public IList<PeakData> ImportFile(TextReader peakViewReader)
{
var peakDatas = new List<PeakData>();
var msFileNames = new List<string>();
var fileReader = new DsvFileReader(peakViewReader, TextUtil.SEPARATOR_TSV);
Assert.AreEqual(fileReader.GetFieldIndex(PROTEIN), 0);
Assert.AreEqual(fileReader.GetFieldIndex(PEPTIDE), 1);
Assert.AreEqual(fileReader.GetFieldIndex(LABEL), 2);
Assert.AreEqual(fileReader.GetFieldIndex(PRECURSOR), 3);
Assert.AreEqual(fileReader.GetFieldIndex(CHARGE), 4);
Assert.AreEqual(fileReader.GetFieldIndex(RT), 5);
Assert.AreEqual(fileReader.GetFieldIndex(DECOY), 6);
for (int i = 7; i < fileReader.NumberOfFields; ++i)
{
msFileNames.Add(fileReader.FieldNames[i]);
}
while (fileReader.ReadLine() != null)
{
string modifiedSequence = fileReader.GetFieldByName(PEPTIDE);
string decoyString = fileReader.GetFieldByName(DECOY);
bool decoy;
Assert.IsTrue(bool.TryParse(decoyString, out decoy));
foreach (var msFileName in msFileNames)
{
string dataFieldString = fileReader.GetFieldByName(msFileName);
double dataField;
Assert.IsTrue(double.TryParse(dataFieldString, out dataField));
var peakData = new PeakData(dataField, modifiedSequence, msFileName, decoy);
peakDatas.Add(peakData);
}
}
return peakDatas;
}
public void DsvHeadersTest()
{
// test reading DSV files with and without headers
string[] lines = {"dog,1.1,cat,2.2", "pony,3.3,fish,4.4"}; // Not L10N
const char csvSeperator = ',';
var withheaders = new DsvFileReader(new StringReader("0,1,2,3\n" + String.Join("\n", lines)), csvSeperator); // Not L10N
var withoutheaders = new DsvFileReader(new StringReader(String.Join("\n", lines)), csvSeperator, hasHeaders: false); // Not L10N
Assert.AreEqual(withheaders.NumberOfFields, withoutheaders.NumberOfFields);
for (int h = 0; h < withoutheaders.NumberOfFields; h++)
{
var f = String.Format("{0}", h); // verify that a headerless CSV file will pretend to have a header of form "0,1,2,..." // Not L10N
Assert.AreEqual(withheaders.GetFieldIndex(f), withoutheaders.GetFieldIndex(f));
}
int linenumber = 0;
while (true)
{
var fields = withoutheaders.ReadLine();
var fieldsTest = withheaders.ReadLine();
Assert.IsTrue((fields == null) == (fieldsTest == null));
if (fields == null)
break;
for (int f = 0; f < withoutheaders.NumberOfFields; f++)
{
Assert.AreEqual(fields[f], fieldsTest[f]); // quick string compare
Assert.AreEqual(lines[linenumber].Split(csvSeperator)[f],fields[f]);
}
linenumber++;
}
Assert.AreEqual(2,linenumber);
// let's also check the precision handling and field exception in AssertEx.FieldsEqual
var A = String.Join("\n", lines).Replace("cat","hamster"); // change col 2, then ignore it // Not L10N
var B = String.Join("\n", lines).Replace("1.1","1.09"); // add error at limits of precision, then allow for it // Not L10N
AssertEx.FieldsEqual(A, B, 4, 2, true);
}
