/dports/biology/lamarc/lamarc-2.1.8/src/datalike/ |
H A D | tipdata.cpp | 32 individual(FLAGLONG), in TipData() 33 m_locus(FLAGLONG), in TipData() 34 m_hap(FLAGLONG), in TipData() 48 individual = FLAGLONG; in Clear() 49 m_locus = FLAGLONG; in Clear() 50 m_hap = FLAGLONG; in Clear() 97 LongVec1d parts(partitions.size(),FLAGLONG); in GetBranchPartitions()
|
H A D | dlcalc.cpp | 75 long firstmrkr = FLAGLONG; in SitePairToMarkerPair() 76 long lastmrkr = FLAGLONG; in SitePairToMarkerPair() 89 return(rangepair(FLAGLONG, FLAGLONG)); in SitePairToMarkerPair() 97 return(rangepair(FLAGLONG,FLAGLONG)); in SitePairToMarkerPair() 119 assert(firstmrkr != FLAGLONG && lastmrkr != FLAGLONG); in SitePairToMarkerPair() 556 if (marker.first == FLAGLONG) continue; in Calculate() 812 if (marker.first != FLAGLONG) in Calculate() 932 if (marker.first != FLAGLONG) in SumNoPanel() 944 if (marker.first != FLAGLONG) in SumNoPanel() 1094 if (marker.first != FLAGLONG) in SumPanel() [all …]
|
H A D | locus.cpp | 38 m_nmarkers(FLAGLONG), in Locus() 39 m_nsites(FLAGLONG), in Locus() 58 m_truesite(FLAGLONG), in Locus() 86 if (m_nsites == FLAGLONG) return m_nmarkers; in GetNsites() 229 if (m_nmarkers == FLAGLONG) in SetNmarkers() 645 return FLAGLONG; in SiteToMarker() 876 if (m_truesite != FLAGLONG) in ReportMappingInfo() 1079 return FLAGLONG; in ChooseVariableSiteFrom()
|
H A D | phenotypes.cpp | 43 : m_regionnum(FLAGLONG), in Phenotypes() 52 assert (m_regionnum != FLAGLONG); in AddPhenotype()
|
H A D | locuscell.cpp | 83 if (dlcells[cell]->DiffersFrom(src.dlcells[cell]) != FLAGLONG) in operator ==()
|
H A D | haplotypes.cpp | 37 m_current_hapindex(FLAGLONG) in Haplotypes() 50 m_current_hapindex(FLAGLONG) in Haplotypes()
|
/dports/biology/lamarc/lamarc-2.1.8/src/control/ |
H A D | chainout.cpp | 18 : m_badtrees(FLAGLONG), in ChainOut() 19 m_tinypoptrees(FLAGLONG), in ChainOut() 20 m_zerodltrees(FLAGLONG), in ChainOut() 21 m_stretchedtrees(FLAGLONG), in ChainOut() 23 m_numtemps(FLAGLONG), in ChainOut()
|
H A D | chainpack.cpp | 233 chout.SetNumBadTrees(FLAGLONG); in SetSummaryOverReps() 234 chout.SetNumTinyPopTrees(FLAGLONG); in SetSummaryOverReps() 235 chout.SetNumStretchedTrees(FLAGLONG); in SetSummaryOverReps() 236 chout.SetNumZeroDLTrees(FLAGLONG); in SetSummaryOverReps() 262 chout.SetNumBadTrees(FLAGLONG); in SetSummaryOverRegions() 263 chout.SetNumTinyPopTrees(FLAGLONG); in SetSummaryOverRegions() 264 chout.SetNumStretchedTrees(FLAGLONG); in SetSummaryOverRegions() 265 chout.SetNumZeroDLTrees(FLAGLONG); in SetSummaryOverRegions()
|
/dports/biology/lamarc/lamarc-2.1.8/src/force/ |
H A D | event.cpp | 115 m_chosenxpart(FLAGLONG), in CoalEvent() 274 m_frompop(FLAGLONG), in MigEvent() 275 m_topop(FLAGLONG) in MigEvent() 368 m_topop = FLAGLONG; in PickTime() 409 m_frompop(FLAGLONG), in DivMigEvent() 410 m_topop(FLAGLONG) in DivMigEvent() 526 m_topop = FLAGLONG; in PickTime() 564 m_startdis(FLAGLONG), in DiseaseEvent() 565 m_enddis(FLAGLONG) in DiseaseEvent() 866 m_pindex = FLAGLONG; in EpochEvent() [all …]
|
H A D | paramstat.cpp | 28 if (groupindex != FLAGLONG) return "be held at zero and ignored in output)"; in ConstraintDescription() 36 if (groupindex != FLAGLONG) in ConstraintDescription() 50 if (groupindex != FLAGLONG) return "stay at the same constant value)"; in ConstraintDescription()
|
H A D | timemanager.cpp | 218 targetxpart = FLAGLONG; in TimeOfActiveCoal() 268 targetxpart = FLAGLONG; in TimeOfInactiveCoal() 329 tiptrait = FLAGLONG; in TimeOfTraitMutation() 330 roottrait = FLAGLONG; in TimeOfTraitMutation() 445 targetxpart = FLAGLONG; in TimeOfActiveCoal() 1611 targetxpart = FLAGLONG; in TimeOfActiveCoal() 1708 targetxpart = FLAGLONG; in TimeOfInactiveCoal() 1738 tiptrait = FLAGLONG; in TimeOfTraitMutation() 1739 roottrait = FLAGLONG; in TimeOfTraitMutation() 1855 tiptrait = FLAGLONG; in TimeOfTraitMutation() [all …]
|
H A D | forceparam.cpp | 45 : m_region(FLAGLONG), in ForceParameters() 57 : m_region(FLAGLONG), in ForceParameters() 607 if (m_region == FLAGLONG) in FillRegionalParamsFromGlobalParams() 626 if (m_region == FLAGLONG) in FillGlobalParamsFromRegionalParams()
|
/dports/biology/lamarc/lamarc-2.1.8/src/bayeslike/ |
H A D | bayesanalyzer_1d.cpp | 491 if (!((region == FLAGLONG) && (m_regioncurves.size() == 1))) in CalcProfiles() 504 if (region==FLAGLONG) in CalcProfiles() 521 if (nregion == FLAGLONG) in CalcProfile() 639 if (region == FLAGLONG) in GetMinParamValFromCurve() 652 if (region == FLAGLONG) in GetMaxParamValFromCurve() 665 if (region == FLAGLONG) in GetBinWidthFromCurve() 706 if (region==FLAGLONG) in WriteCurvesForRegion() 718 if (region==FLAGLONG) in WriteCurvesForRegion() 743 if (region==FLAGLONG) in WriteCurvesForRegion() 749 if ((region != m_currentRegion-1) && (region != FLAGLONG)) in WriteCurvesForRegion() [all …]
|
/dports/biology/lamarc/lamarc-2.1.8/src/tree/ |
H A D | branch.cpp | 90 m_partitions(registry.GetDataPack().GetNPartitionForces(), FLAGLONG), in Branch() 544 if (badmarker == FLAGLONG) continue; in DLCheck() 1208 FLAGLONG, myxpart, FLAGLONG, FLAGLONG, emptyvec, force_COAL); in ScoreEvent() 1235 s, myxpart, FLAGLONG, FLAGLONG, emptyvec, force_COAL); in ScoreEvent() 1482 FLAGLONG, mypop, chpop, FLAGLONG, emptyvec, force_MIG); in ScoreEvent() 1509 s, mypop, chpop, FLAGLONG, emptyvec, force_MIG); in ScoreEvent() 1568 FLAGLONG, mypop, chpop, FLAGLONG, emptyvec, force_DIVMIG); in ScoreEvent() 1595 s, mypop, chpop, FLAGLONG, emptyvec, force_DIVMIG); in ScoreEvent() 1654 FLAGLONG, mydis, chdis, FLAGLONG, emptyvec, force_DISEASE); in ScoreEvent() 1724 FLAGLONG, mypop, chpop, FLAGLONG, emptyvec, force_DIVERGENCE); in ScoreEvent() [all …]
|
H A D | summary.cpp | 208 … m_fakeIntervals.AddDummyInterval(fakeback, 0L, param, FLAGLONG, FLAGLONG, force_COAL); in AdjustSummary() 315 … m_fakeIntervals.AddDummyInterval(fakeback, 0L, frompop, topop, FLAGLONG, force_MIG); in AdjustSummary() 419 … m_fakeIntervals.AddDummyInterval(fakeback, 0L, oldstatus, newstatus, FLAGLONG, force_DISEASE); in AdjustSummary() 557 m_fakeIntervals.AddDummyInterval(fakeback, 0L, FLAGLONG, FLAGLONG, 0L, force_REC); in AdjustSummary()
|
H A D | range.h | 96 virtual long int GetFirstTargetLink_Rg() const { assert(false); return FLAGLONG; }; in GetFirstTargetLink_Rg() 97 virtual long int NumTargetLinks_Rg() const { assert(false); return FLAGLONG; }; in NumTargetLinks_Rg() 99 virtual long int NumNewTargetLinks_Rg() const { assert(false); return FLAGLONG; }; in NumNewTargetLinks_Rg()
|
/dports/biology/recombine/recombine1.41/ |
H A D | getdata.c | 85 return(FLAGLONG); in getdata_numpop() 89 return(FLAGLONG); in getdata_numpop() 113 return(FLAGLONG); in getdata_numloci() 117 return(FLAGLONG); in getdata_numloci() 141 return(FLAGLONG); in getdata_nummarkers() 145 return(FLAGLONG); in getdata_nummarkers() 173 return(FLAGLONG); in getdata_numseq() 204 return(FLAGLONG); in getdata_numtips() 231 return(FLAGLONG); in getdata_sitecount() 258 return(FLAGLONG); in getdata_markersite() [all …]
|
H A D | constants.h | 147 #define FLAGLONG -99L /* a arbitrary special value */ macro
|
H A D | recombine.c | 494 return(FLAGLONG); in findlink() 1794 op->thlb = FLAGLONG; in initoptions() 1795 op->thub = FLAGLONG; in initoptions() 1796 op->reclb = FLAGLONG; in initoptions() 1797 op->recub = FLAGLONG; in initoptions() 2510 p->number = FLAGLONG; in allocate_nodelet() 4249 snpsmooth(op,data,curtree,substart,FLAGLONG,FLAGLONG); in localeval() 4524 sranges[j+1] = FLAGLONG; in finddnasubtrees() 4643 return(FLAGLONG); in sitetorightmarker() 4665 return(FLAGLONG); in sitetomarker() [all …]
|
H A D | jdrop.c | 71 return(FLAGLONG); in countsites() 450 return((double)FLAGLONG); in getnumlinks() 663 if (cutmarker == FLAGLONG) return; in edit_alias() 712 (*newranges)[3] = FLAGLONG; in contrib() 735 (*newranges)[i+2] = FLAGLONG; in contrib() 872 return((p->futileflag == FLAGLONG)); in is_futile() 2945 if (newstart == FLAGLONG) { in updatesegranges() 2977 if (oval == FLAGLONG) in updatesegranges() 2985 if (nval == FLAGLONG) in updatesegranges() 3040 if(newstart != FLAGLONG && newend != FLAGLONG) { in segranges_to_ranges() [all …]
|
/dports/biology/lamarc/lamarc-2.1.8/src/report/ |
H A D | runreport.cpp | 419 (zerodltrees == 0 || zerodltrees == FLAGLONG) && in FormatReport() 420 (stretchedtrees == 0 || stretchedtrees == FLAGLONG)) in FormatReport() 428 if (badtrees == FLAGLONG) in FormatReport() 439 if (tinytrees == FLAGLONG) in FormatReport() 450 if (zerodltrees == FLAGLONG) in FormatReport() 461 if (stretchedtrees == FLAGLONG) in FormatReport()
|
H A D | curvefiles.cpp | 75 double minIndex = ba.GetMinParamValFromCurve(FLAGLONG, paramnum); in getMinIndex() 91 double maxIndex = ba.GetMaxParamValFromCurve(FLAGLONG, paramnum); in getMaxIndex() 107 double increment = ba.GetBinWidthFromCurve(FLAGLONG, paramnum); in getIncrement()
|
/dports/biology/lamarc/lamarc-2.1.8/src/ui_vars/ |
H A D | ui_vars_forces.cpp | 330 if (gindex != FLAGLONG) in SetDoProfile() 361 if (gindex != FLAGLONG) in GetParamstatus() 386 if (gindex == FLAGLONG) in SetParamstatus() 399 if (gindex == FLAGLONG) in GetStartValue() 591 if (gindex != FLAGLONG) in SetUserStartValue() 700 if (gindex == FLAGLONG) in SetPriorType() 725 if (gindex == FLAGLONG) in SetRelativeSampling() 753 if (gindex == FLAGLONG) in SetLowerBound() 972 if (gnum != FLAGLONG) in RemoveParamIfInAGroup() 1041 return FLAGLONG; in ParamInGroup() [all …]
|
/dports/biology/lamarc/lamarc-2.1.8/src/ui_interface/ |
H A D | constraint_interface.cpp | 168 if (gindex == FLAGLONG) in Get() 198 if (gindex != FLAGLONG) in Get()
|
/dports/biology/lamarc/lamarc-2.1.8/src/lamarcmenus/ |
H A D | constraintmenus.cpp | 307 return UIId(FLAGLONG); in GetGroupIdFromLocalId() 370 if (groupId.GetIndex1() != FLAGLONG) in GetHandler()
|