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/dports/biology/canu/canu-2.2/src/overlapInCore/
H A DoverlapInCore-Output.C41 ovs->dat.ovl.span = (olap->s_hi - olap->s_lo); in Output_Overlap()
42 ovs->dat.ovl.span += (olap->t_hi - olap->t_lo); in Output_Overlap()
63 assert(olap->s_lo < olap->s_hi); in Output_Overlap()
64 assert(olap->t_lo < olap->t_hi); in Output_Overlap()
67 assert((olap->s_lo == 0) || (olap->t_lo == 0)); in Output_Overlap()
68 assert((olap->s_hi == S_Len - 1) || (olap->t_hi == T_Len - 1)); in Output_Overlap()
71 if ((olap->s_lo > olap->t_lo) || in Output_Overlap()
74 assert((olap->s_hi == S_Len - 1) || (olap->t_hi == T_Len - 1)); in Output_Overlap()
78 assert((olap->s_hi == S_Len - 1) || (olap->t_hi == T_Len - 1)); in Output_Overlap()
221 ovl->dat.ovl.span = (olap->s_hi - olap->s_lo); in Output_Partial_Overlap()
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H A DoverlapInCore-Process_String_Overlaps.C61 int32 leni = 1 + std::min(olap[i].s_hi - olap[i].s_lo, olap[i].t_hi - olap[i].t_lo); in Combine_Into_One_Olap()
62 int32 lenb = 1 + std::min(olap[best].s_hi - olap[best].s_lo, olap[best].t_hi - olap[best].t_lo); in Combine_Into_One_Olap()
64 if ((olap[i].quality < olap[best].quality) || in Combine_Into_One_Olap()
65 (olap[i].quality == olap[best].quality && leni > lenb)) in Combine_Into_One_Olap()
185 int32 old_diag = olap[i].t_lo - olap[i].s_lo; in Add_Overlap()
228 olap[ct].s_lo = olap[ct].s_left_boundary = s_lo; in Add_Overlap()
229 olap[ct].s_hi = olap[ct].s_right_boundary = s_hi; in Add_Overlap()
230 olap[ct].t_lo = olap[ct].t_left_boundary = t_lo; in Add_Overlap()
231 olap[ct].t_hi = olap[ct].t_right_boundary = t_hi; in Add_Overlap()
296 matching_bases = (1.0 - olap[0].quality) * (2 + olap[0].s_hi - olap[0].s_lo in Choose_Best_Partial()
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/dports/biology/canu/canu-2.2/src/bogart/
H A DAS_BAT_BestOverlapGraph_implementation.H56 BestEdgeOverlap::set(BAToverlap const &olap) { in set() argument
57 _id = olap.b_iid; in set()
58 if (((olap.a_hang <= 0) && (olap.b_hang >= 0)) || // If contained, _e3p just means in set()
59 ((olap.a_hang >= 0) && (olap.b_hang <= 0))) // the other read is flipped in set()
60 _e3p = olap.flipped; in set()
62 _e3p = olap.BEndIs3prime(); // olap is to the 3' end in set()
64 _ahang = olap.a_hang; in set()
65 _bhang = olap.b_hang; in set()
66 _evalue = olap.evalue; in set()
H A DAS_BAT_BestOverlapGraph.C55 if (olap.a_hang > 0) in scoreOverlap()
56 leng = RI->readLength(olap.a_iid) - olap.a_hang; in scoreOverlap()
58 leng = RI->readLength(olap.a_iid) + olap.b_hang; in scoreOverlap()
1062 olap.a_iid, olap.b_iid, in isOverlapBadQuality()
1064 olap.a_hang, in isOverlapBadQuality()
1065 olap.b_hang, in isOverlapBadQuality()
1075 return(olap.filtered); in isOverlapBadQuality()
1089 olap.a_iid, olap.AEndIs3prime() ? '3' : '5', in logEdgeScore()
1090 olap.b_iid, olap.BEndIs3prime() ? '3' : '5', in logEdgeScore()
1091 olap.a_hang, in logEdgeScore()
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H A DAS_BAT_OverlapCache.H99 convert(ovOverlap &olap) { in convert() argument
100 olap.clear(); in convert()
102 olap.a_iid = a_iid; in convert()
103 olap.b_iid = b_iid; in convert()
105 olap.evalue(evalue); in convert()
107 olap.flipped(flipped); in convert()
108 olap.a_hang(a_hang); in convert()
109 olap.b_hang(b_hang); in convert()
H A DAS_BAT_OptimizePositions.C90 BAToverlap &olap, in optimize_isCompatible() argument
101 assert(olap.a_iid == iiid); // The overlap has a_iid == ii. in optimize_isCompatible()
102 assert(olap.b_iid == jjid); in optimize_isCompatible()
149 if ((olap.AisContained() == true) || in optimize_isCompatible()
150 (olap.AisContainer() == true)) in optimize_isCompatible()
165 int32 expJbgn = ip.min() + (ip.isForward() ? olap.a_hang : -olap.b_hang); in optimize_isCompatible()
166 int32 expJend = ip.max() + (ip.isForward() ? olap.b_hang : -olap.a_hang); in optimize_isCompatible()
178 if (((ip.isForward() == jp.isForward()) && (olap.flipped == true)) || in optimize_isCompatible()
179 ((ip.isForward() != jp.isForward()) && (olap.flipped == false))) in optimize_isCompatible()
192 olap.a_hang, olap.b_hang, in optimize_isCompatible()
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/dports/biology/canu/canu-2.2/src/overlapErrorAdjustment/
H A DfindErrors-Process_Olap.C145 Process_Olap(Olap_Info_t *olap, in Process_Olap() argument
152 olap->a_iid, olap->b_iid, in Process_Olap()
153 olap->a_hang, olap->b_hang, in Process_Olap()
154 olap->innie == true ? 'I' : 'N'); in Process_Olap()
160 int32 ri = olap->a_iid - wa->G->bgnID; in Process_Olap()
176 if ((olap->innie == true) && (wa->rev_id != olap->b_iid)) { in Process_Olap()
179 wa->rev_id = olap->b_iid; in Process_Olap()
184 if (olap->a_hang > 0) { in Process_Olap()
185 a_offset = olap->a_hang; in Process_Olap()
189 if (olap->a_hang < 0) { in Process_Olap()
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H A DcorrectOverlaps-Read_Olaps.C44 ovOverlap olap; in Read_Olaps() local
46 while (ovs->readOverlap(&olap)) { in Read_Olaps()
47 G->olaps[G->olapsLen].a_iid = olap.a_iid; in Read_Olaps()
48 G->olaps[G->olapsLen].b_iid = olap.b_iid; in Read_Olaps()
49 G->olaps[G->olapsLen].a_hang = olap.a_hang(); in Read_Olaps()
50 G->olaps[G->olapsLen].b_hang = olap.b_hang(); in Read_Olaps()
52 G->olaps[G->olapsLen].innie = (olap.flipped() == true); in Read_Olaps()
53 G->olaps[G->olapsLen].normal = (olap.flipped() == false); in Read_Olaps()
56 G->olaps[G->olapsLen].evalue = olap.evalue(); in Read_Olaps()
H A DfindErrors-Read_Olaps.C37 ovOverlap olap; in Read_Olaps() local
39 while (ovs->readOverlap(&olap)) { in Read_Olaps()
40 G->olaps[G->olapsLen].a_iid = olap.a_iid; in Read_Olaps()
41 G->olaps[G->olapsLen].b_iid = olap.b_iid; in Read_Olaps()
42 G->olaps[G->olapsLen].a_hang = olap.a_hang(); in Read_Olaps()
43 G->olaps[G->olapsLen].b_hang = olap.b_hang(); in Read_Olaps()
44 G->olaps[G->olapsLen].innie = (olap.flipped() == true); in Read_Olaps()
45 G->olaps[G->olapsLen].normal = (olap.flipped() == false); in Read_Olaps()
H A DcorrectOverlaps-Redo_Olaps.C429 const Olap_Info_t &olap = G->olaps[thisOvl]; in Redo_Olaps() local
431 if (G->secondID != UINT32_MAX && olap.b_iid != G->secondID) in Redo_Olaps()
434 if (olap.normal) { in Redo_Olaps()
443 char *a_part = G->reads[olap.a_iid - G->bgnID].bases; in Redo_Olaps()
444 if (olap.a_hang > 0) { in Redo_Olaps()
445 int32 ha = Hang_Adjust(olap.a_hang, in Redo_Olaps()
446 G->reads[olap.a_iid - G->bgnID].adjusts, in Redo_Olaps()
453 char *b_part = (olap.normal == true) ? fseq : rseq; in Redo_Olaps()
455 if (olap.a_hang < 0) { in Redo_Olaps()
456 int32 ha = olap.normal ? Hang_Adjust(-olap.a_hang, fadj, fadjLen) : in Redo_Olaps()
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/dports/sysutils/py-pywatchman/watchman-4.9.0/java/src/com/facebook/watchman/windowspipe/
H A DWindowsNamedPipe.java105 WinBase.OVERLAPPED olap = new WinBase.OVERLAPPED(); in write() local
106 olap.hEvent = writerWaitable; in write()
107 olap.write(); in write()
109 boolean immediate = API.WriteFile(pipeHandle, data, len, null, olap.getPointer()); in write()
116 if (!API.GetOverlappedResult(pipeHandle, olap.getPointer(), written, true)) { in write()
138 WinBase.OVERLAPPED olap = new WinBase.OVERLAPPED(); in read() local
139 olap.hEvent = readerWaitable; in read()
140 olap.write(); in read()
142 boolean immediate = API.ReadFile(pipeHandle, readBuffer, len, null, olap.getPointer()); in read()
149 if (!API.GetOverlappedResult(pipeHandle, olap.getPointer(), read, true)) { in read()
/dports/devel/flex-sdk/flex-sdk-4.6.0.23201/frameworks/projects/advancedgrids/src/mx/olap/
H A DIOLAPResultAxis.as12 package mx.olap
19 * @see mx.olap.OLAPQuery
20 * @see mx.olap.OLAPQueryAxis
21 * @see mx.olap.OLAPResultAxis
22 * @see mx.olap.IOLAPResult
23 * @see mx.olap.OLAPResult
H A DOLAPMeasure.as12 package mx.olap
15 import mx.olap.aggregators.SumAggregator;
16 import mx.olap.aggregators.AverageAggregator;
17 import mx.olap.aggregators.MaxAggregator;
18 import mx.olap.aggregators.MinAggregator;
19 import mx.olap.aggregators.CountAggregator;
22 [ResourceBundle("olap")]
108 * @see mx.olap.IOLAPCustomAggregator
149 "olap", "invalidAggregator", [value]);
H A DIOLAPResult.as12 package mx.olap
17 * @see mx.olap.OLAPQuery
18 * @see mx.olap.OLAPQueryAxis
19 * @see mx.olap.IOLAPResultAxis
20 * @see mx.olap.OLAPResultAxis
21 * @see mx.olap.OLAPResult
H A DOLAPResultAxis.as12 package mx.olap
21 * @see mx.olap.OLAPQuery
22 * @see mx.olap.OLAPQueryAxis
23 * @see mx.olap.IOLAPResultAxis
24 * @see mx.olap.IOLAPResult
25 * @see mx.olap.OLAPResult
H A DOLAPAxisPosition.as12 package mx.olap
21 * @see mx.olap.IOLAPResultAxis
22 * @see mx.olap.IOLAPResult
23 * @see mx.olap.OLAPResult
H A DIOLAPQuery.as12 package mx.olap
17 * @see mx.olap.OLAPQuery
18 * @see mx.olap.IOLAPQueryAxis
19 * @see mx.olap.OLAPQueryAxis
H A DIOLAPAxisPosition.as12 package mx.olap
19 * @see mx.olap.OLAPQueryAxis
20 * @see mx.olap.OLAPResultAxis
/dports/sysutils/py-pywatchman/watchman-4.9.0/
H A Dstream_win.cpp46 OVERLAPPED olap; member
115 LPOVERLAPPED olap,
121 LPOVERLAPPED olap,
130 LPOVERLAPPED olap, in get_overlapped_result_ex_impl() argument
178 LPOVERLAPPED olap, in probe_get_overlapped_result_ex() argument
195 return func(file, olap, bytes, millis, alertable); in probe_get_overlapped_result_ex()
202 if (CancelIoEx(handle(), &read_pending->olap)) { in ~win_handle()
271 &h->read_pending->olap, in win_read_handle_completion()
427 LPOVERLAPPED olap) { in write_completed() argument
429 struct overlapped_op *op = (overlapped_op*)olap; in write_completed()
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/dports/sysutils/watchman/watchman-4.5.0/watcher/
H A Dwin32.c16 HANDLE ping, olap; member
73 state->olap = CreateEvent(NULL, TRUE, FALSE, NULL); in winwatch_root_init()
74 if (!state->olap) { in winwatch_root_init()
110 CloseHandle(state->olap); in winwatch_root_dtor()
131 OVERLAPPED olap; in readchanges_thread() local
133 HANDLE handles[2] = { state->olap, state->ping }; in readchanges_thread()
146 memset(&olap, 0, sizeof(olap)); in readchanges_thread()
147 olap.hEvent = state->olap; in readchanges_thread()
156 TRUE, filter, NULL, &olap, NULL)) { in readchanges_thread()
198 if (!GetOverlappedResult(state->dir_handle, &olap, in readchanges_thread()
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/
H A Dmgaps.cc85 int olap = A[i].Start2 + A[i].Len - A[j].Start2; in Filter_Matches() local
87 if (olap >= A[i].Len / 2) { in Filter_Matches()
92 if (olap >= A[j].Len / 2) in Filter_Matches()
95 if (olap >= A[i].Len / 2) { in Filter_Matches()
104 int olap = A[i].Start1 + A[i].Len - A[j].Start1; in Filter_Matches() local
106 if (olap >= A[i].Len / 2) { in Filter_Matches()
111 if (olap >= A[j].Len / 2) in Filter_Matches()
115 if (olap >= A[i].Len / 2) { in Filter_Matches()
/dports/sysutils/watchman/watchman-4.5.0/
H A Dstream_win.c15 OVERLAPPED olap; member
43 LPOVERLAPPED olap,
51 LPOVERLAPPED olap, in win7_get_overlapped_result_ex() argument
57 if (GetOverlappedResult(file, olap, bytes, FALSE)) { in win7_get_overlapped_result_ex()
82 LPOVERLAPPED olap, in probe_get_overlapped_result_ex() argument
98 return func(file, olap, bytes, millis, alertable); in probe_get_overlapped_result_ex()
117 if (CancelIoEx(h->h, &h->read_pending->olap)) { in win_close()
123 if (CancelIoEx(h->h, &h->write_pending->olap)) { in win_close()
271 h->read_pending->olap.hEvent = h->waitable; in win_read_non_blocking()
332 LPOVERLAPPED olap) { in write_completed() argument
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/dports/audio/xmcd/xmcd-3.3.2/cdda_d/
H A Dcommon.c71 i = cdp->cdb->olap; in cdda_rd_corrjitter()
72 l = &cdp->cdb->olap[(cdp->cds->search_bytes << 1) - 1]; in cdda_rd_corrjitter()
78 if ((i - cdp->cdb->olap) % 2 == 0) { in cdda_rd_corrjitter()
94 idx = i - cdp->cdb->olap - cdp->cds->search_bytes; in cdda_rd_corrjitter()
102 (void) memcpy(j, cdp->cdb->olap + cdp->cds->search_bytes, idx); in cdda_rd_corrjitter()
/dports/science/libctl/libctl-4.5.0/utils/
H A Dgeomtst.c180 void check_overlap(double tol, double olap0, double olap, int dim, geometric_object o, geom_box b) { in check_overlap() argument
181 if (fabs(olap0 - olap) > 2 * tol * fabs(olap)) { in check_overlap()
186 fabs(olap0 - olap) / fabs(olap), olap, olap0, geometry_lattice.basis1.x, in check_overlap()
195 printf("Got %s %dd overlap %g vs. %g with tol = %e\n", object_name(o), dim, olap, olap0, tol); in check_overlap()
205 double d, olap, olap0; in test_overlap() local
218 olap = box_overlap_with_object(b, o, tol / 100, 10000 / tol); in test_overlap()
220 check_overlap(tol, olap0, olap, dim, o, b); in test_overlap()
/dports/sysutils/py-pywatchman/watchman-4.9.0/watcher/
H A Dwin32.cpp112 OVERLAPPED olap; in readChangesThread() local
134 memset(&olap, 0, sizeof(olap)); in readChangesThread()
135 olap.hEvent = olapEvent; in readChangesThread()
140 dir_handle, &buf[0], size, TRUE, filter, nullptr, &olap, nullptr)) { in readChangesThread()
170 &olap, in readChangesThread()
199 if (!GetOverlappedResult(dir_handle, &olap, &bytes, FALSE)) { in readChangesThread()

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