public void TestPadenaAssemblyToString()
{
ISequence seq2 = new Sequence(Alphabets.DNA, "ACAAAAGCAAC");
ISequence seq1 = new Sequence(Alphabets.DNA, "ATGAAGGCAATACTAGTAGT");
IList <ISequence> contigList = new List <ISequence>();
contigList.Add(seq1);
contigList.Add(seq2);
PadenaAssembly denovoAssembly = new PadenaAssembly();
denovoAssembly.AddContigs(contigList);
string actualString = denovoAssembly.ToString();
string expectedString = "ATGAAGGCAATACTAGTAGT\r\nACAAAAGCAAC\r\n";
Assert.AreEqual(actualString, expectedString);
}
public void ValidatePadenaAssemblyToString()
{
ISequence seq2 = new Sequence(Alphabets.DNA, "ACAAAAGCAAC");
ISequence seq1 = new Sequence(Alphabets.DNA, "ATGAAGGCAATACTAGTAGT");
IList <ISequence> contigList = new List <ISequence>();
contigList.Add(seq1);
contigList.Add(seq2);
var denovoAssembly = new PadenaAssembly();
denovoAssembly.AddContigs(contigList);
string actualString = denovoAssembly.ToString();
string expectedString = "ATGAAGGCAATACTAGTAGT\r\nACAAAAGCAAC\r\n";
Assert.AreEqual(actualString, expectedString);
// read sequences from xml
string sequence1 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode1);
string sequence2 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode2);
IAlphabet alphabet =
Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.AlphabetNameNode));
var seq3 = new Sequence(alphabet, sequence1);
var seq4 = new Sequence(alphabet, sequence2);
IList <ISequence> contigList1 = new List <ISequence>();
contigList1.Add(seq3);
contigList1.Add(seq4);
var denovoAssembly1 = new PadenaAssembly();
denovoAssembly1.AddContigs(contigList1);
string actualString1 = denovoAssembly1.ToString();
string expectedString1 = "GCCAAAATTTAGGC\r\nTTATGGCGCCCACGGA\r\n";
Assert.AreEqual(expectedString1, actualString1);
}
public void ValidatePadenaAssemblyToString()
{
ISequence seq2 = new Sequence(Alphabets.DNA, "ACAAAAGCAAC");
ISequence seq1 = new Sequence(Alphabets.DNA, "ATGAAGGCAATACTAGTAGT");
IList<ISequence> contigList = new List<ISequence>();
contigList.Add(seq1);
contigList.Add(seq2);
var denovoAssembly = new PadenaAssembly();
denovoAssembly.AddContigs(contigList);
string actualString = denovoAssembly.ToString();
string expectedString = "ATGAAGGCAATACTAGTAGT\r\nACAAAAGCAAC\r\n";
Assert.AreEqual(actualString, expectedString);
// read sequences from xml
string sequence1 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode1);
string sequence2 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode2);
IAlphabet alphabet =
Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.AlphabetNameNode));
var seq3 = new Sequence(alphabet, sequence1);
var seq4 = new Sequence(alphabet, sequence2);
IList<ISequence> contigList1 = new List<ISequence>();
contigList1.Add(seq3);
contigList1.Add(seq4);
var denovoAssembly1 = new PadenaAssembly();
denovoAssembly1.AddContigs(contigList1);
string actualString1 = denovoAssembly1.ToString();
string expectedString1 = "GCCAAAATTTAGGC\r\nTTATGGCGCCCACGGA\r\n";
Assert.AreEqual(expectedString1, actualString1);
}