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Searched refs:refpos (Results 1 – 25 of 233) sorted by relevance

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/dports/astro/p5-Astro-Coords/Astro-Coords-0.20/t/
H A Doffset.t58 my @refpos = $coords->array();
60 is (scalar(@refpos), scalar(@newpos), "array() returns same number of items");
61 for my $i (0..$#refpos) {
62 if (defined $refpos[$i] && defined $newpos[$i] &&
63 looks_like_number($refpos[$i])) {
64 delta_ok( $newpos[$i], $refpos[$i], "Compare element $i");
66 is( $newpos[$i], $refpos[$i], "Compare element $i");
/dports/biology/vcflib/vcflib-1.0.2/smithwaterman/
H A Dsmithwaterman.cpp272 int refpos = 0; in main() local
278 gapped_ref.insert(refpos, string(len, '-')); in main()
280 refpos += len; in main()
284 refpos += len; in main()
289 refpos += len; in main()
293 gapped_ref.insert(refpos, string(len, '*')); in main()
294 refpos += len; in main()
/dports/biology/freebayes/freebayes-1.3.5/vcflib/smithwaterman/
H A Dsmithwaterman.cpp272 int refpos = 0; in main() local
278 gapped_ref.insert(refpos, string(len, '-')); in main()
280 refpos += len; in main()
284 refpos += len; in main()
289 refpos += len; in main()
293 gapped_ref.insert(refpos, string(len, '*')); in main()
294 refpos += len; in main()
/dports/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7/
H A Dsmithwaterman.cpp272 int refpos = 0; in main() local
278 gapped_ref.insert(refpos, string(len, '-')); in main()
280 refpos += len; in main()
284 refpos += len; in main()
289 refpos += len; in main()
293 gapped_ref.insert(refpos, string(len, '*')); in main()
294 refpos += len; in main()
/dports/biology/sra-tools/sra-tools-2.11.0/test/samline/
H A Dalig-gen.c235 uint32_t refpos, mapq, bases_in_ref, reflen; member
294 if ( alig->refpos == 0 ) res |= 0x04; /* this fragment is unmapped */ in sam_flags()
295 if ( other != NULL && other->refpos == 0 ) res |= 0x08; /* next fragment is unmapped */ in sam_flags()
326 if ( other != NULL && other->refname != NULL && other->refpos != 0 ) in produce_sam()
329 first = ( alig->refpos < other->refpos ); in produce_sam()
331 r_pos = other->refpos; in produce_sam()
344 alig->refpos, in produce_sam()
363 KOutMsg ( "REFPOS : %d\n", alig->refpos ); in show_alig_details()
588 if ( gctx->alig[ 1 ].refpos > 0 ) in read_context()
595 uint32_t end = alig1->refpos + alig1->reflen; in read_context()
[all …]
/dports/textproc/source-highlight/source-highlight-3.1.9/lib/srchilite/
H A Dctagscollector.cpp78 RefPosition refpos; in collectTags() local
82 refpos = POSTLINE; in collectTags()
84 refpos = refposition; in collectTags()
93 CTagsInfo ctagsInfo(it->filename, gen_info.str(), refpos, false); in collectTags()
/dports/biology/vcflib/vcflib-1.0.2/src/
H A Dvcfremap.cpp223 int refpos = 0; in main() local
257 refss << ref.substr(refpos, len); in main()
259 refpos += len; in main()
266 if (ref.at(refpos + i) == alternateQuery.at(altpos + i)) { in main()
281 refss << ref.substr(refpos, len); in main()
283 refpos += len; in main()
290 refss << ref.substr(refpos, len); in main()
292 refpos += len; in main()
/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/
H A Dvcfremap.cpp212 int refpos = 0; in main() local
246 refss << ref.substr(refpos, len); in main()
248 refpos += len; in main()
255 if (ref.at(refpos + i) == alternateQuery.at(altpos + i)) { in main()
270 refss << ref.substr(refpos, len); in main()
272 refpos += len; in main()
279 refss << ref.substr(refpos, len); in main()
281 refpos += len; in main()
/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/
H A Dvcfremap.cpp212 int refpos = 0; in main() local
246 refss << ref.substr(refpos, len); in main()
248 refpos += len; in main()
255 if (ref.at(refpos + i) == alternateQuery.at(altpos + i)) { in main()
270 refss << ref.substr(refpos, len); in main()
272 refpos += len; in main()
279 refss << ref.substr(refpos, len); in main()
281 refpos += len; in main()
/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/lib/hotint/HotInt_V1/ElementsLib/constraints/
H A Dcontrol.cpp837 center = Vector2D(refpos.X(),refpos.Y()); in DrawElement2D()
905 center = Vector2D(refpos.X(),refpos.Y()); in DrawElement2D()
918 center = Vector2D(refpos.X(),refpos.Y()); in DrawElement2D()
1044 Vector2D center(refpos.X(),refpos.Y()); in DrawBlockSymbol()
1228 Vector2D center(refpos.X(),refpos.Y()); in DrawBlockSymbol()
1705 Vector2D center(refpos.X(),refpos.Y()); in DrawBlockSymbol()
1775 Vector2D center(refpos.X(),refpos.Y()); in DrawBlockSymbol()
1875 Vector2D center(refpos.X(),refpos.Y()); in DrawBlockSymbol()
2141 Vector2D center(refpos.X(),refpos.Y()); in DrawBlockSymbol()
2200 Vector2D center(refpos.X(),refpos.Y()); in DrawBlockSymbol()
[all …]
/dports/print/tex-luatex/texlive-20150521-source/texk/web2c/luatexdir/pdf/
H A Dpdflistout.w341 refpos = pdf->posstruct;
343 localpos.pos = refpos->pos;
488 pos_info.boxpos.pos = refpos->pos;
555 refpos->pos.h = dir_refpos_h(p);
556 refpos->pos.v = dir_refpos_v(p);
785 pdf->posstruct = refpos;
822 refpos = pdf->posstruct;
825 synch_pos_with_cur(pdf->posstruct, refpos, cur);
934 pos_info.boxpos.pos = refpos->pos;
1128 synch_pos_with_cur(pdf->posstruct, refpos, cur);
[all …]
H A Dpdfpage.w74 void synch_pos_with_cur(posstructure * pos, posstructure * refpos,
79 pos->pos.h = refpos->pos.h + cur.h;
80 pos->pos.v = refpos->pos.v - cur.v;
83 pos->pos.h = refpos->pos.h - cur.h;
84 pos->pos.v = refpos->pos.v - cur.v;
87 pos->pos.h = refpos->pos.h + cur.v;
88 pos->pos.v = refpos->pos.v - cur.h;
91 pos->pos.h = refpos->pos.h - cur.v;
92 pos->pos.v = refpos->pos.v - cur.h;
/dports/devel/tex-web2c/texlive-20150521-source/texk/web2c/luatexdir/pdf/
H A Dpdflistout.w341 refpos = pdf->posstruct;
343 localpos.pos = refpos->pos;
488 pos_info.boxpos.pos = refpos->pos;
555 refpos->pos.h = dir_refpos_h(p);
556 refpos->pos.v = dir_refpos_v(p);
785 pdf->posstruct = refpos;
822 refpos = pdf->posstruct;
825 synch_pos_with_cur(pdf->posstruct, refpos, cur);
934 pos_info.boxpos.pos = refpos->pos;
1128 synch_pos_with_cur(pdf->posstruct, refpos, cur);
[all …]
H A Dpdfpage.w74 void synch_pos_with_cur(posstructure * pos, posstructure * refpos,
79 pos->pos.h = refpos->pos.h + cur.h;
80 pos->pos.v = refpos->pos.v - cur.v;
83 pos->pos.h = refpos->pos.h - cur.h;
84 pos->pos.v = refpos->pos.v - cur.v;
87 pos->pos.h = refpos->pos.h + cur.v;
88 pos->pos.v = refpos->pos.v - cur.h;
91 pos->pos.h = refpos->pos.h - cur.v;
92 pos->pos.v = refpos->pos.v - cur.h;
/dports/devel/tex-synctex/texlive-20150521-source/texk/web2c/luatexdir/pdf/
H A Dpdflistout.w341 refpos = pdf->posstruct;
343 localpos.pos = refpos->pos;
488 pos_info.boxpos.pos = refpos->pos;
555 refpos->pos.h = dir_refpos_h(p);
556 refpos->pos.v = dir_refpos_v(p);
785 pdf->posstruct = refpos;
822 refpos = pdf->posstruct;
825 synch_pos_with_cur(pdf->posstruct, refpos, cur);
934 pos_info.boxpos.pos = refpos->pos;
1128 synch_pos_with_cur(pdf->posstruct, refpos, cur);
[all …]
H A Dpdfpage.w74 void synch_pos_with_cur(posstructure * pos, posstructure * refpos,
79 pos->pos.h = refpos->pos.h + cur.h;
80 pos->pos.v = refpos->pos.v - cur.v;
83 pos->pos.h = refpos->pos.h - cur.h;
84 pos->pos.v = refpos->pos.v - cur.v;
87 pos->pos.h = refpos->pos.h + cur.v;
88 pos->pos.v = refpos->pos.v - cur.h;
91 pos->pos.h = refpos->pos.h - cur.v;
92 pos->pos.v = refpos->pos.v - cur.h;
/dports/japanese/tex-ptex/texlive-20150521-source/texk/web2c/luatexdir/pdf/
H A Dpdflistout.w341 refpos = pdf->posstruct;
343 localpos.pos = refpos->pos;
488 pos_info.boxpos.pos = refpos->pos;
555 refpos->pos.h = dir_refpos_h(p);
556 refpos->pos.v = dir_refpos_v(p);
785 pdf->posstruct = refpos;
822 refpos = pdf->posstruct;
825 synch_pos_with_cur(pdf->posstruct, refpos, cur);
934 pos_info.boxpos.pos = refpos->pos;
1128 synch_pos_with_cur(pdf->posstruct, refpos, cur);
[all …]
H A Dpdfpage.w74 void synch_pos_with_cur(posstructure * pos, posstructure * refpos,
79 pos->pos.h = refpos->pos.h + cur.h;
80 pos->pos.v = refpos->pos.v - cur.v;
83 pos->pos.h = refpos->pos.h - cur.h;
84 pos->pos.v = refpos->pos.v - cur.v;
87 pos->pos.h = refpos->pos.h + cur.v;
88 pos->pos.v = refpos->pos.v - cur.h;
91 pos->pos.h = refpos->pos.h - cur.v;
92 pos->pos.v = refpos->pos.v - cur.h;
/dports/print/tex-basic-engines/texlive-20150521-source/texk/web2c/luatexdir/pdf/
H A Dpdflistout.w341 refpos = pdf->posstruct;
343 localpos.pos = refpos->pos;
488 pos_info.boxpos.pos = refpos->pos;
555 refpos->pos.h = dir_refpos_h(p);
556 refpos->pos.v = dir_refpos_v(p);
785 pdf->posstruct = refpos;
822 refpos = pdf->posstruct;
825 synch_pos_with_cur(pdf->posstruct, refpos, cur);
934 pos_info.boxpos.pos = refpos->pos;
1128 synch_pos_with_cur(pdf->posstruct, refpos, cur);
[all …]
H A Dpdfpage.w74 void synch_pos_with_cur(posstructure * pos, posstructure * refpos,
79 pos->pos.h = refpos->pos.h + cur.h;
80 pos->pos.v = refpos->pos.v - cur.v;
83 pos->pos.h = refpos->pos.h - cur.h;
84 pos->pos.v = refpos->pos.v - cur.v;
87 pos->pos.h = refpos->pos.h + cur.v;
88 pos->pos.v = refpos->pos.v - cur.h;
91 pos->pos.h = refpos->pos.h - cur.v;
92 pos->pos.v = refpos->pos.v - cur.h;
/dports/print/tex-aleph/texlive-20150521-source/texk/web2c/luatexdir/pdf/
H A Dpdflistout.w341 refpos = pdf->posstruct;
343 localpos.pos = refpos->pos;
488 pos_info.boxpos.pos = refpos->pos;
555 refpos->pos.h = dir_refpos_h(p);
556 refpos->pos.v = dir_refpos_v(p);
785 pdf->posstruct = refpos;
822 refpos = pdf->posstruct;
825 synch_pos_with_cur(pdf->posstruct, refpos, cur);
934 pos_info.boxpos.pos = refpos->pos;
1128 synch_pos_with_cur(pdf->posstruct, refpos, cur);
[all …]
/dports/print/tex-xetex/texlive-20150521-source/texk/web2c/luatexdir/pdf/
H A Dpdflistout.w341 refpos = pdf->posstruct;
343 localpos.pos = refpos->pos;
488 pos_info.boxpos.pos = refpos->pos;
555 refpos->pos.h = dir_refpos_h(p);
556 refpos->pos.v = dir_refpos_v(p);
785 pdf->posstruct = refpos;
822 refpos = pdf->posstruct;
825 synch_pos_with_cur(pdf->posstruct, refpos, cur);
934 pos_info.boxpos.pos = refpos->pos;
1128 synch_pos_with_cur(pdf->posstruct, refpos, cur);
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/
H A Dcigar.cpp222 TSeqPos refpos = (refsign > 0) ? ref.GetFrom() : ref.GetTo(); in operator ()() local
225 CRef<CSeq_loc> refseg = x_NextChunk(*refid, refpos, in operator ()()
235 refpos += it->len * refscale * refsign; in operator ()()
243 refpos += it->len * refscale * refsign; in operator ()()
247 refpos += refsign; in operator ()()
250 refpos -= refsign; in operator ()()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/
H A Dcigar.cpp222 TSeqPos refpos = (refsign > 0) ? ref.GetFrom() : ref.GetTo(); in operator ()() local
225 CRef<CSeq_loc> refseg = x_NextChunk(*refid, refpos, in operator ()()
235 refpos += it->len * refscale * refsign; in operator ()()
243 refpos += it->len * refscale * refsign; in operator ()()
247 refpos += refsign; in operator ()()
250 refpos -= refsign; in operator ()()
/dports/math/R-cran-pbkrtest/pbkrtest/R/
H A DPB-modcomp.R357 refpos <- ref[ref>0] functionVar
359 npos <- length(refpos)
365 n.extreme <- sum(tobs < refpos)
420 refpos <- ref[ref > 0] functionVar
422 npos <- length(refpos)
424 EE <- mean(refpos)
425 VV <- var(refpos)
431 n.extreme <- sum(tobs < refpos)

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