public void TestEditingWhenIsReadOnlyIsTrue()
{
QualitativeSequence qualSequence = new QualitativeSequence(Alphabets.RNA, FastQFormatType.Illumina, "ACUGGA", 65);
Assert.IsTrue(qualSequence.IsReadOnly);
try
{
qualSequence.Clear();
Assert.Fail();
}
catch
{
Assert.AreEqual(qualSequence.Count, 6);
}
try
{
qualSequence.Add(Alphabets.RNA.AC);
Assert.Fail();
}
catch
{
Assert.AreEqual(qualSequence.Count, 6);
}
try
{
qualSequence.Remove(Alphabets.RNA.AC);
Assert.Fail();
}
catch
{
Assert.AreEqual(qualSequence.Count, 6);
}
try
{
qualSequence.Replace(0, Alphabets.RNA.AC.Symbol);
Assert.Fail();
}
catch
{
Assert.AreEqual(qualSequence.Count, 6);
}
}
public void AllEditableScenarios()
{
string filepathOriginal = @"TestData\FastQ\SRR002012_5.fastq";
FastQParser fastqParser = new FastQParser();
IList <IQualitativeSequence> qualitativeSequences;
string[] expectedSequences = new string[] {
"GGCGCACTTACACCCTACATCCATTG",
"GTCTGCATTATCTACCAGCACTTCCC",
"GCTGTCTTCCCGCTGTTTTATCCCCC",
"GTAGTTTACCTGTTCATATGTTTCTG",
"GGAAGGAAGAGGCTAGCCCAGCCTTT"
};
fastqParser.EnforceDataVirtualization = true;
fastqParser.AutoDetectFastQFormat = false;
fastqParser.FastqType = FastQFormatType.Sanger;
qualitativeSequences = fastqParser.Parse(filepathOriginal, true);
int sequenceCount = qualitativeSequences.Count;
for (int i = 0; i < sequenceCount; i++)
{
QualitativeSequence actualSequence = qualitativeSequences[i] as QualitativeSequence;
actualSequence.IsReadOnly = false;
ISequenceItem item = actualSequence[1];
actualSequence.Add(item);
expectedSequences[i] += item.Symbol;
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.Remove(item);
int indexOfItem = expectedSequences[i].IndexOf(item.Symbol);
expectedSequences[i] = expectedSequences[i].Remove(indexOfItem, 1);
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.RemoveAt(0);
expectedSequences[i] = expectedSequences[i].Remove(0, 1);
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.RemoveRange(2, 5);
expectedSequences[i] = expectedSequences[i].Remove(2, 5);
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.Replace(0, 'C');
expectedSequences[i] = expectedSequences[i].Remove(0, 1);
expectedSequences[i] = expectedSequences[i].Insert(0, "C");
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.ReplaceRange(5, "GG");
expectedSequences[i] = expectedSequences[i].Remove(5, 2);
expectedSequences[i] = expectedSequences[i].Insert(5, "GG");
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.Insert(10, item);
expectedSequences[i] = expectedSequences[i].Insert(10, item.Symbol.ToString());
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.InsertRange(2, "CC");
expectedSequences[i] = expectedSequences[i].Insert(2, "CC");
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
bool actualContainsValue = actualSequence.Contains(actualSequence[3]);
bool expectedContainsValue = expectedSequences[i].Contains(actualSequence[3].Symbol.ToString());
Assert.AreEqual(actualContainsValue, expectedContainsValue);
}
}
public void TestEditingwhenIsReadOnlyIsFalse()
{
QualitativeSequence qualSequence = new QualitativeSequence(Alphabets.RNA, FastQFormatType.Illumina, "ACUGGA", 65);
Assert.IsTrue(qualSequence.IsReadOnly);
qualSequence.IsReadOnly = false;
Assert.AreEqual(qualSequence.Count, 6);
Assert.AreEqual(qualSequence.ToString(), "ACUGGA");
qualSequence.Clear();
Assert.AreEqual(qualSequence.Count, 0);
Assert.AreEqual(qualSequence.Scores.Length, 0);
qualSequence.Add(Alphabets.RNA.A, 65);
Assert.AreEqual(qualSequence.Count, 1);
Assert.AreEqual(qualSequence.Scores.Length, 1);
Assert.AreSame(qualSequence[0], Alphabets.RNA.A);
Assert.AreEqual(qualSequence.Scores[0], 65);
qualSequence.Insert(0, Alphabets.RNA.G, 70);
Assert.AreEqual(qualSequence.Count, 2);
Assert.AreEqual(qualSequence.Scores.Length, 2);
Assert.AreSame(qualSequence[0], Alphabets.RNA.G);
Assert.AreSame(qualSequence[1], Alphabets.RNA.A);
Assert.AreEqual(qualSequence.Scores[0], 70);
Assert.AreEqual(qualSequence.Scores[1], 65);
qualSequence.Replace(0, Alphabets.RNA.U, 75);
Assert.AreEqual(qualSequence.Count, 2);
Assert.AreEqual(qualSequence.Scores.Length, 2);
Assert.AreSame(qualSequence[0], Alphabets.RNA.U);
Assert.AreSame(qualSequence[1], Alphabets.RNA.A);
Assert.AreEqual(qualSequence.Scores[0], 75);
Assert.AreEqual(qualSequence.Scores[1], 65);
qualSequence.Remove(Alphabets.RNA.C);
Assert.AreEqual(qualSequence.Count, 2);
Assert.AreEqual(qualSequence.Scores.Length, 2);
Assert.AreSame(qualSequence[0], Alphabets.RNA.U);
Assert.AreSame(qualSequence[1], Alphabets.RNA.A);
Assert.AreEqual(qualSequence.Scores[0], 75);
Assert.AreEqual(qualSequence.Scores[1], 65);
qualSequence.Remove(Alphabets.RNA.A);
Assert.AreEqual(qualSequence.Count, 1);
Assert.AreEqual(qualSequence.Scores.Length, 1);
Assert.AreSame(qualSequence[0], Alphabets.RNA.U);
Assert.AreEqual(qualSequence.Scores[0], 75);
qualSequence.Add(Alphabets.RNA.A, 65);
Assert.AreEqual(qualSequence.Count, 2);
Assert.AreEqual(qualSequence.Scores.Length, 2);
Assert.AreSame(qualSequence[0], Alphabets.RNA.U);
Assert.AreSame(qualSequence[1], Alphabets.RNA.A);
Assert.AreEqual(qualSequence.Scores[0], 75);
Assert.AreEqual(qualSequence.Scores[1], 65);
qualSequence.RemoveAt(1);
Assert.AreEqual(qualSequence.Count, 1);
Assert.AreEqual(qualSequence.Scores.Length, 1);
}
