public void ValidateDerivedSequenceConvertToString()
{
string seqLargeStr = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeStringNode);
ISequence seqLarge = new Sequence(Alphabets.DNA, seqLargeStr);
ISequence DeriveSeqLarge = new DerivedSequence(seqLarge, false, true);
string ActualLargeString = DeriveSeqLarge.ToString();
string seqLargeExpected = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeExpectedNode);
string expectedLargeString = string.Format(CultureInfo.CurrentCulture,
seqLargeExpected,
(seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(expectedLargeString, ActualLargeString);
// Get input and expected values from xml
string expectedSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.AlphabetNameNode);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
ISequence seq = new Sequence(alphabet, expectedSequence);
var derSequence = new DerivedSequence(seq, false, false);
Assert.AreEqual(expectedSequence.Substring(2, 5), derSequence.ConvertToString(2, 5));
}
public void ValidateDerivedSequenceToString()
{
ISequence seqSmall = new Sequence(Alphabets.DNA, "ATCG");
string seqLargeStr = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeStringNode);
ISequence seqLarge = new Sequence(Alphabets.DNA, seqLargeStr);
ISequence DeriveSeqSmall = new DerivedSequence(seqSmall, false, true);
ISequence DeriveSeqLarge = new DerivedSequence(seqLarge, false, true);
string ActualSmallString = DeriveSeqSmall.ToString();
string ActualLargeString = DeriveSeqLarge.ToString();
string ExpectedSmallString = "TAGC";
string seqLargeExpected = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeExpectedNode);
string expectedLargeString = string.Format(CultureInfo.CurrentCulture,
seqLargeExpected,
(seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(ExpectedSmallString, ActualSmallString);
Assert.AreEqual(expectedLargeString, ActualLargeString);
//read sequences from file
// Get input and expected values from xml
string expectedSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.ExpectedSequence);
string alphabetName = this.utilityObj.xmlUtil.GetTextValue(
Constants.ProteinDerivedSequenceNode, Constants.AlphabetNameNode);
IAlphabet alphabet = Utility.GetAlphabet(alphabetName);
// Create derived Sequence
ISequence seq = new Sequence(alphabet, expectedSequence);
var derSequence = new DerivedSequence(seq, false, false);
string actualDerivedSeqStr = derSequence.ToString();
if (actualDerivedSeqStr.Length > Helper.AlphabetsToShowInToString)
{
//check if the whole sequence string contains the string retrieved from ToString
Assert.IsTrue(
expectedSequence.Contains(derSequence.ToString().Substring(0, Helper.AlphabetsToShowInToString)));
Assert.IsTrue(derSequence.ToString().Contains("... +["));
}
else
{
Assert.AreEqual(expectedSequence, derSequence.ToString());
}
}
public void TestDerivedSequenceToString()
{
ISequence seqSmall = new Sequence(Alphabets.DNA, "ATCG");
ISequence seqLarge = new Sequence(Alphabets.DNA, "ATCGGGGGGGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGTTTTTTTTTTTTTTT");
ISequence DeriveSeqSmall = new DerivedSequence(seqSmall, false, true);
ISequence DeriveSeqLarge = new DerivedSequence(seqLarge, false, true);
string ActualSmallString = DeriveSeqSmall.ToString();
string ActualLargeString = DeriveSeqLarge.ToString();
string ExpectedSmallString = "TAGC";
string expectedLargeString = string.Format(CultureInfo.CurrentCulture, "TAGCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGCCCCCCCCCCAAAAA... +[{0}]", (seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(ExpectedSmallString, ActualSmallString);
Assert.AreEqual(expectedLargeString, ActualLargeString);
}
