private void DisplayLocationDetails(FeatureLocation floc)
{
DeactivateButton.Text = string.Format(
"Deactivate {0} selected activation(s)",
LocationGrid.SelectedRows.Count);
LocationDetailsView.Items.Clear();
if (floc == null) { return; }
AddLocationProperty("Feature Name", floc.Feature.Name);
AddLocationProperty("Feature Id", floc.Feature.Id.ToString());
AddLocationProperty("Scope", floc.Location.ScopeAbbrev);
AddLocationProperty("Location Name", floc.Location.Name);
AddLocationProperty("Location URL", floc.Location.Url);
AddLocationProperty("Location Id", floc.Location.Id.ToString());
if (!string.IsNullOrEmpty(floc.Location.Template.Name))
{
AddLocationProperty("Template Name", floc.Location.Template.Name);
AddLocationProperty("Template Title", floc.Location.Template.Title);
}
switch (floc.Location.Scope)
{
case SPFeatureScope.Site:
AddSiteDetails(floc.Location);
break;
case SPFeatureScope.Web:
AddWebDetails(floc.Location);
break;
}
}
private void DisplayLocationDetails(FeatureLocation floc)
{
DeactivateButton.Text = string.Format(
"Deactivate {0} selected activation(s)",
LocationGrid.SelectedRows.Count);
LocationDetailsView.Items.Clear();
if (floc == null)
{
return;
}
AddLocationProperty("Feature Name", floc.Feature.Name);
AddLocationProperty("Feature Id", floc.Feature.Id.ToString());
AddLocationProperty("Scope", floc.Location.ScopeAbbrev);
AddLocationProperty("Location Name", floc.Location.Name);
AddLocationProperty("Location URL", floc.Location.FullUrl);
AddLocationProperty("Location Id", floc.Location.Id.ToString());
if (!string.IsNullOrEmpty(floc.Location.Template.Name))
{
AddLocationProperty("Template Name", floc.Location.Template.Name);
AddLocationProperty("Template Title", floc.Location.Template.Title);
}
switch (floc.Location.Scope)
{
case SPFeatureScope.Site:
AddSiteDetails(floc.Location);
break;
case SPFeatureScope.Web:
AddWebDetails(floc.Location);
break;
}
}
public virtual AcceptResult AcceptLocationPair(FeatureLocation floc, SAMAlignedLocation sloc)
{
var result = CheckNoPenaltyMutation(floc, sloc);
if (!result.Accepted)
{
return(result);
}
result.OverlapPercentage = floc.OverlapPercentage(sloc);
result.Accepted = result.OverlapPercentage > 0 && result.OverlapPercentage >= Options.MinimumOverlapPercentage;
return(result);
}
public override AcceptResult AcceptLocationPair(FeatureLocation floc, SAMAlignedLocation sloc)
{
var result = base.AcceptLocationPair(floc, sloc);
if (!result.Accepted)
{
return(result);
}
var offset = sloc.Offset(floc);
result.Accepted = Options.Offsets.Contains(offset);
return(result);
}
private AcceptResult CheckNoPenaltyMutation(FeatureLocation floc, SAMAlignedLocation sloc)
{
if (sloc.NumberOfNoPenaltyMutation > 0)
{
var polys = sloc.GetGsnapMismatches();
var mismatch = 0;
if (floc.Strand == sloc.Strand) //the non-penalty mutation has to be T2C
{
mismatch = polys.Count(m => m.RefAllele != 'T' || m.SampleAllele != 'C');
}
else
{
mismatch = polys.Count(m => m.RefAllele != 'A' || m.SampleAllele != 'G');
}
var nnpm = sloc.NumberOfMismatch + sloc.NumberOfNoPenaltyMutation - mismatch;
if (mismatch > Options.MaximumMismatch || nnpm > Options.MaximumNoPenaltyMutationCount)
{
return(new AcceptResult()
{
Accepted = false
});
}
return(new AcceptResult()
{
Accepted = true,
NumberOfMismatch = mismatch,
NumberOfNoPenaltyMutation = sloc.NumberOfMismatch + sloc.NumberOfNoPenaltyMutation - mismatch
});
}
else if (sloc.NumberOfMismatch > Options.MaximumMismatch)
{
return(new AcceptResult()
{
Accepted = false
});
}
else
{
return(new AcceptResult()
{
Accepted = true,
NumberOfMismatch = sloc.NumberOfMismatch,
NumberOfNoPenaltyMutation = 0
});
}
}
private void LocationGrid_SelectionChanged(object sender, EventArgs e)
{
if (LocationGrid.SelectedRows.Count > 0)
{
_selectedFeatureLocations.Clear();
foreach (DataGridViewRow row in LocationGrid.SelectedRows)
{
_selectedFeatureLocations.Add(row.DataBoundItem as FeatureLocation);
}
}
if (LocationGrid.CurrentRow != null)
{
FeatureLocation floc = LocationGrid.CurrentRow.DataBoundItem as FeatureLocation;
DisplayLocationDetails(floc);
}
}
private void dataGridView1_SelectionChanged(object sender, EventArgs e)
{
if (dataGridView1.SelectedRows.Count <= 0)
{
return;
}
object value = dataGridView1.SelectedRows[0].Cells[Table.OIDFieldName].Value;
if (value == null || value == DBNull.Value)
{
return;
}
if (FeatLayer != null)
{
FeatureLocation?.Invoke(this, new FeatureLocationEventArgs(FeatLayer, $"{Table.OIDFieldName} = {value}"));
}
}
private void PopulateLocationGrid()
{
// Create list of FeatureLocations
List <FeatureLocation> list = new List <FeatureLocation>();
foreach (KeyValuePair <Feature, List <FeatureParent> > pair in _FeatureLocations)
{
Feature feature = pair.Key;
List <FeatureParent> locations = pair.Value;
foreach (FeatureParent location in locations)
{
FeatureLocation floc = new FeatureLocation();
floc.Feature = feature;
floc.Location = location;
list.Add(floc);
}
}
this.LocationGrid.DataSource = new SortableBindingList <FeatureLocation>(list);
}
public override AcceptResult AcceptLocationPair(FeatureLocation floc, SAMAlignedLocation sloc)
{
if (sloc.Parent.Sequence.Length < Options.MinimumReadLengthForLongRNA)
{
return(new AcceptResult()
{
Accepted = false
});
}
if (sloc.NumberOfMismatch > Options.MaximumMismatchForLongRNA)
{
return(new AcceptResult()
{
Accepted = false
});
}
return(base.AcceptLocationPair(floc, sloc));
}
public void TestAsArgument()
{
IVariable <IFeatureLocation> a = new Variable <IFeatureLocation>("argument");
IVariable <double> c1 = new Variable <double>("value");
IVariable <string> c2 = new Variable <string>("description");
// f = (a, p)(h)
IFunction f = new Function("rating curve");
f.Arguments.Add(a);
f.Components.Add(c1);
f.Components.Add(c2);
SimpleFeature simpleFeature = new SimpleFeature(10.0);
IFeatureLocation featureLocation = new FeatureLocation {
Feature = simpleFeature
};
// value based argument referencing.
f[featureLocation] = new object[] { 1.0, "jemig de pemig" };
IMultiDimensionalArray <double> c1Value = f.GetValues <double>(new ComponentFilter(f.Components[0]),
new VariableValueFilter <IFeatureLocation>(
f.Arguments[0],
new FeatureLocation
{
Feature = simpleFeature
}));
Assert.AreEqual(1.0, c1Value[0], 1.0e-6);
//IMultiDimensionalArray<string> c2Value = f.GetValues<string>(new ComponentFilter(f.Components[1]),
// new VariableValueFilter<IFeatureLocation>(
// f.Arguments[0], featureLocation));
//Assert.AreEqual("jemig de pemig", c2Value[0]);
}
public FeatureDetail(string name, bool isEnabled, FeatureLocation location)
{
Name = name;
IsEnabled = isEnabled;
FeatureLocation = location;
}
private void PopulateLocationGrid()
{
// Create list of FeatureLocations
List<FeatureLocation> list = new List<FeatureLocation>();
foreach (KeyValuePair<Feature, List<Location>> pair in _FeatureLocations)
{
Feature feature = pair.Key;
List<Location> locations = pair.Value;
foreach (Location location in locations)
{
FeatureLocation floc = new FeatureLocation();
floc.Feature = feature;
floc.Location = location;
list.Add(floc);
}
}
this.LocationGrid.DataSource = new SortableBindingList<FeatureLocation>(list);
}
private void LocationGrid_SelectionChanged(object sender, EventArgs e)
{
FeatureLocation floc = LocationGrid.CurrentRow.DataBoundItem as FeatureLocation;
DisplayLocationDetails(floc);
}
/// <summary>
/// Creates feature detail
/// </summary>
/// <param name="name"></param>
/// <param name="isEnabled"></param>
/// <param name="location"></param>
/// <returns></returns>
private IFeatureDetail Feature(string name, bool isEnabled, FeatureLocation location)
{
return(new FeatureDetail(name, isEnabled, location));
}
