Package org.fhcrc.cpl.toolbox.proteomics

Interface Summary

Clusterer2D.Clusterable	defines values in two dimensions.
PeptideGenerator.PeptideListener
Scan	User: mbellew Date: Feb 8, 2005 Time: 1:56:36 PM

Class Summary

Clusterer2D	_Highly_ generic 2-dimensional clusterer.
Clusterer2D.ClusterDimensionSplitCalculator	abstract class for determining whether to split in each dimension.
Clusterer2D.DefaultClusterDimensionSplitCalculator	Default split calculator is very simple!
Clusterer2D.TreeEntry	A single entry in the clustering tree, aware of its value in only one dimension
Hydrophobicity3	/* /* reference, O.
IdPattern	User: peter@labkey.com Date: Nov 18, 2007 Time: 11:52:56 PM this class implements a regular expression-based recognition of identifiers parsed from the fasta files.
MassCalibrationUtilities	Utilities for recalibrating and characterizing the mass calibration of sets of features, based on an approach that uses theoretical peptide mass clusters.
MassUtilities	Utilities related to peptide mass
ModifiedAminoAcid	This class models a modified amino acid.
MS2Modification	Note: special characters n and c (lowercase) indicate n-terminal and c-terminal mods
MS2ModificationList	User: adam Date: May 8, 2006 Time: 2:17:53 PM
MSRun	User: mbellew Date: May 20, 2004 Time: 9:54:13 AM
Peptide	User: migra Date: Jun 23, 2004 Time: 10:35:50 PM
PeptideGenerator	User: migra Date: Jun 23, 2004 Time: 2:33:14 PM
PeptideUtilities	Utilities for working with peptide sequences and modifications
Protein	User: migra Date: Jun 23, 2004 Time: 10:28:04 PM
Protein.HeaderComparator
Protein.LookupComparator
Protein.SequenceComparator
ProteinUtilities	This class doesn't do parsing of ProtXML files itself.
ProteomicsRegressionUtilities	Utilities for regression analysis specific to msInspect -- mostly making use of Feature.
QuantitationUtilities	Utilities for working with quantitation