public void OnLoadAllPhyloDInteractions(List <PhyloDInteractionCircleViewModel> vms)
{
foreach (var vm in vms)
{
ModelElements.Add(vm);
}
}
public override bool Initialize(IBioDataLoader data)
{
var sdloader = data as IBioDataLoader <IStructureModelBioEntity>;
if (sdloader != null)
{
var basePairs = from bp in sdloader.Entities.OfType <IBasePairEntity>()
select bp;
_sequence = basePairs.First(bp => bp.Sequence != null).Sequence;
//ElementSpacing = (Width - (2 * _xPadding)) / _sequence.RawData.Count;
Width = (2 * _xPadding) + ElementSpacing * _sequence.RawData.Count;
for (int i = 0; i < _sequence.RawData.Count; i++)
{
NestedElementViewModel nevm = new NestedElementViewModel(this, _sequence.RawData[i], i);
_nestedVMs.Add(nevm);
}
_maxBPDistance = basePairs.Max(e => e.ThreePrimeIndex - e.FivePrimeIndex - 1);
_minBPDistance = basePairs.Min(e => e.ThreePrimeIndex - e.FivePrimeIndex - 1);
var basepairVMs = from bp in basePairs
join fpVM in _nestedVMs on bp.FivePrimeIndex equals fpVM.Index
join tpVM in _nestedVMs on bp.ThreePrimeIndex equals tpVM.Index
select new NestedBasePairViewModel(this, fpVM, tpVM);
foreach (NestedBasePairViewModel bp in basepairVMs)
{
ModelElements.Add(bp);
}
foreach (NestedElementViewModel elem in _nestedVMs)
{
ModelElements.Add(elem);
}
var tickElems = from elem in _nestedVMs
where elem.Index == 1 || elem.Index % 10 == 0
select elem;
foreach (NestedElementViewModel elem in tickElems)
{
ModelElements.Add(new NestedElementTickViewModel(this, elem));
}
}
return(base.Initialize(data));
}
public override bool Initialize(IBioDataLoader data)
{
var sdloader = data as IBioDataLoader <IStructureModelBioEntity>;
if (sdloader != null)
{
var basePairs = from bp in sdloader.Entities.OfType <IBasePairEntity>()
select bp;
IBioEntity sequence = basePairs.First(bp => bp.Sequence != null).Sequence;
_seqVM = new CircleSequenceViewModel(sequence);
PhyloDVM = new PhyloDCircleViewModel(_seqVM);
LoadPhyloDDataCommand = new DelegatingCommand(_phyloDVM.OnLoadPhyloDData);
Width = _seqVM.Width;
Height = _seqVM.Height;
var basePairVM = from bp in basePairs
select new CircleBasePairViewModel(_seqVM, bp);
foreach (var vm in basePairVM)
{
ModelElements.Add(vm);
}
ModelElements.Add(_seqVM);
foreach (var vm in _seqVM.Elements)
{
ModelElements.Add(vm);
}
foreach (var vm in _seqVM.TickMarks)
{
ModelElements.Add(vm);
}
foreach (var vm in _seqVM.TickLabels)
{
ModelElements.Add(vm);
}
}
return(base.Initialize(data));
}
public override bool Initialize(IBioDataLoader data)
{
Dictionary <int, SSBasePairViewModel> basePairVMs = new Dictionary <int, SSBasePairViewModel>();
var sdloader = data as IBioDataLoader <IStructureModelBioEntity>;
if (sdloader != null)
{
var basePairs = from bp in sdloader.Entities.OfType <XRNABasePair>()
select bp;
foreach (XRNABasePair bp in basePairs)
{
SSBasePairViewModel bpvm = BuildBasePairViewModel(bp);
ModelElements.Add(bpvm);
ModelElements.Add(bpvm.FivePrimeNucleotide);
ModelElements.Add(bpvm.ThreePrimeNucleotide);
basePairVMs.Add(bpvm.FivePrimeNucleotide.Index, bpvm);
}
var unpairedNt = from nt in sdloader.Entities.OfType <XRNANucleotide>()
select nt;
foreach (XRNANucleotide nt in unpairedNt)
{
SSSymbolViewModel svm = BuildSymbolViewModel(nt);
ModelElements.Add(svm);
}
var allEntities = from entity in sdloader.Entities
select entity;
foreach (IStructureModelBioEntity entity in allEntities)
{
if (entity is XRNABasePairConnector)
{
XRNABasePairConnector lc = (XRNABasePairConnector)entity;
ModelElements.Add(new SSBasePairLineConnectorViewModel(basePairVMs[lc.BasePair.FivePrimeIndex + 1])
{
Color = lc.Color,
Thickness = lc.Thickness,
Visible = lc.Visible
});
}
else if (entity is XRNABasePairConnectorCircle)
{
XRNABasePairConnectorCircle cc = (XRNABasePairConnectorCircle)entity;
ModelElements.Add(new SSBasePairCircleConnectorViewModel(basePairVMs[cc.BasePair.FivePrimeIndex + 1])
{
Color = cc.Color,
Radius = cc.Radius,
Filled = cc.Filled,
Thickness = cc.Thickness
});
}
else if (entity is TextLabel)
{
TextLabel lc = (TextLabel)entity;
ModelElements.Add(new SSTextLabelViewModel(lc.Start.X, lc.Start.Y, lc.Text, new FontFamily(lc.FontFace), (FontStyle)_fscvtr.ConvertFrom(lc.FontStyle),
(FontWeight)_fwcvtr.ConvertFrom(lc.FontWeight), lc.FontSize, (Brush)_colorCvtr.ConvertFrom(lc.Color)));
}
else if (entity is LineLabel)
{
LineLabel ll = (LineLabel)entity;
ModelElements.Add(new SSLineLabelViewModel()
{
X = ll.Start.X,
Y = ll.Start.Y,
X1 = ll.End.X - ll.Start.X,
Y1 = ll.End.Y - ll.Start.Y,
Color = (Brush)_colorCvtr.ConvertFrom(ll.Color),
Thickness = ll.LineWeight
});
}
else if (entity is ParallelogramLabel)
{
ParallelogramLabel lc = (ParallelogramLabel)entity;
SSParallelogramLabelViewModel vm = new SSParallelogramLabelViewModel()
{
CenterX = lc.Center.X,
CenterY = lc.Center.Y,
Side1Length = lc.Side1Length,
RotationAngle = lc.Side1Angle,
Side2Length = lc.Side2Length,
ParallelogramAngle = lc.Side2Angle,
Color = (Brush)_colorCvtr.ConvertFrom(lc.Color),
LineWeight = lc.LineWeight
};
vm.ComputeParallelogram();
ModelElements.Add(vm);
}
else if (entity is ArcLabel)
{
ArcLabel ac = (ArcLabel)entity;
SSArcLabelViewModel vm = new SSArcLabelViewModel()
{
CenterX = ac.Center.X,
CenterY = ac.Center.Y,
Color = (Brush)_colorCvtr.ConvertFrom(ac.Color),
LineWeight = ac.LineWeight,
Radius = ac.Radius,
Angle1 = ac.Angle1,
Angle2 = ac.Angle2,
};
vm.ComputeArc();
ModelElements.Add(vm);
}
else if (entity is ArrowLabel)
{
ArrowLabel al = (ArrowLabel)entity;
SSArrowLabelViewModel vm = new SSArrowLabelViewModel()
{
ArrowTipX = al.ArrowTip.X,
ArrowTipY = al.ArrowTip.Y,
LeftTipX = al.LeftTip.X,
LeftTipY = al.LeftTip.Y,
Color = (Brush)_colorCvtr.ConvertFrom(al.Color),
LineWeight = al.LineWeight,
TailLength = al.TailLength,
RotationAngle = al.Angle
};
vm.ComputeArrow();
ModelElements.Add(vm);
}
}
MeasureAndArrangeCanvas();
return(base.Initialize(data));
}
return(false);
}