public void TestSequenceAlignmentToString()
{
ISequenceAligner aligner = SequenceAligners.NeedlemanWunsch;
IAlphabet alphabet = Alphabets.Protein;
const string origSequence1 = "KRIPKSQNLRSIHSIFPFLEDKLSHLN";
const string origSequence2 = "LNIPSLITLNKSIYVFSKRKKRLSGFLHN";
// Create input sequences
var inputSequences = new List <ISequence>
{
new Sequence(alphabet, origSequence1),
new Sequence(alphabet, origSequence2)
};
// Get aligned sequences
IList <ISequenceAlignment> alignments = aligner.Align(inputSequences);
ISequenceAlignment alignment = new SequenceAlignment();
foreach (var alignedSequence in alignments[0].AlignedSequences)
{
alignment.AlignedSequences.Add(alignedSequence);
}
const string expected = "XXIPXXXXLXXXXXXFXXXXXXLSXXLHN\r\n" +
"KRIPKSQNLRSIHSIFPFLEDKLSHL--N\r\n" +
"LNIPSLITLNKSIYVFSKRKKRLSGFLHN\r\n\r\n";
Assert.AreEqual(expected.Replace("\r\n", Environment.NewLine), alignment.ToString());
}
public void ValidateSequenceAlignmentToString()
{
ISequenceAligner aligner = SequenceAligners.NeedlemanWunsch;
IAlphabet alphabet = Alphabets.Protein;
string origSequence1 = "KRIPKSQNLRSIHSIFPFLEDKLSHLN";
string origSequence2 = "LNIPSLITLNKSIYVFSKRKKRLSGFLHN";
// 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> alignments = aligner.Align(inputSequences);
ISequenceAlignment alignment = new SequenceAlignment();
for (int ialigned = 0; ialigned < alignments[0].AlignedSequences.Count; ialigned++)
{
alignment.AlignedSequences.Add(alignments[0].AlignedSequences[ialigned]);
}
foreach (string key in alignments[0].Metadata.Keys)
{
alignment.Metadata.Add(key, alignments[0].Metadata[key]);
}
string actualSequenceAlignmentString = alignment.ToString();
string ExpectedSequenceAlignmentString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants
.SequenceAlignmentExpectedNode);
Assert.AreEqual(ExpectedSequenceAlignmentString.Replace("\\r\\n", ""),
actualSequenceAlignmentString.Replace(System.Environment.NewLine, ""));
}
public void TestSequenceAlignmentToString()
{
ISequenceAligner aligner = SequenceAligners.NeedlemanWunsch;
IAlphabet alphabet = Alphabets.Protein;
string origSequence1 = "KRIPKSQNLRSIHSIFPFLEDKLSHLN";
string origSequence2 = "LNIPSLITLNKSIYVFSKRKKRLSGFLHN";
// Create input sequences
List <ISequence> inputSequences = new List <ISequence>();
inputSequences.Add(new Sequence(alphabet, origSequence1));
inputSequences.Add(new Sequence(alphabet, origSequence2));
// Get aligned sequences
IList <ISequenceAlignment> alignments = aligner.Align(inputSequences);
ISequenceAlignment alignment = new SequenceAlignment();
for (int ialigned = 0; ialigned < alignments[0].AlignedSequences.Count; ialigned++)
{
alignment.AlignedSequences.Add(alignments[0].AlignedSequences[ialigned]);
}
foreach (string key in alignments[0].Metadata.Keys)
{
alignment.Metadata.Add(key, alignments[0].Metadata[key]);
}
string actualSequenceAlignmentString = alignment.ToString();
string ExpectedSequenceAlignmentString = "XXIPXXXXLXXXXXXFXXXXXXLSGFXXN\r\nKRIPKSQNLRSIHSIFPFLEDKLS--HLN\r\nLNIPSLITLNKSIYVFSKRKKRLSGFLHN\r\n\r\n";
Assert.AreEqual(ExpectedSequenceAlignmentString, actualSequenceAlignmentString);
}