestLength = slength + rlength; in minLengthInChars() 567 int32_t rlength = 0; in minLengthInChars() local 573 rlength = minLengthInChars(ceList, roffset, history); in minLengthInChars() 576 if (rlength < 0) { in minLengthInChars() 580 shortestLength = 1 + rlength; in minLengthInChars() 584 int32_t rlength = 0; in minLengthInChars() local 618 if (rlength < 0) { in minLengthInChars() [all …]
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/dports/devel/icu-lx/icu/source/test/intltest/ |
H A D | colldata.cpp | 537 int32_t rlength = 0; in minLengthInChars() local 542 if (rlength <= 0) { in minLengthInChars() 551 if (shortestLength > slength + rlength) { in minLengthInChars() 552 shortestLength = slength + rlength; in minLengthInChars() 567 int32_t rlength = 0; in minLengthInChars() local 573 rlength = minLengthInChars(ceList, roffset, history); in minLengthInChars() 576 if (rlength < 0) { in minLengthInChars() 580 shortestLength = 1 + rlength; in minLengthInChars() 584 int32_t rlength = 0; in minLengthInChars() local 618 if (rlength < 0) { in minLengthInChars() [all …]
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/dports/biology/subread/subread-2.0.2-source/src/ |
H A D | gen_rand_reads.c | 514 if(rlength < 1)break; in grc_summary_fasta() 515 …if(rlength >= TRANSCRIPT_FASTA_LINE_WIDTH -1 || clinebuf[rlength]!='\0' || clinebuf[rlength-1]!='\… in grc_summary_fasta() 547 clinebuf[rlength-1]=0; in grc_summary_fasta() 559 seq_name=malloc(rlength); in grc_summary_fasta() 567 seq_len += rlength-1; // no \n in grc_summary_fasta() 759 if(rlength < 1)break; in grc_load_env() 760 …if(rlength >= TRANSCRIPT_FASTA_LINE_WIDTH -1 || clinebuf[rlength]!='\0' || clinebuf[rlength-1]!='\… in grc_load_env() 785 clinebuf[rlength-1]=0; in grc_load_env() 806 if(lbuf_cap - lbuf_used < rlength + 1){ in grc_load_env() 815 *(lbuf+lbuf_used+rlength-1)=0; // '\n' => 0 in grc_load_env() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/phy_tree/fastme/ |
H A D | newickstring.cpp | 309 int slength, llength, rlength; in NewickPrintSubtreeString() local 320 rlength = NewickPrintSubtreeString(T,right,s+2+llength); in NewickPrintSubtreeString() 321 s[2 + rlength + llength]=')'; in NewickPrintSubtreeString() 322 slength = 3 + rlength + llength; in NewickPrintSubtreeString() 359 int i,slength, llength, rlength; in NewickPrintTreeString() local 380 rlength = NewickPrintSubtreeString(T,right,s+2+llength); in NewickPrintTreeString() 381 s[2 + rlength + llength]=','; in NewickPrintTreeString() 382 i = 3 + rlength + llength; in NewickPrintTreeString()
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/dports/www/aria2/aria2-1.36.0/test/ |
H A D | DHTConnectionImplTest.cc | 50 ssize_t rlength = con2.receiveMessage(readbuffer, sizeof(readbuffer), in testWriteAndReadData() local 52 CPPUNIT_ASSERT_EQUAL((ssize_t)message1.size(), rlength); in testWriteAndReadData() 54 std::string(&readbuffer[0], &readbuffer[rlength])); in testWriteAndReadData()
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