IndexedMzMLDecoder

class pyopenms.IndexedMzMLDecoder

Bases: object

Cython implementation of _IndexedMzMLDecoder

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1IndexedMzMLDecoder.html

Specifically, this class allows one to extract the offsets of the <indexList> tag and of all <spectrum> and <chromatogram> tag using the indices found at the end of the indexedmzML XML structure —– While findIndexListOffset tries extracts the offset of the indexList tag from the last 1024 bytes of the file, this offset allows the function parseOffsets to extract all elements contained in the <indexList> tag and thus get access to all spectra and chromatogram offsets

__init__()

  • Cython signature: void IndexedMzMLDecoder()

  • Cython signature: void IndexedMzMLDecoder(IndexedMzMLDecoder &)

Methods

__init__

  • Cython signature: void IndexedMzMLDecoder()

findIndexListOffset

Cython signature: streampos findIndexListOffset(String in_, int buffersize)
findIndexListOffset()

Cython signature: streampos findIndexListOffset(String in_, int buffersize)

This function reads by default the last few (1024) bytes of the given input file and tries to read the content of the <indexListOffset> tag The idea is that somewhere in the last parts of the file specified by the input string, the string <indexListOffset>xxx</indexListOffset> occurs This function returns the xxx part converted to an integer —– Since this function cannot determine where it will start reading the XML, no regular XML parser can be used for this. Therefore it uses regex to do its job. It matches the <indexListOffset> part and any numerical characters that follow —– :param in: Filename of the input indexedmzML file :param buffersize: How many bytes of the input file should be searched for the tag :returns: A positive integer containing the content of the indexListOffset tag, returns -1 in case of failure no tag was found (you can re-try with a larger buffersize but most likely its not an indexed mzML). Using -1 is what the reference docu recommends: http://en.cppreference.com/w/cpp/io/streamoff :raises:

Exception: FileNotFound is thrown if file cannot be found

Raises

Exception: ParseError if offset cannot be parsed