mzml writing output does not work for TDPortal

[stefanks]

• [x] MsConvert
• [x] SeeMs

Need to:

• [x] Write chromatogram
• [x] Write Indexed mzml

[stefanks]

Maybe instead of writing index it is easier to write an unindexed mzml file

[stefanks]

Rough structure of a method for writing indexed mzmls:

1. Write non-indexed mzML to memory
2. Calculated indices of scans by reading the stream as a binary stream
3. Discard the non-indexed mzML from memory
4. Write the indexed mzML using the xsd generated class and the computed indices

The specification is here: https://github.com/HUPO-PSI/mzML/raw/master/specification_document/mzML1.1.0_specificationDocument.doc

Note that there is a need to also write the indexListOffset element, which is the file pointer offset (in bytes) of the 'indexList' element, and the fileChecksum element which is the SHA-1 checksum from beginning of file to end of 'fileChecksum' open tag.