com.compomics.util.experiment.io.massspectrometry

Class MgfIndex

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.io.massspectrometry.MgfIndex

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public class MgfIndex
extends ExperimentObject

This class contains the indexes of an mgf file after indexing mapped with the title of the spectrum.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
MgfIndex(java.util.ArrayList<java.lang.String> spectrumTitles, java.util.HashMap<java.lang.String,java.lang.Integer> duplicatedSpectrumTitles, java.util.HashMap<java.lang.String,java.lang.Long> indexMap, java.lang.String fileName, double minRT, double maxRT, double maxMz, double maxIntensity, int maxCharge, int maxPeakCount, long lastModified) Constructor.
MgfIndex(java.util.ArrayList<java.lang.String> spectrumTitles, java.util.HashMap<java.lang.String,java.lang.Long> indexMap, java.lang.String fileName, double minRT, double maxRT, double maxMz, double maxIntensity, int maxCharge, int maxPeakCount, long lastModified) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	containsSpectrum(java.lang.String spectrumTitle) Returns a boolean indicating whether the spectrum title is implemented in this index.
java.util.HashMap<java.lang.String,java.lang.Integer>	getDuplicatedSpectrumTitles() Returns a map of the duplicated spectrum titles, can be null.
java.lang.String	getFileName() Returns the name of the indexed file.
java.lang.Long	getIndex(java.lang.String spectrumTitle) Returns the index corresponding to the desired spectrum.
java.lang.Long	getLastModified() Returns when the file was last modified.
java.lang.Integer	getMaxCharge() Returns the maximal charge found in the mgf file.
java.lang.Double	getMaxIntensity() Returns the maximum precursor intensity in this file.
java.lang.Double	getMaxMz() Returns the maximum m/z in this file.
java.lang.Integer	getMaxPeakCount() Returns the maximum peak count in this file.
java.lang.Double	getMaxRT() Returns the maximal RT in this file.
java.lang.Double	getMinRT() Returns the minimum RT in this file.
int	getNSpectra() Returns the number of imported spectra.
java.util.ArrayList<java.lang.String>	getSpectrumTitles() Returns an ordered list of all spectrum titles.
void	setMaxCharge(java.lang.Integer maxCharge) Sets the maximum charge in this file.
void	setMaxIntensity(java.lang.Double maxIntensity) Sets the maximum precursor intensity in this file.
void	setMaxMz(java.lang.Double maxMz) Sets the maximum m/z in this file.
void	setMaxPeakCount(java.lang.Integer maxPeakCount) Sets the maximum peak count in this file.
void	setMaxRT(java.lang.Double maxRT) Sets the maximal RT in this file.
void	setMinRT(java.lang.Double minRT) Sets the minimum RT in this file.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

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

Constructor Detail

MgfIndex

public MgfIndex(java.util.ArrayList<java.lang.String> spectrumTitles,
        java.util.HashMap<java.lang.String,java.lang.Long> indexMap,
        java.lang.String fileName,
        double minRT,
        double maxRT,
        double maxMz,
        double maxIntensity,
        int maxCharge,
        int maxPeakCount,
        long lastModified)

Constructor.

Parameters:

spectrumTitles - an ordered list of all spectrum titles

indexMap - map of all indexes: spectrum title -> index in the file

fileName - the mgf file name

maxRT - the maximum retention time

minRT - the minimum retention tome

maxMz - the maximum m/z value

maxIntensity - the maximum precursor intensity

maxCharge - the maximum peak precursor charge

maxPeakCount - the maximum peak count

lastModified - a long indicating the last time the indexed file was modified

MgfIndex

public MgfIndex(java.util.ArrayList<java.lang.String> spectrumTitles,
        java.util.HashMap<java.lang.String,java.lang.Integer> duplicatedSpectrumTitles,
        java.util.HashMap<java.lang.String,java.lang.Long> indexMap,
        java.lang.String fileName,
        double minRT,
        double maxRT,
        double maxMz,
        double maxIntensity,
        int maxCharge,
        int maxPeakCount,
        long lastModified)

Constructor.

Parameters:

spectrumTitles - an ordered list of all spectrum titles

duplicatedSpectrumTitles - a map of duplicated spectrum titles, and how often each title is duplicated

indexMap - map of all indexes: spectrum title -> index in the file

fileName - the mgf file name

maxRT - the maximum retention time

minRT - the minimum retention tome

maxMz - the maximum m/z value

maxIntensity - the maximum precursor intensity

maxCharge - the maximum peak precursor charge

maxPeakCount - the maximum peak count

lastModified - a long indicating the last time the indexed file was modified

Method Detail

getIndex

public java.lang.Long getIndex(java.lang.String spectrumTitle)

Returns the index corresponding to the desired spectrum.

Parameters:

spectrumTitle - the desired spectrum

Returns:

the corresponding index

containsSpectrum

public boolean containsSpectrum(java.lang.String spectrumTitle)

Returns a boolean indicating whether the spectrum title is implemented in this index.

Parameters:

spectrumTitle - the spectrum title

Returns:

a boolean indicating whether the spectrum title is implemented in this index

getSpectrumTitles

public java.util.ArrayList<java.lang.String> getSpectrumTitles()

Returns an ordered list of all spectrum titles.

Returns:

an ordered list of all spectrum titles

getDuplicatedSpectrumTitles

public java.util.HashMap<java.lang.String,java.lang.Integer> getDuplicatedSpectrumTitles()

Returns a map of the duplicated spectrum titles, can be null.

Returns:

a map of the duplicated spectrum titles, can be null

getFileName

public java.lang.String getFileName()

Returns the name of the indexed file.

Returns:

the name of the indexed file

getMaxRT

public java.lang.Double getMaxRT()

Returns the maximal RT in this file.

Returns:

the maximal RT in this file

setMaxRT

public void setMaxRT(java.lang.Double maxRT)

Sets the maximal RT in this file.

Parameters:

maxRT - the maximal RT in this file

getMaxMz

public java.lang.Double getMaxMz()

Returns the maximum m/z in this file.

Returns:

the maximum m/z in this file

setMaxCharge

public void setMaxCharge(java.lang.Integer maxCharge)

Sets the maximum charge in this file.

Parameters:

maxCharge - the maximum charge in this file

getMaxCharge

public java.lang.Integer getMaxCharge()

Returns the maximal charge found in the mgf file.

Returns:

the maximal charge found in the mgf file

setMaxMz

public void setMaxMz(java.lang.Double maxMz)

Sets the maximum m/z in this file.

Parameters:

maxMz - the maximum m/z in this file

getMaxIntensity

public java.lang.Double getMaxIntensity()

Returns the maximum precursor intensity in this file.

Returns:

the maximum precursor intensity in this file

setMaxIntensity

public void setMaxIntensity(java.lang.Double maxIntensity)

Sets the maximum precursor intensity in this file.

Parameters:

maxIntensity - the maximum precursor intensity in this file

getMinRT

public java.lang.Double getMinRT()

Returns the minimum RT in this file.

Returns:

the minimum RT in this file

setMinRT

public void setMinRT(java.lang.Double minRT)

Sets the minimum RT in this file.

Parameters:

minRT - the minimum RT in this file

getMaxPeakCount

public java.lang.Integer getMaxPeakCount()

Returns the maximum peak count in this file.

Returns:

the maximum peak count in this file

setMaxPeakCount

public void setMaxPeakCount(java.lang.Integer maxPeakCount)

Sets the maximum peak count in this file.

Parameters:

maxPeakCount - the maximum peak count in this file

getNSpectra

public int getNSpectra()

Returns the number of imported spectra.

Returns:

the number of imported spectra

getLastModified

public java.lang.Long getLastModified()

Returns when the file was last modified. Null if not set or for utilities versions older than 3.11.30.

Returns:

a long indicating when the file was last modified