/// <summary>
/// Writes out a grouping of ISequenceRange objects to a specified
/// file location.
/// </summary>
/// <param name="rangeGroup">The range grouping to be formatted.</param>
/// <param name="fileName">The file where the formatted data is to be written.</param>
public void Format(SequenceRangeGrouping rangeGroup, string fileName)
{
if (rangeGroup == null)
{
throw new ArgumentNullException("rangeGroup");
}
Format(rangeGroup.Flatten(), fileName);
}
public void ValidateFlatten()
{
// Get values from xml.
string expectedRangeIDs = Utility._xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.IDNode);
string expectedStartIndex = Utility._xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.StartNode);
string expectedEndIndex = Utility._xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.EndNode);
string expectedSequenceRangeCount = Utility._xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.SequenceRangeCountNode);
string actualRangeStarts = string.Empty;
string actualRangeEnds = string.Empty;
string actualRangeIDs = string.Empty;
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
SequenceRangeGrouping seqRangeGrouping = new SequenceRangeGrouping();
List <ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
SequenceRange seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i]), long.Parse(rangeEnds[i]));
seqRangeGrouping.Add(seqRange);
}
//Convert SequenceRangeGroup to SequenceRangeList.
rangeList = seqRangeGrouping.Flatten();
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
actualRangeIDs = string.Concat(actualRangeIDs, seqRange.ID.ToString(), ",");
actualRangeStarts = string.Concat(actualRangeStarts, seqRange.Start.ToString(), ",");
actualRangeEnds = string.Concat(actualRangeEnds, seqRange.End.ToString(), ",");
}
Assert.AreEqual(expectedSequenceRangeCount, rangeList.Count.ToString());
Assert.AreEqual(expectedRangeIDs, actualRangeIDs.Substring(0,
actualRangeIDs.Length - 1));
Assert.AreEqual(expectedStartIndex, actualRangeStarts.Substring(0,
actualRangeStarts.Length - 1));
Assert.AreEqual(expectedEndIndex, actualRangeEnds.Substring(0,
actualRangeEnds.Length - 1));
Console.WriteLine(
"SequenceRange BVT : Successfully validated the SequenceStart,SequenceID and SequenceEnd.");
}
/// <summary>
/// Writes out a grouping of ISequenceRange objects to a specified
/// text writer.
/// </summary>
/// <param name="rangeGroup">The range grouping to be formatted.</param>
/// <param name="writer">The writer stream where the formatted data is to be written.</param>
public void Format(SequenceRangeGrouping rangeGroup, TextWriter writer)
{
if (rangeGroup == null)
{
throw new ArgumentNullException("rangeGroup");
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
Format(rangeGroup.Flatten(), writer);
}
/// <summary>
/// Writes out a grouping of ISequenceRange objects to a specified
/// stream.
/// </summary>
/// <param name="stream">The stream where the formatted data is to be written, it will be closed at the end.</param>
/// <param name="rangeGroup">The range grouping to be formatted.</param>
public void Format(Stream stream, SequenceRangeGrouping rangeGroup)
{
if (stream == null)
{
throw new ArgumentNullException("stream");
}
if (rangeGroup == null)
{
throw new ArgumentNullException("rangeGroup");
}
this.Format(stream, rangeGroup.Flatten());
}
public void ValidateFlatten()
{
// Get values from xml.
string expectedRangeIDs = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.IDNode);
string expectedStartIndex = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.StartNode);
string expectedEndIndex = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.EndNode);
string expectedSequenceRangeCount = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.SequenceRangeCountNode);
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
SequenceRangeGrouping seqRangeGrouping = new SequenceRangeGrouping();
List <ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
SequenceRange seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i], (IFormatProvider)null),
long.Parse(rangeEnds[i], (IFormatProvider)null));
seqRangeGrouping.Add(seqRange);
}
//Convert SequenceRangeGroup to SequenceRangeList.
rangeList = seqRangeGrouping.Flatten();
int j = 0;
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
Assert.AreEqual(rangeStarts[j], seqRange.Start.ToString((IFormatProvider)null));
Assert.AreEqual(rangeEnds[j], seqRange.End.ToString((IFormatProvider)null));
Assert.AreEqual(rangeIDs[j], seqRange.ID.ToString((IFormatProvider)null));
j++;
}
Assert.AreEqual(expectedSequenceRangeCount, rangeList.Count.ToString((IFormatProvider)null));
Console.WriteLine(
"SequenceRange BVT : Successfully validated the SequenceStart,SequenceID and SequenceEnd.");
}
/// <summary>
/// Writes out a grouping of ISequenceRange objects to a specified
/// stream.
/// </summary>
/// <param name="stream">The stream where the formatted data is to be written, it will be closed at the end.</param>
/// <param name="rangeGroup">The range grouping to be formatted.</param>
public void Format(Stream stream, SequenceRangeGrouping rangeGroup)
{
if (stream == null)
{
throw new ArgumentNullException("stream");
}
if (rangeGroup == null)
{
throw new ArgumentNullException("rangeGroup");
}
this.Format(stream, rangeGroup.Flatten());
}
public void ValidateFlatten()
{
// Get values from xml.
string expectedRangeIDs = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.IDNode);
string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.StartNode);
string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.EndNode);
string expectedSequenceRangeCount = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.SequenceRangeCountNode);
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
var seqRangeGrouping = new SequenceRangeGrouping();
List<ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
var seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i], null),
long.Parse(rangeEnds[i], null));
seqRangeGrouping.Add(seqRange);
}
//Convert SequenceRangeGroup to SequenceRangeList.
rangeList = seqRangeGrouping.Flatten();
int j = 0;
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
Assert.AreEqual(rangeStarts[j], seqRange.Start.ToString((IFormatProvider) null));
Assert.AreEqual(rangeEnds[j], seqRange.End.ToString((IFormatProvider) null));
Assert.AreEqual(rangeIDs[j], seqRange.ID.ToString(null));
j++;
}
Assert.AreEqual(expectedSequenceRangeCount, rangeList.Count.ToString((IFormatProvider) null));
ApplicationLog.WriteLine("SequenceRange BVT : Successfully validated the SequenceStart,SequenceID and SequenceEnd.");
}
/// <summary>
/// Writes out a grouping of ISequenceRange objects to a specified
/// text writer.
/// </summary>
public void Format(SequenceRangeGrouping rangeGroup, TextWriter writer)
{
Format(rangeGroup.Flatten(), writer);
}
/// <summary>
/// Writes out a grouping of ISequenceRange objects to a specified
/// file location.
/// </summary>
public void Format(SequenceRangeGrouping rangeGroup, string fileName)
{
Format(rangeGroup.Flatten(), fileName);
}