Mascot results file module

Modules
	Examples for the results file module
	UML Class Diagram
	Issues with backward compatibility for results files
	Error Handling
	Peptide mass fingerprint mixtures
	Grouping proteins together
	Unassigned peptides list
	Treatment of duplicate peptides
	Detecting ambiguous peptide matches
	Error tolerant searches
	Crosslinked search results
	Using the singleHit parameter to return a single protein
	Automated repeating of searches
	Target-decoy searches and false discovery rate
	Using Percolator scores
	Caching Mascot Results
	Combining multiple results files
	Query-level modifications
	Spectral libraries
	Spectral library score threshold (advanced reading)

Classes
class	ms_inputquery
	This class encapsulates the input queries (peak lists) in the Mascot results file. More...
class	ms_linker_site
	Position of an intact link between alpha and beta peptide or a looplink. More...
class	ms_linker_site_vector
	A vector of linker sites. More...
class	ms_mascotresfile_dat
	Class for parsing and reading files in dat28 format. More...
class	ms_mascotresfile_msr
	Class for parsing and reading files in MSR format. More...
class	ms_mascotresfilebase
	Abstract base class of ms_mascotresfile_dat and ms_mascotresfile_msr. More...
class	ms_mascotresults
	Abstract class for either ms_peptidesummary or ms_proteinsummary. More...
class	ms_mascotresults_params
	Class which provides constructor parameters for either ms_peptidesummary or ms_proteinsummary. More...
class	ms_msr2dat28
	This class converts a Mascot Search Results (MSR) file to legacy .dat format. More...
class	ms_peptide
	This class encapsulates a peptide from the mascot results file. More...
class	ms_peptidesummary
	Use this class to get peptide summary results. More...
class	ms_protein
	This class encapsulates a protein in the mascot results file. More...
class	ms_proteinsummary
class	ms_searchparams
	This class encapsulates the search parameters in the Mascot results file. More...
class	ms_unigene
	This class encapsulates a complete unigene file. More...
class	ms_unigene_entry
	This class encapsulates a single entry from a unigene file. More...

Detailed Description

The Mascot results files module is used for parsing information from the results files. This data is typically used to populate a database with search results, or to provide custom reports. The standard Mascot reports uses this module.