Home
last modified time | relevance | path

Searched refs:rlength (Results 1 – 25 of 393) sorted by relevance

12345678910>>...16

/dports/biology/gmap/gmap-2020-09-12/src/
H A Ddynprog_end.c372 *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 …]
H A Ddynprog_single.c372 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 …]
H A Ddynprog_simd.c2467 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 …]
H A Ddynprog.c218 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 …]
H A Ddynprog_simd.h20 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,
H A Ddynprog_genome.c635 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 …]
/dports/databases/hbase/hbase-1.2.1/hbase-common/src/main/java/org/apache/hadoop/hbase/
H A DKeyValue.java620 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 …]
/dports/biology/jalview/jalview/src/jalview/datamodel/
H A DCigarBase.java82 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 …]
/dports/converters/p5-Convert-BinHex/Convert-BinHex-1.125/bin/
H A Dbinhex.pl104 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);
/dports/editors/led/led-2.0/src/
H A Dmacro.c39 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()
/dports/biology/vt/vt-0.57721/lib/pcre2/
H A Dpcre2_substitute.c78 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()
/dports/graphics/xfractint/xfractint-20.04p16/common/
H A Dbiginit.c96 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 …]
/dports/math/R-cran-zoo/zoo/R/
H A Dna.trim.R9 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)
/dports/net/openmpi3/openmpi-3.1.6/test/datatype/
H A Dto_self.c194 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 …]
/dports/security/libksba/libksba-1.6.0/src/
H A Doid.c183 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()
/dports/java/openjdk16/jdk16u-jdk-16.0.2-7-1/src/jdk.incubator.vector/share/classes/jdk/incubator/vector/
H A DAbstractVector.java537 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 …]
/dports/java/openjdk17/jdk17u-jdk-17.0.1-12-1/src/jdk.incubator.vector/share/classes/jdk/incubator/vector/
H A DAbstractVector.java537 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 …]
/dports/databases/hbase/hbase-1.2.1/hbase-server/src/main/java/org/apache/hadoop/hbase/mapreduce/
H A DCellCreator.java68 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()
/dports/net/openmpi/openmpi-4.1.1/test/datatype/
H A Dto_self.c345 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 …]
/dports/biology/sra-tools/sra-tools-2.11.0/tools2/assemble-fragments/
H A Dfragment.hpp116 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()
/dports/devel/icu/icu/source/test/intltest/
H A Dcolldata.cpp537 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 …]
/dports/devel/icu-lx/icu/source/test/intltest/
H A Dcolldata.cpp537 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 …]
/dports/biology/subread/subread-2.0.2-source/src/
H A Dgen_rand_reads.c514 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/phy_tree/fastme/
H A Dnewickstring.cpp309 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()
/dports/www/aria2/aria2-1.36.0/test/
H A DDHTConnectionImplTest.cc50 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()

12345678910>>...16