/// <summary>
/// Adds a broad phase overlap if the collision rules permit it.
/// </summary>
/// <param name="entryA">First entry of the overlap.</param>
/// <param name="entryB">Second entry of the overlap.</param>
protected internal void TryToAddOverlap(BroadPhaseEntry entryA, BroadPhaseEntry entryB)
{
CollisionRule rule;
if ((rule = GetCollisionRule(entryA, entryB)) < CollisionRule.NoBroadPhase)
{
overlapAddLock.Enter();
Overlaps.Add(new BroadPhaseOverlap(entryA, entryB, rule));
overlapAddLock.Exit();
}
}
public void Insert(int index, Overlap value)
{
if (index < Overlaps.Count)
{
Overlaps.Insert(index, value);
}
else
{
Overlaps.Add(value);
}
}
public void Insert(int index, Point p)
{
var e = new Overlap();
e.X = (byte)p.X;
e.Y = (byte)p.Y;
if (index < Overlaps.Count)
{
Overlaps.Insert(index, e);
}
else
{
Overlaps.Add(e);
}
}
/// <summary>
/// Calculate a list of which views overlap this handle.
/// </summary>
/// <param name="group">The parent texture group, used to find a view's base CPU VA offset</param>
/// <param name="views">The list of views to search for overlaps</param>
public void RecalculateOverlaps(TextureGroup group, List <Texture> views)
{
// Overlaps can be accessed from the memory tracking signal handler, so access must be atomic.
lock (Overlaps)
{
int endOffset = Offset + Size;
Overlaps.Clear();
foreach (Texture view in views)
{
int viewOffset = group.FindOffset(view);
if (viewOffset < endOffset && Offset < viewOffset + (int)view.Size)
{
Overlaps.Add(view);
}
}
}
}
/// <summary>
/// Construct initialization.
/// </summary>
/// <param name="fragList">Fragment list.</param>
/// <param name="maxOverlapLen">Minimum overlap length.</param>
private void Init(ObservableCollection <Fragment> fragList, DesignerSettings settings)
{
this.Overlaps = new List <Overlap>();
this.Settings = settings;
//forward
String seq5 = "";
String seq3 = "";
String name = "";
List <MiscFeature> featList = new List <MiscFeature>();
for (int i = 0; i < fragList.Count; i++)
{
name += fragList[i].Name;
seq3 = fragList[i].GetString();
int len5 = Math.Min(settings.MaxOverlapLen, seq5.Length);
int len3 = Math.Min(settings.MaxGeneSpecificLen, seq3.Length);
String overlapping = seq5.Substring(seq5.Length - len5, len5);
String geneSpecific = seq3.Substring(0, len3);
String loc = (seq5.Length + 1).ToString() + ".." + (seq5.Length + seq3.Length).ToString();
MiscFeature gene = new MiscFeature(loc);
gene.StandardName = fragList[i].Name;
featList.Add(gene);
seq5 += seq3;
if (i == 0)
{
Overlaps.Add(new Overlap(fragList[i].Name + "_fwd", new Sequence(Alphabets.DNA, geneSpecific)));
}
else
{
Overlaps.Add(new Overlap(fragList[i].Name + "_fwd", new Sequence(Alphabets.DNA, overlapping), new Sequence(Alphabets.DNA, geneSpecific)));
}
}
this.Sequence = new Sequence(Alphabets.DNA, seq5);
//meta
GenBankMetadata meta = new GenBankMetadata();
meta.Locus = new GenBankLocusInfo();
meta.Locus.MoleculeType = MoleculeType.DNA;
meta.Locus.Name = name;
meta.Locus.Date = System.DateTime.Now;
meta.Locus.SequenceLength = seq5.Length;
meta.Comments.Add("designed with mufasa");
meta.Definition = "synthetic construct";
meta.Features = new SequenceFeatures();
meta.Features.All.AddRange(featList);
this.Sequence.Metadata.Add("GenBank", meta);
//reverse
fragList.Add(new Fragment(fragList[0]));
fragList.RemoveAt(0);
seq5 = "";
seq3 = "";
for (int i = fragList.Count - 1; i >= 0; i--)
{
seq5 = fragList[i].GetReverseComplementString();
int len3 = Math.Min(settings.MaxOverlapLen, seq3.Length);
int len5 = Math.Min(settings.MaxGeneSpecificLen, seq5.Length);
String overlapping = seq3.Substring(seq3.Length - len3, len3);
String geneSpecific = seq5.Substring(0, len5);
seq3 += seq5;
if (i == fragList.Count - 1)
{
Overlaps.Add(new Overlap(fragList[i].Name + "_rev", new Sequence(Alphabets.DNA, geneSpecific)));
}
else
{
Overlaps.Add(new Overlap(fragList[i].Name + "_rev", new Sequence(Alphabets.DNA, overlapping), new Sequence(Alphabets.DNA, geneSpecific)));
}
}
TermoOptimizeOverlaps();
}
protected internal void AddOverlap(BroadPhaseOverlap overlap)
{
overlapAddLock.Enter();
Overlaps.Add(overlap);
overlapAddLock.Exit();
}
