Home
last modified time | relevance | path

Searched refs:gaps (Results 1 – 25 of 6359) sorted by relevance

12345678910>>...255

/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/
H A Dtest_align_gaps.h128 TGaps gaps; in testAlignGapsSetSource() local
142 TGaps gaps; in testAlignGapsSetSource() local
164 TGaps gaps; in testAlignGapsAssignSource() local
711 ss << gaps; in testAlignGapsSequenceInterfaceUngapped()
746 ss << gaps; in testAlignGapsSequenceInterfaceGapsCenter()
781 ss << gaps; in testAlignGapsSequenceInterfaceGapsLeading()
816 ss << gaps; in testAlignGapsSequenceInterfaceGapsTrailing()
1349 TGaps gaps; in testAlignGapsSourceIsNothing() local
1574 TGaps gaps; in SEQAN_DEFINE_TEST() local
1588 clear(gaps); in SEQAN_DEFINE_TEST()
[all …]
H A Dtest_align_gaps_iterator.h79 TGaps gaps(seq); in testAlignGapsIteratorTrivialIteratorFunctions()
98 TGaps gaps(seq); in testAlignGapsIteratorRootedRandomAccessIteratorFunctions()
161 TGaps gaps(seq); in testAlignGapsIteratorMovement()
296 TGaps gaps(seq); in testAlignGapsIteratorRelations()
333 TGaps gaps(seq); in testAlignGapsIteratorPointerArithmetic()
360 TGaps gaps(seq); in testAlignGapsIteratorForwardIteration()
390 TGaps gaps(seq); in testAlignGapsIteratorReverseIteration()
422 TGaps gaps(seq); in testAlignGapsIteratorCountGapsCountCharactersIsGap()
523 TGaps gaps(seq); in testAlignGapsIteratorClippedCountGapsCountCharactersIsGap()
536 ss << gaps; in testAlignGapsIteratorClippedCountGapsCountCharactersIsGap()
[all …]
H A Dtest_align_stream.h46 seqan::Gaps<seqan::Dna5String> gaps; in SEQAN_DEFINE_TEST() local
47 assignSource(gaps, "CGATTTAT"); in SEQAN_DEFINE_TEST()
48 insertGaps(gaps, 8, 2); in SEQAN_DEFINE_TEST()
49 insertGaps(gaps, 5, 1); in SEQAN_DEFINE_TEST()
50 insertGaps(gaps, 0, 2); in SEQAN_DEFINE_TEST()
53 ss << gaps; in SEQAN_DEFINE_TEST()
65 assignSource(gaps, "CGATTTAT"); in SEQAN_DEFINE_TEST()
66 insertGaps(gaps, 8, 2); in SEQAN_DEFINE_TEST()
67 insertGaps(gaps, 5, 1); in SEQAN_DEFINE_TEST()
68 insertGaps(gaps, 0, 2); in SEQAN_DEFINE_TEST()
[all …]
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Dgaps_array.h245 gaps._sourceEndPos = gaps._clippingEndPos; in _setLength()
261 _setLength(gaps, length(value(gaps._source))); in _reinitArrayGaps()
339 return gaps._clippingEndPos - gaps._clippingBeginPos; in length()
482 return gaps._array[0] - clippedBeginPosition(gaps);
668 gaps._array[i - 1] += gaps._array[i + 1]; in removeGaps()
764 gaps._sourceEndPos = length(value(gaps._source)); in clearClipping()
768 gaps._clippingEndPos += gaps._array[i]; in clearClipping()
781 … gaps._sourceBeginPos = toSourcePosition(gaps, unclippedViewPosition - clippedBeginPosition(gaps)); in setClippedBeginPosition()
793 gaps._sourceEndPos = toSourcePosition(gaps, unclippedViewPosition - clippedBeginPosition(gaps)); in setClippedEndPosition()
829 … setClippedBeginPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); in setBeginPosition()
[all …]
H A Dgaps_anchor.h267 gaps.data_cutEnd = 0; in _reinitAnchorGaps()
429 clear(gaps.data_gaps); in clear()
431 gaps.data_cutEnd = 0; in clear()
613 …return toSourcePosition(gaps, _unclippedLength(gaps) - (gaps.data_viewCutEnd + gaps.data_viewCutBe… in endPosition()
620 …return toSourcePosition(gaps, _unclippedLength(gaps) - (gaps.data_viewCutEnd + gaps.data_viewCutBe… in endPosition()
631 … setClippedBeginPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); in setBeginPosition()
642 setClippedEndPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); in setEndPosition()
885 return positionSeqToGap(gaps, sourcePosition) - gaps.data_viewCutBegin - gaps.data_cutBegin; in toViewPosition()
898 return positionGapToSeq(gaps, clippedViewPos + gaps.data_viewCutBegin + gaps.data_cutBegin); in toSourcePosition()
920 gaps.data_viewCutEnd = _unclippedLength(gaps) - unclippedViewPosition; in setClippedEndPosition()
[all …]
H A Dgaps_base.h449 insertGaps(gaps, clippedViewPos, 1u);
535 countLeadingGaps(TGaps const & gaps)
537 return toViewPosition(gaps, 0);
557 countTrailingGaps(TGaps const & gaps)
559 return length(gaps) - toViewPosition(gaps, length(source(gaps)) - 1) - 1;
795 write(it, gaps);
885 …return infix(source(gaps), toSourcePosition(gaps, clippedBeginPosition(gaps)), toSourcePosition(ga…
892 …return infix(source(gaps), toSourcePosition(gaps, clippedBeginPosition(gaps)), toSourcePosition(ga…
915 assign(source(gaps), value);
1032 clearGaps(gaps);
[all …]
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Dgaps_array.h253 gaps._sourceEndPos = gaps._clippingEndPos; in _setLength()
269 _setLength(gaps, length(value(gaps._source))); in _reinitArrayGaps()
347 return gaps._clippingEndPos - gaps._clippingBeginPos; in length()
531 return gaps._array[0] - clippedBeginPosition(gaps);
702 gaps._array[i - 1] += gaps._array[i + 1]; in removeGaps()
798 gaps._sourceEndPos = length(value(gaps._source)); in clearClipping()
802 gaps._clippingEndPos += gaps._array[i]; in clearClipping()
815 … gaps._sourceBeginPos = toSourcePosition(gaps, unclippedViewPosition - clippedBeginPosition(gaps)); in setClippedBeginPosition()
827 gaps._sourceEndPos = toSourcePosition(gaps, unclippedViewPosition - clippedBeginPosition(gaps)); in setClippedEndPosition()
863 … setClippedBeginPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); in setBeginPosition()
[all …]
H A Dgaps_anchor.h273 gaps.data_cutEnd = 0; in _reinitAnchorGaps()
435 clear(gaps.data_gaps); in clear()
437 gaps.data_cutEnd = 0; in clear()
593 …return toSourcePosition(gaps, _unclippedLength(gaps) - (gaps.data_viewCutEnd + gaps.data_viewCutBe… in endPosition()
600 …return toSourcePosition(gaps, _unclippedLength(gaps) - (gaps.data_viewCutEnd + gaps.data_viewCutBe… in endPosition()
611 … setClippedBeginPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); in setBeginPosition()
622 setClippedEndPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); in setEndPosition()
874 return positionSeqToGap(gaps, sourcePosition) - gaps.data_viewCutBegin - gaps.data_cutBegin; in toViewPosition()
889 …return positionGapToSeq(gaps, clippedViewPos + gaps.data_viewCutBegin + gaps.data_cutBegin, TProje… in toSourcePosition()
911 gaps.data_viewCutEnd = _unclippedLength(gaps) - unclippedViewPosition; in setClippedEndPosition()
[all …]
H A Dgaps_base.h291 value(Gaps<TSequence, TSpec> & gaps,
613 countLeadingGaps(TGaps const & gaps)
615 return toViewPosition(gaps, 0);
637 return length(gaps) - toViewPosition(gaps, length(source(gaps)) - 1) - 1;
657 countGapOpens(TGaps const & gaps)
965 write(it, gaps);
1055 …return infix(source(gaps), toSourcePosition(gaps, clippedBeginPosition(gaps)), toSourcePosition(ga…
1062 …return infix(source(gaps), toSourcePosition(gaps, clippedBeginPosition(gaps)), toSourcePosition(ga…
1085 assign(source(gaps), value);
1202 clearGaps(gaps);
[all …]
H A Dgap_anchor.h256 begin(gaps, Standard()),
257 end(gaps, Standard()),
272 begin(gaps, Standard()),
273 end(gaps, Standard()),
288 begin(gaps, Standard()),
289 end(gaps, Standard()),
305 end(gaps, Standard()),
325 end(gaps, Standard()),
341 end(gaps, Standard()),
357 end(gaps, Standard()),
[all …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Dgaps_array.h253 gaps._sourceEndPos = gaps._clippingEndPos; in _setLength()
269 _setLength(gaps, length(value(gaps._source))); in _reinitArrayGaps()
347 return gaps._clippingEndPos - gaps._clippingBeginPos; in length()
531 return gaps._array[0] - clippedBeginPosition(gaps);
702 gaps._array[i - 1] += gaps._array[i + 1]; in removeGaps()
798 gaps._sourceEndPos = length(value(gaps._source)); in clearClipping()
802 gaps._clippingEndPos += gaps._array[i]; in clearClipping()
815 … gaps._sourceBeginPos = toSourcePosition(gaps, unclippedViewPosition - clippedBeginPosition(gaps)); in setClippedBeginPosition()
827 gaps._sourceEndPos = toSourcePosition(gaps, unclippedViewPosition - clippedBeginPosition(gaps)); in setClippedEndPosition()
863 … setClippedBeginPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); in setBeginPosition()
[all …]
H A Dgaps_anchor.h273 gaps.data_cutEnd = 0; in _reinitAnchorGaps()
435 clear(gaps.data_gaps); in clear()
437 gaps.data_cutEnd = 0; in clear()
593 …return toSourcePosition(gaps, _unclippedLength(gaps) - (gaps.data_viewCutEnd + gaps.data_viewCutBe… in endPosition()
600 …return toSourcePosition(gaps, _unclippedLength(gaps) - (gaps.data_viewCutEnd + gaps.data_viewCutBe… in endPosition()
611 … setClippedBeginPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); in setBeginPosition()
622 setClippedEndPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); in setEndPosition()
874 return positionSeqToGap(gaps, sourcePosition) - gaps.data_viewCutBegin - gaps.data_cutBegin; in toViewPosition()
889 …return positionGapToSeq(gaps, clippedViewPos + gaps.data_viewCutBegin + gaps.data_cutBegin, TProje… in toSourcePosition()
911 gaps.data_viewCutEnd = _unclippedLength(gaps) - unclippedViewPosition; in setClippedEndPosition()
[all …]
H A Dgaps_base.h291 value(Gaps<TSequence, TSpec> & gaps,
613 countLeadingGaps(TGaps const & gaps)
615 return toViewPosition(gaps, 0);
637 return length(gaps) - toViewPosition(gaps, length(source(gaps)) - 1) - 1;
657 countGapOpens(TGaps const & gaps)
965 write(it, gaps);
1055 …return infix(source(gaps), toSourcePosition(gaps, clippedBeginPosition(gaps)), toSourcePosition(ga…
1062 …return infix(source(gaps), toSourcePosition(gaps, clippedBeginPosition(gaps)), toSourcePosition(ga…
1085 assign(source(gaps), value);
1202 clearGaps(gaps);
[all …]
/dports/biology/bbmap/bbmap/current/align2/
H A DGapTools.java38 int gN=gaps[gaps.length-1]; in fixGaps()
42 if(gaps[0]!=a){gaps[0]=a; changed++;} in fixGaps()
43 if(gaps[gaps.length-1]!=b){gaps[gaps.length-1]=b; changed++;} in fixGaps()
45 if(gaps[i]<a){gaps[i]=a; changed++;} in fixGaps()
46 else if(gaps[i]>b){gaps[i]=b; changed++;} in fixGaps()
52 if(gaps[i-1]>gaps[i]){gaps[i]=gaps[i-1]; changed++;} in fixGaps()
60 gaps[gaps.length-1]=b; in fixGaps()
65 gaps[i]=Tools.constrict(gaps[i], a, b); in fixGaps()
66 gaps[i+1]=Tools.constrict(gaps[i+1], a, b); in fixGaps()
67 if(gaps[i]==gaps[i+1]){remove++;} in fixGaps()
[all …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/howto/
H A Dalign_gaps_clipping.cpp14 Gaps<CharString> gaps(seq); in main() local
17 insertGaps(gaps, 2, 2); in main()
18 insertGap(gaps, 6); in main()
19 insertGap(gaps, 10); in main()
22 std::cout << "gaps\t" << gaps << "\n" in main()
36 setClippedBeginPosition(gaps, 3); in main()
37 setClippedEndPosition(gaps, 10); in main()
39 std::cout << "gaps\t" << gaps << "\n" in main()
40 << "seq \t" << infix(seq, beginPosition(gaps), endPosition(gaps)) << "\n\n"; in main()
68 …std::cout << "3 clipped gapped => " << toSourcePosition(gaps, 3) - beginPosition(gaps) << " clippe… in main()
[all …]
H A Dalign_gaps_clipping.cpp.stdout1 gaps AB--CD-EFG-HIJ
4 beginPosition(gaps) == 0
5 endPosition(gaps) == 10
6 clippedBeginPosition(gaps) == 0
7 clippedEndPosition(gaps) == 14
9 gaps -CD-EFG
12 beginPosition(gaps) == 2
13 endPosition(gaps) == 7
14 clippedBeginPosition(gaps) == 3
15 clippedEndPosition(gaps) == 10
/dports/x11-wm/i3-gaps/i3-4.20.1/src/
H A Dconfig_directives.c275 assignment->gaps.inner = gaps.inner; in create_gaps_assignment()
277 assignment->gaps.top = gaps.top; in create_gaps_assignment()
278 assignment->gaps.right = gaps.right; in create_gaps_assignment()
279 assignment->gaps.bottom = gaps.bottom; in create_gaps_assignment()
280 assignment->gaps.left = gaps.left; in create_gaps_assignment()
282 assignment->gaps.top = gaps.top; in create_gaps_assignment()
285 assignment->gaps.right = gaps.right; in create_gaps_assignment()
286 assignment->gaps.left = gaps.left; in create_gaps_assignment()
288 assignment->gaps.top = gaps.top; in create_gaps_assignment()
290 assignment->gaps.right = gaps.right; in create_gaps_assignment()
[all …]
/dports/devel/spark/spark-2.1.1/core/src/test/scala/org/apache/spark/util/random/
H A DRandomSamplerSuite.scala154 d = medianKSD(gaps(sample(Iterator.from(0), 0.5)), gaps(sample(Iterator.from(0), 0.5)))
159 d = medianKSD(gaps(sample(Iterator.from(0), 0.4)), gaps(sample(Iterator.from(0), 0.5)))
163 d = medianKSD(gaps(sampleWR(Iterator.from(0), 0.5)), gaps(sampleWR(Iterator.from(0), 0.5)))
167 d = medianKSD(gaps(sampleWR(Iterator.from(0), 0.5)), gaps(sampleWR(Iterator.from(0), 0.6)))
179 d = medianKSD(gaps(sampler.sample(Iterator.from(0))), gaps(sample(Iterator.from(0), 0.5)))
184 d = medianKSD(gaps(sampler.sample(Iterator.from(0))), gaps(sample(Iterator.from(0), 0.7)))
189 d = medianKSD(gaps(sampler.sample(Iterator.from(0))), gaps(sample(Iterator.from(0), 0.9)))
195 d = medianKSD(gaps(sampler.sample(Iterator.from(0))), gaps(sample(Iterator.from(0), 0.6)))
242 d = medianKSD(gaps(sampler.sample(Iterator.from(0))), gaps(sample(Iterator.from(0), 0.1)))
247 d = medianKSD(gaps(sampler.sample(Iterator.from(0))), gaps(sample(Iterator.from(0), 0.3)))
[all …]
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/tasks/
H A DExternalToolRunTask.cpp524 QVariantMap gaps; in getScoresGapDependencyMap() local
525 gaps["2 2"] = "2 2"; in getScoresGapDependencyMap()
526 gaps["1 2"] = "1 2"; in getScoresGapDependencyMap()
527 gaps["0 2"] = "0 2"; in getScoresGapDependencyMap()
528 gaps["2 1"] = "2 1"; in getScoresGapDependencyMap()
529 gaps["1 1"] = "1 1"; in getScoresGapDependencyMap()
533 gaps.clear(); in getScoresGapDependencyMap()
542 gaps.clear(); in getScoresGapDependencyMap()
553 gaps.clear(); in getScoresGapDependencyMap()
562 gaps.clear(); in getScoresGapDependencyMap()
[all …]
/dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/align/
H A Dgaps_example.cpp12 Gaps<Dna5String> gaps(seq); in main() local
16 insertGap(gaps, 3); in main()
17 insertGap(gaps, 5); in main()
18 insertGaps(gaps, 7, 2); in main()
21 setClippedBeginPosition(gaps, 1); in main()
22 setClippedEndPosition(gaps, 8); in main()
25 std::cout << "Resulting gaps: " << gaps << "\n" in main()
26 << "toSourcePosition(gaps, 0) == " << toSourcePosition(gaps, 0) << "\n" in main()
27 << "toSourcePosition(gaps, 4) == " << toSourcePosition(gaps, 4) << "\n" in main()
28 << "toViewPosition(gaps, 0) == " << toViewPosition(gaps, 0) << "\n" in main()
[all …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/align/
H A Dgaps_example.cpp12 Gaps<Dna5String> gaps(seq); in main() local
16 insertGap(gaps, 3); in main()
17 insertGap(gaps, 5); in main()
18 insertGaps(gaps, 7, 2); in main()
21 setClippedBeginPosition(gaps, 1); in main()
22 setClippedEndPosition(gaps, 8); in main()
25 std::cout << "Resulting gaps: " << gaps << "\n" in main()
26 << "toSourcePosition(gaps, 0) == " << toSourcePosition(gaps, 0) << "\n" in main()
27 << "toSourcePosition(gaps, 4) == " << toSourcePosition(gaps, 4) << "\n" in main()
28 << "toViewPosition(gaps, 0) == " << toViewPosition(gaps, 0) << "\n" in main()
[all …]
/dports/games/vavoom/vavoom-1.33/source/
H A Dsv_world.cpp258 if (!gaps) in SV_FindThingGap()
264 return gaps; in SV_FindThingGap()
271 while (gaps) in SV_FindThingGap()
282 gaps = gaps->next; in SV_FindThingGap()
289 return gaps; in SV_FindThingGap()
313 gaps = gaps->next; in SV_FindThingGap()
363 if (!gaps) in SV_FindOpening()
369 return gaps; in SV_FindOpening()
373 while (gaps) in SV_FindOpening()
382 return gaps; in SV_FindOpening()
[all …]
/dports/x11-wm/i3-gaps/i3-4.20.1/
H A DREADME.md6 # i3-gaps
8 ## What is i3-gaps?
14 ## How do I install i3-gaps?
28 ### gaps subsection
39 …Note:* Outer gaps are added to the inner gaps, i.e., the gaps between a screen edge and a containe…
60 gaps inner all set 20
61 gaps outer current plus 5
62 gaps horizontal current plus 40
63 gaps outer current toggle 60
78 # Only enable outer gaps when there is exactly one container
[all …]
/dports/biology/subread/subread-2.0.2-source/src/
H A Dinterval_merge.c88 void print_gaps(unsigned int * gaps, int gapn) in print_gaps() argument
92 printf("{%d,%d} ", gaps[ii*2], gaps[ii*2+1]); in print_gaps()
111 print_gaps(outbuff, gaps); in main()
114 gaps = mergeIntervals(inbuff, outbuff, 6); in main()
115 print_gaps(outbuff, gaps); in main()
118 gaps = mergeIntervals(inbuff, outbuff, 6); in main()
119 print_gaps(outbuff, gaps); in main()
122 gaps = mergeIntervals(inbuff, outbuff, 6); in main()
123 print_gaps(outbuff, gaps); in main()
126 gaps = mergeIntervals(inbuff, outbuff, 6); in main()
[all …]
/dports/audio/cuetools/cuetools-1.4.1/src/tools/
H A Dcuebreakpoints.c76 void print_breaks(Cd *cd, int gaps) in print_breaks() argument
93 if (gaps == PREPEND || gaps == SPLIT) { in print_breaks()
99 } else if (gaps == APPEND && 1 < i) { in print_breaks()
104 if (gaps == SPLIT && 0 < pg) { in print_breaks()
110 int breaks(char *name, int format, int gaps) in breaks() argument
120 print_breaks(cd, gaps); in breaks()
128 int gaps = APPEND; in main() local
166 gaps = APPEND; in main()
169 gaps = PREPEND; in main()
172 gaps = SPLIT; in main()
[all …]

12345678910>>...255