/// <summary>
/// Validate aligned sequence instance using different aligners
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="aligner">sw/nw/pw aligners</param>
private void ValidateAlignedSequence(string nodeName, ISequenceAligner aligner)
{
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
string origSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string origSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
// Create input sequences
var inputSequences = new List <ISequence>();
inputSequences.Add(new Sequence(alphabet, origSequence1));
inputSequences.Add(new Sequence(alphabet, origSequence2));
// Get aligned sequences
IList <ISequenceAlignment> alignment = aligner.Align(inputSequences);
// Create AlignedSequence instance
IAlignedSequence sequence = alignment[0].AlignedSequences[0];
// Validate the alignedsequence properties
Assert.AreEqual(alignment[0].AlignedSequences[0].Sequences, sequence.Sequences);
Assert.AreEqual(alignment[0].AlignedSequences[0].Metadata, sequence.Metadata);
ApplicationLog.WriteLine(@"Alignment BVT : Validation of aligned sequence completed successfully");
}
/// <summary>
/// Clear the view
/// </summary>
public void Clear()
{
this.sequences = null;
this.alignedSequence = null;
this.contig = null;
this.Children.Clear();
}
/// <summary>
/// Set dource data for the panel
/// This will trigger a redraw of this panel
/// </summary>
/// <param name="sourceList">Alignment to plot</param>
/// <param name="maximumWidthInChars">Maximum span of the sequences</param>
public void SetDataSource(IAlignedSequence alignedSequence, int maximumWidthInChars)
{
this.sequences = null;
this.contig = null;
this.contigSequences = null;
this.alignedSequence = alignedSequence;
this.maxLength = maximumWidthInChars;
InvalidateMeasure();
}
/// <summary>
/// Set dource data for the panel
/// This will trigger a redraw of this panel
/// </summary>
/// <param name="sourceList">List of seuqences to plot</param>
/// <param name="maximumWidthInChars">Maximum span of the sequences</param>
public void SetDataSource(IList <ISequence> sourceList, int maximumWidthInChars)
{
this.contig = null;
this.alignedSequence = null;
this.contigSequences = null;
this.sequences = sourceList;
this.maxLength = maximumWidthInChars;
InvalidateMeasure();
}
/// <summary>
/// Set dource data for the panel
/// This will trigger a redraw of this panel
/// </summary>
/// <param name="sourceList">Contig to plot</param>
/// <param name="maximumWidthInChars">Maximum span of the sequences</param>
/// <param name="basePaddingLeft">Padding to be added to left of all sequences</param>
public void SetDataSource(Contig contig, int maximumWidthInChars, int basePaddingLeft)
{
this.sequences = null;
this.alignedSequence = null;
this.contig = contig;
this.basePaddingLeft = basePaddingLeft;
this.maxLength = maximumWidthInChars;
contigSequences = contig.Sequences.OrderBy(s => s.Position);
InvalidateMeasure();
}
/// <summary>
/// Used to set datasource if the control is to display the output of an assembly.
/// </summary>
/// <param name="alignment">Contig retrieved after doing the assembly.</param>
public void SetDataSource(IAlignedSequence alignment)
{
this.referenceSequence = null;
this.sequenceList = new List <ISequence>();
this.sequencePropertiesList = new List <SequenceProperties>();
List <int> startOffsets = null;
List <int> endOffsets = null;
if (alignment.Metadata.ContainsKey(StartOffsetString))
{
startOffsets = alignment.Metadata[StartOffsetString] as List <int>;
}
if (alignment.Metadata.ContainsKey(EndOffsetString))
{
endOffsets = alignment.Metadata[EndOffsetString] as List <int>;
}
if (startOffsets == null || startOffsets.Count != alignment.Sequences.Count) // remove offset info if the counts are not matching
{
startOffsets = null;
endOffsets = null;
this.sequencePropertiesList = null;
}
for (int i = 0; i < alignment.Sequences.Count; i++)
{
ISequence currentSeq = alignment.Sequences[i];
sequenceList.Add(currentSeq);
if (startOffsets != null && endOffsets != null)
{
sequencePropertiesList.Add(new SequenceProperties
{
AlignPosition = startOffsets[i],
ReadStartAlignPosition = 0,
AlignmentLength = startOffsets[i] + currentSeq.Count,
IsComplemented = false,
IsReversed = false,
IsAlignment = true
});
}
}
DataSourceUpdated();
}
public void ValidateReadOnlyAlignedSeqCopyTo()
{
ReadOnlyAlignedSequenceCollection readOnlyAlignedSeq =
GetReadOnlyAlignedSequence(Constants.SAMFileWithAllFieldsNode);
IAlignedSequence[] IAlignedSeqArray = new
IAlignedSequence[readOnlyAlignedSeq.Count];
readOnlyAlignedSeq.CopyTo(IAlignedSeqArray, 0);
for (int index = 0; index < readOnlyAlignedSeq.Count; index++)
{
Assert.AreEqual(IAlignedSeqArray[index].Sequences[0].ToString(),
readOnlyAlignedSeq[index].Sequences[0].ToString());
}
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"ReadOnlyAlignedSeqCollection Bvt : Validated the ReadOnlyAlignedSeq CopyTo"));
Console.WriteLine(string.Format((IFormatProvider)null,
"ReadOnlyAlignedSeqCollection Bvt : Validated the ReadOnlyAlignedSeq CopyTo"));
}
/// <summary>
/// Writes SAMAlignedSequence to specified text writer.
/// </summary>
/// <param name="alignedSequence">SAM aligned sequence to write</param>
/// <param name="writer">Text writer.</param>
public static void WriteSAMAlignedSequence(IAlignedSequence alignedSequence, TextWriter writer)
{
if (writer == null)
{
throw new ArgumentNullException("writer");
}
if (alignedSequence == null)
{
throw new ArgumentNullException("alignedSequence");
}
SAMAlignedSequenceHeader alignedHeader = alignedSequence.Metadata[Helper.SAMAlignedSequenceHeaderKey] as SAMAlignedSequenceHeader;
if (alignedHeader == null)
{
throw new ArgumentException(Resource.SAM_AlignedSequenceHeaderMissing);
}
ISequence sequence = alignedSequence.Sequences[0];
if (sequence.Alphabet != Alphabets.DNA)
{
throw new ArgumentException(Resource.SAMFormatterSupportsDNAOnly);
}
List <int> dotSymbolIndices = new List <int>(alignedHeader.DotSymbolIndices);
List <int> equalSymbolIndices = new List <int>(alignedHeader.EqualSymbolIndices);
string seq = "*";
if (sequence.Count > 0)
{
char[] symbols = new char[sequence.Count];
for (int i = 0; i < sequence.Count; i++)
{
char symbol = sequence[i].Symbol;
if (dotSymbolIndices.Count > 0)
{
if (dotSymbolIndices.Contains(i))
{
symbol = '.';
dotSymbolIndices.Remove(i);
}
}
if (equalSymbolIndices.Count > 0)
{
if (equalSymbolIndices.Contains(i))
{
symbol = '=';
equalSymbolIndices.Remove(i);
}
}
symbols[i] = symbol;
}
seq = new string(symbols);
}
string qualValues = "*";
QualitativeSequence qualSeq = sequence as QualitativeSequence;
if (qualSeq != null)
{
byte[] bytes = qualSeq.Scores;
qualValues = System.Text.ASCIIEncoding.ASCII.GetString(bytes);
}
writer.Write(AlignedSequenceFormat,
alignedHeader.QName, (int)alignedHeader.Flag, alignedHeader.RName,
alignedHeader.Pos, alignedHeader.MapQ, alignedHeader.CIGAR,
alignedHeader.MRNM.Equals(alignedHeader.RName) ? "=" : alignedHeader.MRNM,
alignedHeader.MPos, alignedHeader.ISize, seq, qualValues);
for (int j = 0; j < alignedHeader.OptionalFields.Count; j++)
{
writer.Write(OptionalFieldFormat, alignedHeader.OptionalFields[j].Tag,
alignedHeader.OptionalFields[j].VType, alignedHeader.OptionalFields[j].Value);
}
writer.WriteLine();
}
/// <summary>
/// Initializes a new instance of the AlignedSequence class
/// Internal constructor to create AlignedSequence instance from IAlignedSequence.
/// </summary>
/// <param name="alignedSequence">IAlignedSequence instance.</param>
internal AlignedSequence(IAlignedSequence alignedSequence)
{
this.Metadata = alignedSequence.Metadata;
this.Sequences = new List <ISequence>(alignedSequence.Sequences);
}
/// <summary>
/// Writes SAMAlignedSequence to specified text writer.
/// </summary>
/// <param name="alignedSequence">SAM aligned sequence to write</param>
/// <param name="writer">Text writer.</param>
public static void WriteSAMAlignedSequence(IAlignedSequence alignedSequence, TextWriter writer)
{
if (writer == null)
{
throw new ArgumentNullException("writer");
}
if (alignedSequence == null)
{
throw new ArgumentNullException("alignedSequence");
}
SAMAlignedSequenceHeader alignedHeader = alignedSequence.Metadata[Helper.SAMAlignedSequenceHeaderKey] as SAMAlignedSequenceHeader;
if (alignedHeader == null)
{
throw new ArgumentException(Properties.Resource.SAM_AlignedSequenceHeaderMissing);
}
ISequence sequence = alignedSequence.Sequences[0];
if (!(sequence.Alphabet is DnaAlphabet))
{
throw new ArgumentException(Properties.Resource.SAMFormatterSupportsDNAOnly);
}
string seq = "*";
if (sequence.Count > 0)
{
char[] symbols = new char[sequence.Count];
for (int i = 0; i < sequence.Count; i++)
{
symbols[i] = (char)sequence[i];
}
seq = new string(symbols);
}
string qualValues = "*";
QualitativeSequence qualSeq = sequence as QualitativeSequence;
if (qualSeq != null)
{
byte[] bytes = qualSeq.GetEncodedQualityScores();
// if FormatType is not sanger then convert the quality scores to sanger.
if (qualSeq.FormatType != FastQFormatType.Sanger)
{
bytes = QualitativeSequence.ConvertEncodedQualityScore(qualSeq.FormatType, FastQFormatType.Sanger, bytes);
}
qualValues = System.Text.ASCIIEncoding.ASCII.GetString(bytes);
}
writer.Write(AlignedSequenceFormat,
alignedHeader.QName, (int)alignedHeader.Flag, alignedHeader.RName,
alignedHeader.Pos, alignedHeader.MapQ, alignedHeader.CIGAR,
alignedHeader.MRNM.Equals(alignedHeader.RName) ? "=" : alignedHeader.MRNM,
alignedHeader.MPos, alignedHeader.ISize, seq, qualValues);
foreach (var j in alignedHeader.OptionalFields)
{
writer.Write(OptionalFieldFormat, j.Tag,
j.VType, j.Value);
}
writer.WriteLine();
}
/// <summary>
/// Initializes a new instance of the PairwiseAlignedSequence class
/// Internal constructor for creating new instance of
/// PairwiseAlignedSequence from specified IAlignedSequence.
/// </summary>
/// <param name="alignedSequence">IAlignedSequence instance.</param>
internal PairwiseAlignedSequence(IAlignedSequence alignedSequence)
: base(alignedSequence)
{
// Impl.
}
/// <summary>
/// Initializes a new instance of the AlignedSequence class
/// Internal constructor to create AlignedSequence instance from IAlignedSequence.
/// </summary>
/// <param name="alignedSequence">IAlignedSequence instance.</param>
internal AlignedSequence(IAlignedSequence alignedSequence)
{
this.Metadata = alignedSequence.Metadata;
this.Sequences = new List<ISequence>(alignedSequence.Sequences);
}
/// <summary>
/// Получить значение весовой функции выровненных последовательностей.
/// </summary>
public static long GetScore(this IAlignedSequence alignedSequence)
{
return(alignedSequence.Metadata.TryGetValue("Score", out var score)
? (long)score
: long.MinValue);
}
/// <summary>
/// Writes SAMAlignedSequence to specified text writer.
/// </summary>
/// <param name="writer">Text writer.</param>
/// <param name="alignedSequence">SAM aligned sequence to write</param>
public static void WriteSAMAlignedSequence(TextWriter writer, IAlignedSequence alignedSequence)
{
if (writer == null)
{
throw new ArgumentNullException("writer");
}
if (alignedSequence == null)
{
throw new ArgumentNullException("alignedSequence");
}
SAMAlignedSequenceHeader alignedHeader = alignedSequence.Metadata[Helper.SAMAlignedSequenceHeaderKey] as SAMAlignedSequenceHeader;
if (alignedHeader == null)
{
throw new ArgumentException(Properties.Resource.SAM_AlignedSequenceHeaderMissing);
}
ISequence sequence = alignedSequence.Sequences[0];
if (!(sequence.Alphabet is DnaAlphabet))
{
throw new ArgumentException(Properties.Resource.SAMFormatterSupportsDNAOnly);
}
string seq = "*";
if (sequence.Count > 0)
{
char[] symbols = new char[sequence.Count];
for (int i = 0; i < sequence.Count; i++)
{
symbols[i] = (char)sequence[i];
}
seq = new string(symbols);
}
string qualValues = "*";
QualitativeSequence qualSeq = sequence as QualitativeSequence;
if (qualSeq != null)
{
byte[] bytes = qualSeq.GetEncodedQualityScores();
// if FormatType is not sanger then convert the quality scores to sanger.
if (qualSeq.FormatType != FastQFormatType.Sanger)
{
bytes = QualitativeSequence.ConvertEncodedQualityScore(qualSeq.FormatType, FastQFormatType.Sanger, bytes);
}
qualValues = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
}
writer.Write(AlignedSequenceFormat,
alignedHeader.QName, (int)alignedHeader.Flag, alignedHeader.RName,
alignedHeader.Pos, alignedHeader.MapQ, alignedHeader.CIGAR,
alignedHeader.MRNM.Equals(alignedHeader.RName) ? "=" : alignedHeader.MRNM,
alignedHeader.MPos, alignedHeader.ISize, seq, qualValues);
foreach (SAMOptionalField t in alignedHeader.OptionalFields)
{
writer.Write(OptionalFieldFormat, t.Tag,
t.VType, t.Value);
}
writer.WriteLine();
}
/// <summary>
/// Initializes a new instance of the PairwiseAlignedSequence class
/// Internal constructor for creating new instance of
/// PairwiseAlignedSequence from specified IAlignedSequence.
/// </summary>
/// <param name="alignedSequence">IAlignedSequence instance.</param>
internal PairwiseAlignedSequence(IAlignedSequence alignedSequence)
: base(alignedSequence)
{
// Impl.
}
