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); }