/// <summary>
/// Initialize a MzMlReader object
/// </summary>
/// <param name="filePath">Path to mzML file</param>
/// <param name="randomAccess">If mzML reader should be configured for random access</param>
/// <param name="tryReducingMemoryUsage">If mzML reader should try to avoid reading all spectra into memory. This will reduce memory usage for a non-random access MzMLReader, as long as ReadMassSpectrum(int) isn't used.</param>
public MzMLReader(string filePath, bool randomAccess = false, bool tryReducingMemoryUsage = true)
{
_filePath = filePath;
_instrument = Instrument.Unknown;
_version = MzML_Version.mzML1_1_0;
_randomAccess = randomAccess;
_reduceMemoryUsage = tryReducingMemoryUsage;
_unzippedFilePath = _filePath;
ConfigureFileHandles();
}
/// <summary>
/// Read and parse a .mzML file
/// Files are commonly larger than 100 MB, so use a streaming reader instead of a DOM reader
/// Vary conditional, depending on configuration
/// </summary>
private void ReadMzMl()
{
if (_randomAccess && _haveIndex && _haveMetaData)
{
return;
}
// Handle disposal of allocated object correctly
var reader = XmlReader.Create(_fileReader, _xSettings);
// Guarantee a move to the root node
reader.MoveToContent();
if (_encoding == null)
{
_encoding = _fileReader.CurrentEncoding;
}
XmlReader indexReader = null;
if (reader.Name == "indexedmzML")
{
indexReader = reader;
// Read to the mzML root tag, and ignore the extra indexedmzML data
reader.ReadToDescendant("mzML");
if (_randomAccess && !_haveIndex)
{
// run to the end of the file (using stream.position = stream.length) and jump backwards to read the index first, and then read the file for needed data
ReadIndexFromEnd();
}
reader = reader.ReadSubtree();
reader.MoveToContent();
}
string schemaName = reader.GetAttribute("xsi:schemaLocation");
// We automatically assume it uses the mzML_1.1.0 schema. Check for the old version.
//if (!schemaName.Contains("mzML1.1.0.xsd"))
if (schemaName.Contains("mzML1.0.0.xsd"))
{
_version = MzML_Version.mzML1_0_0;
}
// Consume the mzML root tag
// Throws exception if we are not at the "mzML" tag.
// This is a critical error; we want to stop processing for this file if we encounter this error
reader.ReadStartElement("mzML");
bool continueReading = true;
// Read the next node - should be the first child node
while (reader.ReadState == ReadState.Interactive && continueReading)
{
// Handle exiting out properly at EndElement tags
if (reader.NodeType != XmlNodeType.Element)
{
reader.Read();
continue;
}
// Handle each 1st level as a chunk
switch (reader.Name)
{
case "cvList":
// Schema requirements: one instance of this element
reader.Skip();
break;
case "fileDescription":
// Schema requirements: one instance of this element
if (!_randomAccess || (_randomAccess && !_haveMetaData))
{
ReadFileDescription(reader.ReadSubtree());
reader.ReadEndElement(); // "fileDescription" must have child nodes
}
else
{
reader.Skip();
}
break;
case "referenceableParamGroupList":
// Schema requirements: zero to one instances of this element
if (!_randomAccess || (_randomAccess && !_haveMetaData))
{
ReadReferenceableParamGroupList(reader.ReadSubtree());
reader.ReadEndElement(); // "referenceableParamGroupList" must have child nodes
}
else
{
reader.Skip();
}
break;
case "sampleList":
// Schema requirements: zero to one instances of this element
reader.Skip();
break;
case "softwareList":
// Schema requirements: one instance of this element
reader.Skip();
break;
case "scanSettingsList":
// Schema requirements: zero to one instances of this element
reader.Skip();
break;
case "instrumentConfigurationList":
// Schema requirements: one instance of this element
reader.Skip();
break;
case "dataProcessingList":
// Schema requirements: one instance of this element
reader.Skip();
break;
case "acquisitionSettingsList": // mzML 1.0.0 compatibility
// Schema requirements: zero to one instances of this element
reader.Skip();
break;
case "run":
// Schema requirements: one instance of this element
// Use reader.ReadSubtree() to provide an XmlReader that is only valid for the element and child nodes
ReadRunData(reader.ReadSubtree());
if (_randomAccess || _reduceMemoryUsage)
{
// Kill the read, since we already have a valid index
continueReading = false;
// don't worry about the skip, since it can take some time.
//reader.Skip();
}
else
{
// "run" might not have any child nodes
// We will either consume the EndElement, or the same element that was passed to ReadRunData (in case of no child nodes)
reader.Read();
}
break;
default:
// We are not reading anything out of the tag, so bypass it
reader.Skip();
break;
}
}
_haveMetaData = true;
if (!_randomAccess && !_reduceMemoryUsage)
{
_allRead = true;
}
//_numSpectra = _spectrumOffsets.Offsets.Count;
/* // Now read before any of the metadata.
if (indexReader != null)
{
reader = indexReader;
//_reader.ReadStartElement("mzML");
// Read the next node - should be the first child node
while (reader.ReadState == ReadState.Interactive)
{
// Handle exiting out properly at EndElement tags
if (reader.NodeType != XmlNodeType.Element)
{
reader.Read();
continue;
}
// Handle each 1st level as a chunk
switch (reader.Name)
{
case "indexList":
// Schema requirements: one instance of this element
ReadIndexList(reader.ReadSubtree());
reader.ReadEndElement(); // "fileDescription" must have child nodes
break;
case "indexListOffset":
// Schema requirements: zero to one instances of this element
_indexListOffset = Int64.Parse(reader.ReadElementContentAsString());
break;
case "fileChecksum":
// Schema requirements: zero to one instances of this element
reader.Skip();
break;
default:
// We are not reading anything out of the tag, so bypass it
reader.Skip();
break;
}
}
reader.Close();
} */
if (!_reduceMemoryUsage)
{
// Don't worry about closing the subtree readers, just close the root reader.
// reader is the root if it is not an indexed mzML file.
if (indexReader == null)
{
reader.Close();
}
else
{
indexReader.Close();
}
}
}
