/dports/biology/canu/canu-2.2/src/overlapInCore/ |
H A D | overlapInCore-Output.C | 41 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() [all …]
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H A D | overlapInCore-Process_String_Overlaps.C | 61 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() [all …]
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/dports/biology/canu/canu-2.2/src/bogart/ |
H A D | AS_BAT_BestOverlapGraph_implementation.H | 56 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()
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H A D | AS_BAT_BestOverlapGraph.C | 55 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() [all …]
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H A D | AS_BAT_OverlapCache.H | 99 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()
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H A D | AS_BAT_OptimizePositions.C | 90 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() [all …]
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/dports/biology/canu/canu-2.2/src/overlapErrorAdjustment/ |
H A D | findErrors-Process_Olap.C | 145 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() [all …]
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H A D | correctOverlaps-Read_Olaps.C | 44 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()
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H A D | findErrors-Read_Olaps.C | 37 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()
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H A D | correctOverlaps-Redo_Olaps.C | 429 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() [all …]
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/dports/sysutils/py-pywatchman/watchman-4.9.0/java/src/com/facebook/watchman/windowspipe/ |
H A D | WindowsNamedPipe.java | 105 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()
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/dports/devel/flex-sdk/flex-sdk-4.6.0.23201/frameworks/projects/advancedgrids/src/mx/olap/ |
H A D | IOLAPResultAxis.as | 12 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
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H A D | OLAPMeasure.as | 12 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]);
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H A D | IOLAPResult.as | 12 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
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H A D | OLAPResultAxis.as | 12 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
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H A D | OLAPAxisPosition.as | 12 package mx.olap 21 * @see mx.olap.IOLAPResultAxis 22 * @see mx.olap.IOLAPResult 23 * @see mx.olap.OLAPResult
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H A D | IOLAPQuery.as | 12 package mx.olap 17 * @see mx.olap.OLAPQuery 18 * @see mx.olap.IOLAPQueryAxis 19 * @see mx.olap.OLAPQueryAxis
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H A D | IOLAPAxisPosition.as | 12 package mx.olap 19 * @see mx.olap.OLAPQueryAxis 20 * @see mx.olap.OLAPResultAxis
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/dports/sysutils/py-pywatchman/watchman-4.9.0/ |
H A D | stream_win.cpp | 46 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() [all …]
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/dports/sysutils/watchman/watchman-4.5.0/watcher/ |
H A D | win32.c | 16 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() [all …]
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/ |
H A D | mgaps.cc | 85 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()
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/dports/sysutils/watchman/watchman-4.5.0/ |
H A D | stream_win.c | 15 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 [all …]
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/dports/audio/xmcd/xmcd-3.3.2/cdda_d/ |
H A D | common.c | 71 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()
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/dports/science/libctl/libctl-4.5.0/utils/ |
H A D | geomtst.c | 180 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()
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/dports/sysutils/py-pywatchman/watchman-4.9.0/watcher/ |
H A D | win32.cpp | 112 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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