/dports/astro/p5-Astro-Coords/Astro-Coords-0.20/t/ |
H A D | offset.t | 58 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");
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/dports/biology/vcflib/vcflib-1.0.2/smithwaterman/ |
H A D | smithwaterman.cpp | 272 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()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/smithwaterman/ |
H A D | smithwaterman.cpp | 272 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()
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/dports/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7/ |
H A D | smithwaterman.cpp | 272 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/test/samline/ |
H A D | alig-gen.c | 235 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 …]
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/dports/textproc/source-highlight/source-highlight-3.1.9/lib/srchilite/ |
H A D | ctagscollector.cpp | 78 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()
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/dports/biology/vcflib/vcflib-1.0.2/src/ |
H A D | vcfremap.cpp | 223 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()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
H A D | vcfremap.cpp | 212 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()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
H A D | vcfremap.cpp | 212 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()
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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/lib/hotint/HotInt_V1/ElementsLib/constraints/ |
H A D | control.cpp | 837 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 …]
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/dports/print/tex-luatex/texlive-20150521-source/texk/web2c/luatexdir/pdf/ |
H A D | pdflistout.w | 341 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 …]
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H A D | pdfpage.w | 74 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;
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/dports/devel/tex-web2c/texlive-20150521-source/texk/web2c/luatexdir/pdf/ |
H A D | pdflistout.w | 341 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 …]
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H A D | pdfpage.w | 74 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;
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/dports/devel/tex-synctex/texlive-20150521-source/texk/web2c/luatexdir/pdf/ |
H A D | pdflistout.w | 341 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 …]
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H A D | pdfpage.w | 74 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;
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/dports/japanese/tex-ptex/texlive-20150521-source/texk/web2c/luatexdir/pdf/ |
H A D | pdflistout.w | 341 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 …]
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H A D | pdfpage.w | 74 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;
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/dports/print/tex-basic-engines/texlive-20150521-source/texk/web2c/luatexdir/pdf/ |
H A D | pdflistout.w | 341 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 …]
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H A D | pdfpage.w | 74 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;
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/dports/print/tex-aleph/texlive-20150521-source/texk/web2c/luatexdir/pdf/ |
H A D | pdflistout.w | 341 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 …]
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/dports/print/tex-xetex/texlive-20150521-source/texk/web2c/luatexdir/pdf/ |
H A D | pdflistout.w | 341 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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/ |
H A D | cigar.cpp | 222 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 ()()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/ |
H A D | cigar.cpp | 222 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 ()()
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/dports/math/R-cran-pbkrtest/pbkrtest/R/ |
H A D | PB-modcomp.R | 357 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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