This class handles parsing and storage of database information from mzIDentML files, residing at the /MzIdentML/SequenceCollection/DBSequence node.
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An mzIDevidence object
An mzIDdatabase object
Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?
The content of the class is stored in a data.frame with columns depending on the content of the mzIdentML file. Required information for files conforming to the mzIdentML standard are: 'accession', 'searchDatabase_ref' and 'id', while additional information can fx be 'length' (number of residues), 'description' (from the fasta file) and 'sequence' (the actual sequence).
show: Short summary of the content of the object
length: Report the number of proteins in the database
database: Get the database used for searching
A data.frame containing references to all the database sequences from the mzIdentML file
Objects of mzIDdatabase are not meant to be created explicitly but as part of
mzID-class. Still object can be created with the
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