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 TestDerivedSequenceConvertToString()
{
Sequence baseSeq = new Sequence(Alphabets.DNA, "ATCGATCGGATCGATCGGCTACTAATATCGATCGGCTACGATCGGCTAATCGATCGATCGGCTAATCGATCGATCGGCTAGCTA");
DerivedSequence seq = new DerivedSequence(baseSeq, false, false);
const string expectedValue = "TCGATCGGCT";
string actualValue = seq.ConvertToString(10, 10);
Assert.AreEqual(expectedValue, actualValue);
}
public void TestDerivedSequenceConvertToString()
{
Sequence baseSeq = new Sequence(Alphabets.DNA, "ATCGATCGGATCGATCGGCTACTAATATCGATCGGCTACGATCGGCTAATCGATCGATCGGCTAATCGATCGATCGGCTAGCTA");
DerivedSequence seq = new DerivedSequence(baseSeq, false, false);
const string expectedValue = "TCGATCGGCT";
string actualValue = seq.ConvertToString(10, 10);
Assert.AreEqual(expectedValue, actualValue);
}
public void InvalidateDerivedSequenceConvertToString()
{
try
{
//check with blank sequene
var baseSeq = new Sequence(Alphabets.DNA, "");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, 3);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with length greater than actual length
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, 30);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with length < 0
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, -30);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with start index < 0
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(-10, 3);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with start index greater than actual length
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(30, 3);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with null sequence
Sequence baseSeq = null;
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, 3);
Assert.Fail();
}
catch (NullReferenceException nre)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + nre.Message);
}
}
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 InvalidateDerivedSequenceConvertToString()
{
try
{
//check with blank sequene
var baseSeq = new Sequence(Alphabets.DNA, "");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, 3);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with length greater than actual length
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, 30);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with length < 0
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, -30);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with start index < 0
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(-10, 3);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with start index greater than actual length
var baseSeq = new Sequence(Alphabets.DNA, "ATGCCCC");
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(30, 3);
Assert.Fail();
}
catch (ArgumentOutOfRangeException aorex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + aorex.Message);
}
try
{
//check with null sequence
Sequence baseSeq = null;
var seq = new DerivedSequence(baseSeq, false, false);
string seqStr = seq.ConvertToString(0, 3);
Assert.Fail();
}
catch (NullReferenceException nre)
{
ApplicationLog.WriteLine("Successfully caught ArgumentOutOfRangeException : " + nre.Message);
}
}
