mobios.type
Class TandemSpectra

java.lang.Object
  mobios.type.IndexObject
      mobios.type.DoubleVector
          mobios.type.Spectra
              mobios.type.TandemSpectra

All Implemented Interfaces:

Externalizable, Serializable, Comparable<IndexObject>

public class TandemSpectra
extends Spectra

TandemSpectra represents a given spectra and its attached precursor mass.

Version:

2004.11.29

Author:

Smriti Ramakrishnan, Willard

See Also:

Serialized Form

Constructor Summary

TandemSpectra()
Necessary for readExternal() and writeExternal().

TandemSpectra(mobios.db.Table table, int rowID, double precursorMass, double[] spectra)
Main constructor using an array of doubles to define the Spectra.

TandemSpectra(mobios.db.Table table, int rowID, double precursorMass, String spectra)
Constructs a TandemSpectra object from a {@link String representing the tandem spectra.

Method Summary

int	compareTo(IndexObject oThat)
boolean	equals(Object that)
IndexObject[]	expand() This method is necessary to implement bucketing, so that similar objects are only stored once in the database.
double	getPrecursorMass()
int	hashCode()
void	readExternal(ObjectInput in)
String	toString() all implementing classes are required to override toString
void	writeExternal(ObjectOutput out)

Methods inherited from class mobios.type.Spectra

getMax, getMin, sortAsc

Methods inherited from class mobios.type.DoubleVector

compareTo, getData, size

Methods inherited from class mobios.type.IndexObject

getRowID, setRowID, setRowIDLength

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

TandemSpectra

public TandemSpectra()

Necessary for readExternal() and writeExternal().

TandemSpectra

public TandemSpectra(mobios.db.Table table,
                     int rowID,
                     double precursorMass,
                     String spectra)

Constructs a TandemSpectra object from a {@link String representing the tandem spectra. The only difference between a Spectra and a TandemSpectra is that a TandemSpectra includes the precursor mass.

Parameters:

table - the corresponding TandemSpectraTable for this object

rowID - the rowID in the TandemSpectraTable.

precursorMass - the precursor mass of the spectra itself.

spectra - a space-seperated String representation of a single fragmentation spectra.

TandemSpectra

public TandemSpectra(mobios.db.Table table,
                     int rowID,
                     double precursorMass,
                     double[] spectra)

Main constructor using an array of doubles to define the Spectra.

Parameters:

table - the corresponding TandemSpectraTable for this object

rowID - the rowID in the TandemSpectraTable.

precursorMass - the precursor mass of the spectra itself.

spectra -

Method Detail

getPrecursorMass

public double getPrecursorMass()

Returns:

the precursor mass for this tandem spectra.

expand

public IndexObject[] expand()

Description copied from class: IndexObject

This method is necessary to implement bucketing, so that similar objects are only stored once in the database. If you do not want to implement bucketing for your object, you can just return an array of length one containing this object.

Overrides:

expand in class Spectra

Returns:

an array of IndexObjects

compareTo

public int compareTo(IndexObject oThat)

Specified by:

compareTo in interface Comparable<IndexObject>

Overrides:

compareTo in class DoubleVector

equals

public boolean equals(Object that)

Overrides:

equals in class DoubleVector

hashCode

public int hashCode()

Overrides:

hashCode in class DoubleVector

toString

public String toString()

Description copied from class: IndexObject

all implementing classes are required to override toString

Overrides:

toString in class DoubleVector

readExternal

public void readExternal(ObjectInput in)
                  throws ClassNotFoundException,
                         IOException

Specified by:

readExternal in interface Externalizable

Overrides:

readExternal in class DoubleVector

Throws:

ClassNotFoundException

IOException

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Specified by:

writeExternal in interface Externalizable

Overrides:

writeExternal in class DoubleVector

Throws:

IOException