Package org.fhcrc.cpl.viewer.amt

Interface Summary

AmtFeatureSetMatcher

Interface that must be implemented by any FeatureSetMatcher class.

Class Summary

AcrylamideHydrophobicityAdjuster	This class knows how to adjust normalized hydrophobicities based on the effect of acrylamide, vs.
AmtDatabase	A representation of a full AMT database.
AmtDatabaseBuilder	Builds AMT databases, in various ways If you want to build an AMT database in some other way, put a method in here to do it your way.
AmtDatabaseFeatureSetGenerator	This class Generates FeatureSets based on AMT Database entries.
AmtDatabaseManager	Manages AMT databases -- prunes outliers of various kinds
AmtDatabaseMatcher	This class performs simple matching between an AMT database and a feature files.
AmtDatabaseMatcher.PeptideProphetComparatorDesc
AmtFeatureSetMatcher.FeatureMatchingResult	This class represents the result of running FeatureSetMatcher.matchFeatures().
AmtFeatureSetMatcherFactory	Creates instances of particular FeatureSetMatchers
AMTFileRestrictor
AmtLabeledQuant	Methods for performing labeled quantitation on AMT data.
AmtMatchedProtein	Created by IntelliJ IDEA.
AmtMatchedProtein.AmtMatchedPeptide
AmtMatchProbabilityAssigner	This class assigns a probability to every AMT match, based on the distribution of target and decoy mass and H errors.
AmtPeptideEntry	Encapsulates everything we need to retrieve from / store into an AMT database.
AmtPeptideEntry.AmtPeptideModificationStateEntry	Represents an entry for a specific modification state
AmtPeptideEntry.AmtPeptideObservation	Represents a single peptide observation.
AmtRunEntry	Encapsulates everything we need to retrieve from / store into an AMT database related to a run.
AmtTsvReader	A class for writing AMT TSV files.
AmtTsvReader.AmtTsvRow	Used by TabLoader to represent one row.
AmtUtilities	Utilities related to AMT
AmtXmlReader	A restrictive wrapper for reading AmtXml files.
AmtXmlWriter	A restrictive wrapper for writing AmtXml files.
BaseAmtFeatureSetMatcherImpl	Base implementing class for FeatureSetMatcher classes.
ClusteringFeatureSetMatcher	Attempts to match one feature set against another
HydrophobicityNormalizer	Converts hydrophobicity values from various algorithms to normalized values.
PeptideMatcher
ProteinDisplay	Methods for HTML display of protein sequences.
ProteinMatcher
RecursiveFeatureSetMatcher	Attempts to match one feature set against another.
Window2DFeatureSetMatcher	Attempts to match one feature set against another using a window of minimum and maximum mass and elution time differences, not necessarily centered at 0.