Package com.compomics.util.experiment.mass_spectrometry.indexes

Class PrecursorMap

java.lang.Object

com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap

public class PrecursorMap
extends Object

This map stores the precursors indexed by mass.

Author:

Marc Vaudel

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	PrecursorMap.PrecursorWithTitle	Convenience class storing the precursor and corresponding spectrum title.

Constructor Summary

Constructors

Constructor	Description
PrecursorMap()	Empty default constructor
PrecursorMap(HashMap<String,Precursor> precursors, double precursorTolerance, boolean ppm)	Builds a precursor map.

Method Summary

Modifier and Type	Method	Description
ArrayList<Integer>	getBins()	Returns the bins in the map.
Double	getMass(int bin)	Returns the mass associated with the given bin, the middle of the bin.
ArrayList<PrecursorMap.PrecursorWithTitle>	getMatchingSpectra(double referenceMz)	Returns a list containing the precursors matching the given m/z.
Double	getMaxMz()	Returns the maximal m/z encountered among the precursors.
Double	getMinMz()	Returns the minimal m/z encountered among the precursors.
HashMap<Double,ArrayList<PrecursorMap.PrecursorWithTitle>>	getPrecursorsInBin(int bin)	Returns the precursors at the given bin indexed by mass.

Methods inherited from class java.lang.Object

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

Constructor Details

PrecursorMap

public PrecursorMap()

Empty default constructor

PrecursorMap

public PrecursorMap(HashMap<String,Precursor> precursors,
 double precursorTolerance,
 boolean ppm)

Builds a precursor map.

Parameters:

precursors - map of the precursors indexed by spectrum title

precursorTolerance - the precursor mass tolerance to use

ppm - boolean indicating whether the tolerance is in ppm

Method Details

getMatchingSpectra

public ArrayList<PrecursorMap.PrecursorWithTitle> getMatchingSpectra(double referenceMz)

Returns a list containing the precursors matching the given m/z. TODO: check only one/two bins when possible

Parameters:

referenceMz - a mz to query

Returns:

a list containing the precursors matching the given m/z

getBins

public ArrayList<Integer> getBins()

Returns the bins in the map.

Returns:

the bins in the map

getPrecursorsInBin

public HashMap<Double,ArrayList<PrecursorMap.PrecursorWithTitle>> getPrecursorsInBin(int bin)

Returns the precursors at the given bin indexed by mass. Null if none found.

Parameters:

bin - the bin number

Returns:

the precursors at the given bin

getMass

public Double getMass(int bin)

Returns the mass associated with the given bin, the middle of the bin.

Parameters:

bin - the bin number

Returns:

the mass associated with the given bin

getMinMz

public Double getMinMz()

Returns the minimal m/z encountered among the precursors.

Returns:

the minimal m/z encountered among the precursors

getMaxMz

public Double getMaxMz()

Returns the maximal m/z encountered among the precursors.

Returns:

the maximal m/z encountered among the precursors