public override int GetHashCode()
{
unchecked // Overflow is fine, just wrap
{
int hashCode = 41;
if (AnnotationPosition != null)
{
hashCode = hashCode * 59 + AnnotationPosition.GetHashCode();
}
if (AnnotationTail != null)
{
hashCode = hashCode * 59 + AnnotationTail.GetHashCode();
}
if (AnnotationText != null)
{
hashCode = hashCode * 59 + AnnotationText.GetHashCode();
}
if (AxisTitleText != null)
{
hashCode = hashCode * 59 + AxisTitleText.GetHashCode();
}
if (ColorbarPosition != null)
{
hashCode = hashCode * 59 + ColorbarPosition.GetHashCode();
}
if (ColorbarTitleText != null)
{
hashCode = hashCode * 59 + ColorbarTitleText.GetHashCode();
}
if (LegendPosition != null)
{
hashCode = hashCode * 59 + LegendPosition.GetHashCode();
}
if (LegendText != null)
{
hashCode = hashCode * 59 + LegendText.GetHashCode();
}
if (ShapePosition != null)
{
hashCode = hashCode * 59 + ShapePosition.GetHashCode();
}
if (TitleText != null)
{
hashCode = hashCode * 59 + TitleText.GetHashCode();
}
return(hashCode);
}
}
private static AnnotationPosition FindProperStartPosition(AnnotationPosition genomicPosition, IIntervalForest <IGene> geneIntervalForest, IDictionary <string, IChromosome> refNameToChromosome)
{
var chromosome = ReferenceNameUtilities.GetChromosome(refNameToChromosome, genomicPosition.Chromosome);
int currentPosition = genomicPosition.Position;
IGene[] overlappingGenes;
while ((overlappingGenes = geneIntervalForest.GetAllOverlappingValues(chromosome.Index,
currentPosition, currentPosition)) != null)
{
if (overlappingGenes.Length > 0)
{
currentPosition = overlappingGenes.Select(x => x.Start).Min() - 1;
}
}
// Always return the position right before the overlapping genes to KISS
return(new AnnotationPosition(genomicPosition.Chromosome, currentPosition < 1 ? 1 : currentPosition));
}
private static AnnotationPosition[] AdjustPartitionGenomicStarts(IReadOnlyList <long> blockBasedOffsets, string vcfUrl,
IIntervalForest <IGene> geneIntervalForest, IDictionary <string, IChromosome> refNameToChromosome)
{
var allAdjustedStarts = new AnnotationPosition[blockBasedOffsets.Count];
for (var index = 0; index < blockBasedOffsets.Count; index++)
{
long blockBasedOffset = blockBasedOffsets[index];
using (var stream = PersistentStreamUtils.GetReadStream(vcfUrl, blockBasedOffset))
using (var gzipStream = new BlockGZipStream(stream, CompressionMode.Decompress))
{
var annotationPosition = GetFirstGenomicPosition(gzipStream, index == 0);
allAdjustedStarts[index] = FindProperStartPosition(annotationPosition, geneIntervalForest, refNameToChromosome);
}
}
AnnotationPosition[] adjustedStarts = MergeConsecutiveEqualValues(allAdjustedStarts).ToArray();
return(adjustedStarts);
}
PointF getAnnotationTextPos(AnnotationPosition pos, SizeF stringSize)
{
var ret = new PointF();
if (pos == AnnotationPosition.StartPoint)
{
var dx = Point1.X - Point0.X;
var dy = Point1.Y - Point0.Y;
float ox = 0;
float oy = 0;
if (dx > 0 && dy > 0)
{
ox -= stringSize.Width;
}
ret = new PointF(Point0.X + ox, Point0.Y + oy);
}
else if (pos == AnnotationPosition.EndPoint)
{
var dx = Point0.X - Point1.X;
var dy = Point0.Y - Point1.Y;
float ox = 0;
float oy = 0;
if (dx > 0 && dy > 0)
{
ox -= stringSize.Width;
}
ret = new PointF(Point1.X + ox, Point1.Y + oy);
}
else
{
// mid point
ret.X = (Point0.X + Point1.X) / 2;
ret.Y = (Point0.Y + Point1.Y) / 2;
}
return(ret);
}
/// <inheritdoc />
public bool Equals([AllowNull] Edits other)
{
if (other == null)
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
return
((
AnnotationPosition == other.AnnotationPosition ||
AnnotationPosition != null &&
AnnotationPosition.Equals(other.AnnotationPosition)
) &&
(
AnnotationTail == other.AnnotationTail ||
AnnotationTail != null &&
AnnotationTail.Equals(other.AnnotationTail)
) &&
(
AnnotationText == other.AnnotationText ||
AnnotationText != null &&
AnnotationText.Equals(other.AnnotationText)
) &&
(
AxisTitleText == other.AxisTitleText ||
AxisTitleText != null &&
AxisTitleText.Equals(other.AxisTitleText)
) &&
(
ColorbarPosition == other.ColorbarPosition ||
ColorbarPosition != null &&
ColorbarPosition.Equals(other.ColorbarPosition)
) &&
(
ColorbarTitleText == other.ColorbarTitleText ||
ColorbarTitleText != null &&
ColorbarTitleText.Equals(other.ColorbarTitleText)
) &&
(
LegendPosition == other.LegendPosition ||
LegendPosition != null &&
LegendPosition.Equals(other.LegendPosition)
) &&
(
LegendText == other.LegendText ||
LegendText != null &&
LegendText.Equals(other.LegendText)
) &&
(
ShapePosition == other.ShapePosition ||
ShapePosition != null &&
ShapePosition.Equals(other.ShapePosition)
) &&
(
TitleText == other.TitleText ||
TitleText != null &&
TitleText.Equals(other.TitleText)
));
}
string getAnnotationText(AnnotationPosition pos)
{
return(_annotationTexts[(int)pos]);
}
void setAnnotationText(AnnotationPosition pos, string text)
{
_annotationTexts[(int)pos] = text;
}
