public IEnumerable <ISimplePosition> Recompose(List <ISimplePosition> simplePositions, List <int> functionBlockRanges)
{
var positionSet = PositionSet.CreatePositionSet(simplePositions, functionBlockRanges);
var alleleSet = positionSet.AlleleSet;
var alleleIndexBlockToSampleIndex = positionSet.AlleleBlockToSampleHaplotype;
int numSamples = positionSet.NumSamples;
_sequenceProvider.LoadChromosome(alleleSet.Chromosome);
int regionStart = alleleSet.Starts[0];
string lastRefAllele = alleleSet.VariantArrays.Last()[0];
int regionEnd = alleleSet.Starts.Last() + lastRefAllele.Length + 100; // make it long enough
if (regionEnd > _sequenceProvider.Sequence.Length)
{
regionEnd = _sequenceProvider.Sequence.Length;
}
string totalRefSequence = _sequenceProvider.Sequence.Substring(regionStart - 1, regionEnd - regionStart); // VCF positions are 1-based
var recomposedAlleleSet = new RecomposedAlleleSet(positionSet.ChrName, numSamples);
foreach (var(alleleIndexBlock, sampleAlleles) in alleleIndexBlockToSampleIndex)
{
(int start, _, string refAllele, string altAllele, var varPosIndexesInAlleleBlock, List <string> decomposedVids) = GetPositionsAndRefAltAlleles(alleleIndexBlock, alleleSet, totalRefSequence, regionStart, simplePositions);
var variantSite = new VariantSite(start, refAllele);
if (!recomposedAlleleSet.RecomposedAlleles.TryGetValue(variantSite, out var variantInfo))
{
variantInfo = GetVariantInfo(positionSet, alleleIndexBlock);
recomposedAlleleSet.RecomposedAlleles[variantSite] = variantInfo;
}
variantInfo.AddAllele(altAllele, sampleAlleles, decomposedVids);
variantInfo.UpdateSampleFilters(varPosIndexesInAlleleBlock, sampleAlleles);
}
return(recomposedAlleleSet.GetRecomposedPositions(_sequenceProvider.RefNameToChromosome));
}
public void LoadData(ObservableCollection <PlaceData> listOfPlaces)
{
string pathData = Properties.Settings.Default.Path + Properties.Settings.Default.DataFileName;
string[] lines = System.IO.File.ReadAllLines(pathData, UTF8Encoding.UTF8); // , UTF8Encoding.UTF7
PositionSet positionSet;
foreach (string line in lines)
{
PlaceData placeData = new PlaceData();
string[] data = line.Split('|');
placeData.PlaceIndex = Int32.Parse(data[0]);
placeData.PlaceId = Int32.Parse(data[1]);
placeData.PlaceName = data[2];
for (int i = 3; i < data.GetUpperBound(0); i = i + 2)
{
positionSet = new PositionSet(data[i].ConvertStringToVertex(), data[i + 1].ConvertStringToVertex());
placeData.PositionList.Add(positionSet);
}
listOfPlaces.Add(placeData);
}
}
private static VariantInfo GetVariantInfo(PositionSet positionSet, AlleleIndexBlock alleleIndexBlock)
{
string filter = "PASS";
var positions = positionSet.SimplePositions;
var startIndex = alleleIndexBlock.PositionIndex;
var numPositions = alleleIndexBlock.AlleleIndexes.Count;
var numSamples = positionSet.NumSamples;
string[] quals = new string[numPositions];
for (int i = startIndex; i < startIndex + numPositions; i++)
{
quals[i - startIndex] = positions[i].VcfFields[VcfCommon.QualIndex];
string thisFilter = positions[i].VcfFields[VcfCommon.FilterIndex];
if (filter == "PASS" && thisFilter != "PASS" && thisFilter != ".")
{
filter = FailedFilterTag;
}
}
string qual = GetStringWithMinValueOrDot(quals);
string[] gqValues = new string[numSamples];
for (int i = 0; i < numSamples; i++)
{
gqValues[i] = GetStringWithMinValueOrDot(new ArraySegment <string>(positionSet.GqInfo[i], startIndex, numPositions).ToArray());
}
string[] psValues = new string[numSamples];
for (int i = 0; i < numSamples; i++)
{
// PS tags are the same in the decomposed variants
psValues[i] = positionSet.PsInfo[i][startIndex];
}
return(new VariantInfo(qual, filter, gqValues, psValues));
}
private void SetScale(object sender, Pose pose)
{
markerHolder.localScale = Vector3.one * lastMessage.PhysicalSideLength;
markerDisplay.SetActive(true);
PositionSet?.Invoke(this, pose);
audioSource.Play();
}
public PositionSet(PositionSet other) : this(bwapiPINVOKE.new_PositionSet__SWIG_1(PositionSet.getCPtr(other)), true)
{
if (bwapiPINVOKE.SWIGPendingException.Pending)
{
throw bwapiPINVOKE.SWIGPendingException.Retrieve();
}
}
public PositionSetEnumerator(PositionSet collection)
{
collectionRef = collection;
keyCollection = new global::System.Collections.Generic.List <Position>(collection.Values);
currentIndex = -1;
currentObject = null;
currentSize = collectionRef.Count;
}
public void GetPhaseSetTagIndexes_NoPS_Return_NegativeOne()
{
var position = new Mock<ISimplePosition>();
var vcfFields = new string[VcfCommon.MinNumColumnsSampleGenotypes];
vcfFields[VcfCommon.FormatIndex] = "GT";
position.SetupGet(x => x.VcfFields).Returns(vcfFields);
var functionBlockRanges = new List<int> { 102 };
var positionSet = new PositionSet(new List<ISimplePosition> { position.Object }, functionBlockRanges);
Assert.Equal(new[] { new []{-1} }, positionSet.GetSampleTagIndexes(new[] { "PS" }));
}
private static VariantInfo GetVariantInfo(PositionSet positionSet, AlleleBlock alleleBlock)
{
var positions = positionSet.SimplePositions;
int startIndex = alleleBlock.PositionIndex;
int numPositions = alleleBlock.AlleleIndexes.Length;
int numSamples = positionSet.NumSamples;
string qual = GetStringWithMinValueOrDot(Enumerable.Range(startIndex, numPositions)
.Select(x => positions[x].VcfFields[VcfCommon.QualIndex]));
var filters = Enumerable.Range(startIndex, numPositions)
.Select(i => positions[i].VcfFields[VcfCommon.FilterIndex])
.ToArray();
var gqValues = new string[numSamples];
for (var i = 0; i < numSamples; i++)
{
gqValues[i] = GetStringWithMinValueOrDot(
new ArraySegment <string>(positionSet.GqInfo.Values[i], startIndex, numPositions).ToArray());
}
var psValues = new string[numSamples];
for (var i = 0; i < numSamples; i++)
{
var psTagsThisSample =
new ArraySegment <string>(positionSet.PsInfo.Values[i], startIndex, numPositions);
var isHomozygous = new ArraySegment <bool>(
positionSet.GtInfo.Values[i].Select(x => x.IsHomozygous).ToArray(), startIndex, numPositions);
psValues[i] = GetPhaseSetForRecomposedVariant(psTagsThisSample, isHomozygous);
}
var homoReferenceSamplePloidy = new int?[numSamples];
for (var i = 0; i < numSamples; i++)
{
if (Genotype.IsAllHomozygousReference(positionSet.GtInfo.Values[i], startIndex, numPositions))
{
homoReferenceSamplePloidy[i] = positionSet.GtInfo.Values[i][startIndex].AlleleIndexes.Length;
}
}
var sampleFilters = new List <bool> [numSamples];
for (var i = 0; i < numSamples; i++)
{
sampleFilters[i] = new List <bool>();
}
return(new VariantInfo(qual, filters, gqValues, psValues, homoReferenceSamplePloidy, sampleFilters));
}
public void InsertInPosition(BadgeEventSet be, FieldSet f, double posX, double posY, string fontFamily, int fontSize)
{
PositionSet p = new PositionSet();
p.BadgeEventSet = be;
p.FieldSet = f;
p.Position_X = posX;
p.Position_Y = posY;
p.FontFamily = fontFamily;
p.FontSize = fontSize;
p.FontStyle = System.Drawing.FontStyle.Regular.ToString();
var repo = this._repostitoryFactory.GetPositionRepository(this._dbContext);
repo.Insert(p);
repo.SaveChanges();
}
public void GetPhaseSetTagIndexes_Return_Correct_PSIndex()
{
var position1 = new Mock<ISimplePosition>();
var vcfFields1 = new string[VcfCommon.MinNumColumnsSampleGenotypes];
vcfFields1[VcfCommon.FormatIndex] = "GT:PS";
position1.SetupGet(x => x.VcfFields).Returns(vcfFields1);
var position2 = new Mock<ISimplePosition>();
var vcfFields2 = new string[VcfCommon.MinNumColumnsSampleGenotypes];
vcfFields2[VcfCommon.FormatIndex] = "GT:AA:PS";
position2.SetupGet(x => x.VcfFields).Returns(vcfFields2);
var position3 = new Mock<ISimplePosition>();
var vcfFields3 = new string[VcfCommon.MinNumColumnsSampleGenotypes];
vcfFields3[VcfCommon.FormatIndex] = "GT:AA:BB:PS";
position3.SetupGet(x => x.VcfFields).Returns(vcfFields3);
var positionSet = new PositionSet(new List<ISimplePosition> { position1.Object, position2.Object, position3.Object }, new List<int>());
Assert.Equal(new[] {new[] { 1, 2, 3 }}, positionSet.GetSampleTagIndexes(new[] { "PS" }));
}
public IEnumerable <ISimplePosition> Recompose(List <ISimplePosition> recomposablePositions, List <int> functionBlockRanges)
{
var positionSet = PositionSet.CreatePositionSet(recomposablePositions, functionBlockRanges);
var alleleSet = positionSet.AlleleSet;
var alleleIndexBlockToSampleIndex = positionSet.AlleleIndexBlockToSampleIndex;
var numSamples = positionSet.NumSamples;
_sequenceProvider.LoadChromosome(alleleSet.Chromosome);
int regionStart = alleleSet.Starts[0];
string lastRefAllele = alleleSet.VariantArrays.Last()[0];
int regionEnd = alleleSet.Starts.Last() + lastRefAllele.Length + 100; // make it long enough
if (regionEnd > _sequenceProvider.Sequence.Length)
{
regionEnd = _sequenceProvider.Sequence.Length;
}
string totalRefSequence = _sequenceProvider.Sequence.Substring(regionStart - 1, regionEnd - regionStart); // VCF positions are 1-based
var recomposedAlleleSet = new RecomposedAlleleSet(positionSet.ChrName, numSamples);
var decomposedPosVarIndex = new HashSet <(int PosIndex, int VarIndex)>();
foreach (var(alleleIndexBlock, sampleAlleles) in alleleIndexBlockToSampleIndex)
{
var(start, _, refAllele, altAllele) = GetPositionsAndRefAltAlleles(alleleIndexBlock, alleleSet, totalRefSequence, regionStart, decomposedPosVarIndex);
var variantSite = new VariantSite(start, refAllele);
if (!recomposedAlleleSet.RecomposedAlleles.TryGetValue(variantSite, out var variantInfo))
{
variantInfo = GetVariantInfo(positionSet, alleleIndexBlock);
recomposedAlleleSet.RecomposedAlleles[variantSite] = variantInfo;
}
variantInfo.AddAllele(altAllele, sampleAlleles);
}
// Set decomposed tag to positions used for recomposition
foreach (var indexTuple in decomposedPosVarIndex)
{
recomposablePositions[indexTuple.PosIndex].IsDecomposed[indexTuple.VarIndex] = true;
}
return(recomposedAlleleSet.GetRecomposedVcfRecords().Select(x => SimplePosition.GetSimplePosition(x, _sequenceProvider.RefNameToChromosome, true)));
}
protected virtual void RaiseProgressSetEvent(object sender, ProgressEventArgs e) => InvokeActionOnMainThread(() => PositionSet?.Invoke(sender, e));
public virtual PositionSet getNukeDots()
{
PositionSet ret = new PositionSet(bwapiPINVOKE.Game_getNukeDots(swigCPtr), false);
return(ret);
}
public void ExtractSamplePhaseSet_NegativePSIndex_ReturnDot()
{
Assert.Equal(".", PositionSet.ExtractSampleValue(-1, new[] { "0|1", "." }));
}
public override PositionSet getNukeDots() {
PositionSet ret = new PositionSet(bwapiclientPINVOKE.GameImpl_getNukeDots(swigCPtr), false);
return ret;
}
public void showData()
{
Radix radix = agent.rpCase.radix;
lbl_datetime.Text = radix.datetime;
lbl_location.Text = radix.location;
lbl_coordinates.Text = radix.coordinatesText;
PositionSet positionSet = radix.positionSet;
ArrayList planetaryPositions = positionSet.planetaryPositions;
dgvPositions.CellBorderStyle = DataGridViewCellBorderStyle.None;
dgvPositions.RowsDefaultCellStyle.BackColor = Color.AliceBlue;
dgvPositions.AlternatingRowsDefaultCellStyle.BackColor = Color.NavajoWhite;
DataGridViewTextBoxColumn col1 = new DataGridViewTextBoxColumn();
DataGridViewTextBoxColumn col2 = new DataGridViewTextBoxColumn();
DataGridViewTextBoxColumn col3 = new DataGridViewTextBoxColumn();
DataGridViewTextBoxColumn col4 = new DataGridViewTextBoxColumn();
DataGridViewTextBoxColumn col5 = new DataGridViewTextBoxColumn();
DataGridViewTextBoxColumn col6 = new DataGridViewTextBoxColumn();
DataGridViewTextBoxColumn col7 = new DataGridViewTextBoxColumn();
DataGridViewTextBoxColumn col8 = new DataGridViewTextBoxColumn();
col2.HeaderText = ResourceBundle.RB_FRM_SHOWPOSITIONS_TXT_LONGITUDE;
col4.HeaderText = ResourceBundle.RB_FRM_SHOWPOSITIONS_TXT_LATITUDE;
col5.HeaderText = ResourceBundle.RB_FRM_SHOWPOSITIONS_TXT_RIGHTASCENSION;
col6.HeaderText = ResourceBundle.RB_FRM_SHOWPOSITIONS_TXT_DECLINATION;
col7.HeaderText = ResourceBundle.RB_FRM_SHOWPOSITIONS_TXT_SPEED;
col8.HeaderText = ResourceBundle.RB_FRM_SHOWPOSITIONS_TXT_DISTANCE;
col1.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleCenter;
col2.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleRight;
col3.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleLeft;
col4.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleRight;
col5.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleRight;
col6.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleRight;
col7.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleRight;
col8.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleRight;
col1.DefaultCellStyle.Font = listBodyGlyphs;
col1.Width = 24;
col3.DefaultCellStyle.Font = listSignGlyphs;
col3.Width = 24;
col2.SortMode = DataGridViewColumnSortMode.NotSortable;
col3.SortMode = DataGridViewColumnSortMode.NotSortable;
col4.SortMode = DataGridViewColumnSortMode.NotSortable;
col5.SortMode = DataGridViewColumnSortMode.NotSortable;
col6.SortMode = DataGridViewColumnSortMode.NotSortable;
col7.SortMode = DataGridViewColumnSortMode.NotSortable;
col8.SortMode = DataGridViewColumnSortMode.NotSortable;
dgvPositions.Columns.AddRange(
new DataGridViewTextBoxColumn[] { col1, col2, col3, col4, col5, col6, col7, col8 });
int nrOfBodies = radix.positionSet.planetaryPositions.Count;
int nrOfRows = Math.Max(nrOfBodies, 20);
DataGridViewRow[] dgvr = new DataGridViewRow[nrOfBodies];
ArrayList pos = radix.positionSet.planetaryPositions;
PlanetaryPosition pp;
for (int i = 0; i < nrOfBodies; i++)
{
pp = (PlanetaryPosition)pos[i];
dgvr[i] = new DataGridViewRow();
dgvr[i].CreateCells(dgvPositions);
dgvr[i].Cells[0].Value = Conversions.bodyGlyphFromIndex(pp.planetId);
dgvr[i].Cells[1].Value = Conversions.deg2sexagesimal(pp.longitude, true, true);
dgvr[i].Cells[2].Value = Conversions.signGlyphFromLong(pp.longitude);
dgvr[i].Cells[3].Value = Conversions.deg2sexagesimalInRange(pp.latitude, -180, 180, true);
dgvr[i].Cells[4].Value = Conversions.deg2sexagesimal(pp.rightAscension, true, false);
dgvr[i].Cells[5].Value = Conversions.deg2sexagesimalInRange(pp.declination, -90.0, 90.0, true);
dgvr[i].Cells[6].Value = Conversions.deg2sexagesimalInRange(pp.speedLongitude, -90.0, 90.0, true);
dgvr[i].Cells[7].Value = Conversions.fixedFraction(pp.distance, 6);
}
dgvPositions.Rows.AddRange(dgvr);
lbl_name.Text = radix.name;
}
public void ExtractSamplePhaseSet_PSIsDot_ReturnDot()
{
Assert.Equal(".", PositionSet.ExtractSampleValue(1, new[] { "0|1", "." }));
}
public virtual PositionSet getNukeDots() {
PositionSet ret = new PositionSet(bwapiPINVOKE.Game_getNukeDots(swigCPtr), false);
return ret;
}
private void SetScale(object sender, Pose pose)
{
PositionSet?.Invoke(this, pose);
}
internal static global::System.Runtime.InteropServices.HandleRef getCPtr(PositionSet obj)
{
return((obj == null) ? new global::System.Runtime.InteropServices.HandleRef(null, global::System.IntPtr.Zero) : obj.swigCPtr);
}
public void ExtractSamplePhaseSet_PSIsNum_ReturnTheNum()
{
Assert.Equal("123", PositionSet.ExtractSampleValue(1, new[] { "0|1", "123" }));
}
/// <summary>
/// Analysis for a radix, supports a set of analysing techniques
/// </summary>
/// <param name="positionSet">Postions of bodies and houses</param>
/// <param name="aspectTypes">Supported aspecttypes</param>
/// <param name="midpointOrb">Orbis for midpoints</param>
public RadixAnalysis(PositionSet positionSet, ArrayList aspectTypes, double midpointOrb)
{
aspectsAnalysis = new AspectsAnalysis(aspectTypes, positionSet.planetaryPositions, positionSet.housePositionSet);
midpointsAnalysis = new MidpointsAnalysis(positionSet.planetaryPositions, positionSet.housePositionSet, midpointOrb);
}
public static ObservableCollection <PlaceData> ImportData()
{
ObservableCollection <PlaceData> listOfData = new ObservableCollection <PlaceData>();
PositionSet positionSet;
string process;
int startIndex;
try
{
string pathData = Properties.Settings.Default.Path + Properties.Settings.Default.ImportFileName;
string[] lines = System.IO.File.ReadAllLines(pathData, UTF8Encoding.UTF7);
foreach (string line in lines)
{
PlaceData place = new PlaceData();
process = line;
startIndex = line.IndexOf("(");
if (startIndex > 0)
{
process = process.Substring(startIndex + 2);
}
else
{
process = process.Substring(1);
}
// check if line contain data formatted as expected
int indexPosition = process.IndexOf("\'");
if (indexPosition > 0)
{
// parse index at end of line
int index;
Int32.TryParse(process.Substring(indexPosition + 1), out index);
place.PlaceIndex = index;
// remove trailing 'x [index]
process = process.Substring(0, indexPosition - 1);
// remove trailing ")
indexPosition = process.IndexOf("\")");
process = process.Substring(0, indexPosition);
// data ready - parse to object
string[] data = process.Split('|');
place.PlaceId = Int32.Parse(data[0]);
place.PlaceName = data[1];
for (int i = 2; i < data.GetUpperBound(0); i = i + 2)
{
positionSet = new PositionSet(data[i].ConvertStringToVertex(), data[i + 1].ConvertStringToVertex());
place.PositionList.Add(positionSet);
}
}
if (indexPosition > 0) // only add to collection if data is meaningfull
{
listOfData.Add(place);
}
}
}
catch (Exception e)
{
MessageBox.Show("Error while importing data: " + e.Message);
}
return(listOfData);
}
