public pHistBumpViewModel()
{
// Initialize this view model with default values
searchParams = new SearchParams();
mgf = null;
}
/// <summary>
/// Initializes the search.
/// </summary>
/// <returns>Returns error messages</returns>
public string parseMGF()
{
string errors = searchParams.validateSearchParamsAndConvertToNum();
if (errors != string.Empty)
return errors;
mgf = null;
mgf = new MGFFile(searchParams.mgfFilePath);
if (!mgf.parseText_Linear())
return "Error: Failed to parse MGF input file.";
return String.Empty;
}
public void parseText_Linear_wellFormedIonListProvided_IonSpectraListPopulated()
{
string[] fileLines = sampleData_wellFormed;
string filePath = createTestMgfFile(fileLines);
MGFFile target = new MGFFile(filePath);
bool expected = true;
bool actual;
actual = target.parseText_Linear();
Assert.AreEqual(expected, actual);
IonSpectrum spectrum1 = getIonSpectrum1();
IonSpectrum spectrum2 = getIonSpectrum2();
if (target.ionSpectra.Count != 2)
Assert.Fail("Parser did not accumulate the same amount of spectra");
if (!AreSpectraEqual(target.ionSpectra[0], spectrum1))
Assert.Fail("Spectrum 1 was not parsed correctly");
if (!AreSpectraEqual(target.ionSpectra[1], spectrum2))
Assert.Fail("Spectrum 2 was not parsed correctly");
}
public void parseText_Linear_illFormedIonListProvided_parseFails()
{
string[] fileLines = sampleData_poorlyFormed;
string filePath = createTestMgfFile(fileLines);
MGFFile target = new MGFFile(filePath);
bool expected = false;
bool actual;
actual = target.parseText_Linear();
Assert.AreEqual(expected, actual);
}
public void parseSpectrum_validSpectrumLineIndex_validParseResult()
{
string[] fileLines = sampleData_wellFormed;
string filePath = createTestMgfFile(fileLines);
MGFFile target = new MGFFile(filePath);
int ionStartLineIndex = 16;
IonSpectrum expected = getIonSpectrum2();
IonSpectrum actual;
System.IO.StreamReader sr = getStreamReaderAtLine(filePath, ionStartLineIndex);
actual = target.parseSpectrum(ionStartLineIndex, sr);
if (!AreSpectraEqual(expected, actual))
Assert.Fail("Expected and actual spectra are not equal.");
}
public void parseSpectrum_invalidSpectrumLineIndex_nullResult()
{
string[] fileLines = sampleData_wellFormed;
string filePath = createTestMgfFile(fileLines);
MGFFile target = new MGFFile(filePath);
int ionStartLineIndex = -1;
IonSpectrum expected = null;
IonSpectrum actual;
System.IO.StreamReader sr = getStreamReaderAtLine(filePath, ionStartLineIndex);
actual = target.parseSpectrum(ionStartLineIndex, sr);
Assert.AreEqual(expected, actual);
}
public void MGFFileConstructor_givenProperMGFFile_ParsesCorrectly()
{
string filePath = "C:\\Users\\vbhatia\\Desktop\\pHistBump\\assets\\pH-SHY-PtsI_SythPep-sample.mgf";
MGFFile target = new MGFFile(filePath);
target.parseText_Linear();
if (target.ionSpectra == null || target.ionSpectra.Count < 1)
Assert.Fail("Failed to parse file correctly.");
}
public void identifyIonsStartIndices_validInputMGFText_correctIndices()
{
string[] fileLines = sampleData_wellFormed;
string filePath = createTestMgfFile(fileLines);
MGFFile target = new MGFFile(filePath);
List<int> expected = new List<int>();
expected.Add(1);
expected.Add(16);
List<int> actual;
actual = target.identifyIonsStartIndices();
if (expected.Count != actual.Count)
Assert.Fail("Incorrect number of start indices found.");
foreach (int index in expected)
if (!actual.Contains(index))
Assert.Fail("Expected and actual start indices are not equivalent.");
}