public void Parse_ShouldAcceptGaps()
{
string expectedSequence = "ABC-";
var aminoAcidSequenceData = AminoAcidSequence.Parse(expectedSequence);
Assert.AreEqual(expectedSequence, aminoAcidSequenceData.Characters);
}
public void Parse_ShouldAcceptTranslationStop()
{
string expectedSequence = "ABC*";
var aminoAcidSequenceData = AminoAcidSequence.Parse(expectedSequence);
Assert.AreEqual(expectedSequence, aminoAcidSequenceData.Characters);
}
public void ToString_ProducesExpectedOutput()
{
string expectedSequence = "ABC-";
var aminoAcidSequenceData = AminoAcidSequence.Parse(expectedSequence);
Assert.AreEqual(expectedSequence, aminoAcidSequenceData.ToString());
}
public void ToInterleavedLines_ShouldProduceExpectedOutputForNonDefaultLineLength()
{
string inputSequence = "MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS"
+ "EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL";
IEnumerable <string> expectedOutputLines = new string[] {
">lcl|123",
"MDSKGSSQ",
"KGSRLLLL",
"LVVSNLLL",
"CQGVVSTP",
"VCPNGPGN",
"CQVSLRDL",
"FDRAVMVS",
"HYIHDLSS",
"EMFNEFDK",
"RYAQGKGF",
"ITMALNSC",
"HTSSLPTP",
"EDKEQAQQ",
"THHEVLMS",
"LILGLLRS",
"WNDPLYHL"
};
Identifier identifier = new LocalIdentifier("123");
Header header = new Header(identifier);
IActualSequence sequence = AminoAcidSequence.Parse(inputSequence);
var singleFASTAFileData = new Sequence(header, sequence);
IEnumerable <string> actualOutputLines = singleFASTAFileData.ToInterleavedLines(8);
CollectionAssert.AreEqual(expectedOutputLines.ToList(), actualOutputLines.ToList());
}
public void ToLines_RejectsNegativeLineLength()
{
string sequence = "ABCDEF";
var aminoAcidSequenceData = AminoAcidSequence.Parse(sequence);
_ = aminoAcidSequenceData.ToLines(-1);
}
public void ToLines_RejectsLineLengthOfZero()
{
string sequence = "ABCDEF";
var aminoAcidSequenceData = AminoAcidSequence.Parse(sequence);
_ = aminoAcidSequenceData.ToLines(0);
}
public void ToLines_ProducesExpectedOutput()
{
string sequence = "ABCDEF";
var expectedLines = new string[] { "ABCD", "EF" };
var aminoAcidSequenceData = AminoAcidSequence.Parse(sequence);
IEnumerable <string> actualLines = aminoAcidSequenceData.ToLines(4);
Assert.IsTrue(actualLines.SequenceEqual(expectedLines));
}
public void ToMultilineString_ProducesExpectedOutput()
{
string sequence = "ABCDEF";
string expectedLines = $"ABCD{Environment.NewLine}EF";
var aminoAcidSequenceData = AminoAcidSequence.Parse(sequence);
string actualLines = aminoAcidSequenceData.ToMultilineString(4);
Assert.AreEqual(expectedLines, actualLines);
}
public void ToInterleavedLines_ShouldRejectLineLengthOfZero()
{
string inputSequence = "MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS"
+ "EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL";
Identifier identifier = new LocalIdentifier("123");
Header header = new Header(identifier);
IActualSequence sequence = AminoAcidSequence.Parse(inputSequence);
var singleFASTAFileData = new Sequence(header, sequence);
_ = singleFASTAFileData.ToInterleavedLines(0).ToList();
}
public void Parse_ShouldConvertMultilineSequenceToSingleLine()
{
var aminoAcidSequenceData = AminoAcidSequence.Parse("ABC\nDEF");
Assert.AreEqual("ABCDEF", aminoAcidSequenceData.Characters);
}
public void Parse_ShouldConvertLowercaseSequenceToUppercase()
{
var aminoAcidSequenceData = AminoAcidSequence.Parse("abc");
Assert.AreEqual("ABC", aminoAcidSequenceData.Characters);
}
public void Parse_ShouldRejectInvalidCharacterAtEnd()
{
_ = AminoAcidSequence.Parse("ABC2");
}
public void Parse_ShouldRejectInvalidCharacterAtStart()
{
_ = AminoAcidSequence.Parse("2ABC");
}
public void Parse_ShouldRejectNullString()
{
_ = AminoAcidSequence.Parse(null);
}