org.fhcrc.cpl.viewer.amt
Class AmtDatabaseFeatureSetGenerator

java.lang.Object
  org.fhcrc.cpl.viewer.amt.AmtDatabaseFeatureSetGenerator

public class AmtDatabaseFeatureSetGenerator
extends java.lang.Object

This class Generates FeatureSets based on AMT Database entries. These featuresets are what's actually used in matching.

Field Summary

protected AmtDatabase

amtDatabase

Constructor Summary

AmtDatabaseFeatureSetGenerator(AmtDatabase amtDatabase)

Method Summary

protected static Feature	createFeatureForPeptideWithMods(AmtPeptideEntry peptideEntry, double observedHydrophobicity, java.util.List<MS2Modification> modifications) Modifications are applied all-or-nothing.
FeatureSet	createFeatureSetForRun(AmtRunEntry runEntry, MS2Modification[] modifications) create a featureset that represents all the features from a run within an amt database, with their original times.
Feature[]	createFeaturesForModifications(MS2Modification[] modifications) Create a feature set based on this AMT database, accounting for expected modifications.
static java.util.List<Feature>	generateModFeaturesForPeptide(AmtPeptideEntry peptideEntry, double observedHydrophobicity, java.util.List<MS2Modification> staticMods, java.util.List<MS2Modification> varMods) Note: Assumes that a variable modification is either fully applied, to all residues in the peptide, or not applied at all
protected static java.util.List<Feature>	recursivelyAddFeaturesForMods(AmtPeptideEntry peptideEntry, double observedHydrophobicity, java.util.List<MS2Modification> appliedMods, java.util.List<MS2Modification> modsRemaining) Recursively generate features for all possible masses, given the list of variable modifications known to exist in this peptide and the list of modifications already applied

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

amtDatabase

protected AmtDatabase amtDatabase

Constructor Detail

AmtDatabaseFeatureSetGenerator

public AmtDatabaseFeatureSetGenerator(AmtDatabase amtDatabase)

Method Detail

createFeaturesForModifications

public Feature[] createFeaturesForModifications(MS2Modification[] modifications)

Create a feature set based on this AMT database, accounting for expected modifications. That is, bump up the mass by the mass of any static modifications, and create duplicate features for any variable modifictions TODO: maybe interrogate modifications[] to see if any of these match up with TODO: the mods we've already got in the db, and get the hydrophobicity accordingly

Parameters:

modifications -

Returns:

generateModFeaturesForPeptide

public static java.util.List<Feature> generateModFeaturesForPeptide(AmtPeptideEntry peptideEntry,
                                                                    double observedHydrophobicity,
                                                                    java.util.List<MS2Modification> staticMods,
                                                                    java.util.List<MS2Modification> varMods)

Note: Assumes that a variable modification is either fully applied, to all residues in the peptide, or not applied at all

Parameters:

peptideEntry -

observedHydrophobicity -

staticMods -

varMods -

Returns:

recursivelyAddFeaturesForMods

protected static java.util.List<Feature> recursivelyAddFeaturesForMods(AmtPeptideEntry peptideEntry,
                                                                       double observedHydrophobicity,
                                                                       java.util.List<MS2Modification> appliedMods,
                                                                       java.util.List<MS2Modification> modsRemaining)

Recursively generate features for all possible masses, given the list of variable modifications known to exist in this peptide and the list of modifications already applied

Parameters:

peptideEntry -

observedHydrophobicity -

appliedMods -

modsRemaining -

Returns:

createFeatureForPeptideWithMods

protected static Feature createFeatureForPeptideWithMods(AmtPeptideEntry peptideEntry,
                                                         double observedHydrophobicity,
                                                         java.util.List<MS2Modification> modifications)

Modifications are applied all-or-nothing. If we modify one residue, we modify all of that residue

Parameters:

peptideEntry -

observedHydrophobicity -

modifications -

Returns:

createFeatureSetForRun

public FeatureSet createFeatureSetForRun(AmtRunEntry runEntry,
                                         MS2Modification[] modifications)

create a featureset that represents all the features from a run within an amt database, with their original times. Note: scan will be incorrectB.

Parameters:

runEntry -

modifications -

Returns: