com.compomics.util.experiment.identification
Class NeutralLossesMap

java.lang.Object
  extended by com.compomics.util.experiment.identification.NeutralLossesMap
All Implemented Interfaces:
java.io.Serializable

public class NeutralLossesMap
extends java.lang.Object
implements java.io.Serializable

This class contains the informations relative to the accounting of neutral losses

Author:
Marc Vaudel
See Also:
Serialized Form

Constructor Summary
NeutralLossesMap()
          Constructor
 
Method Summary
 void addNeutralLoss(NeutralLoss neutralLoss, int bStart, int yStart)
          Adds a new neutral loss to the map
 void clearNeutralLosses()
          Clears the mapping
 boolean containsLoss(NeutralLoss neutralLoss)
          Returns a boolean indicating whether a loss is implemented in the mapping
 java.util.ArrayList<NeutralLoss> getAccountedNeutralLosses()
          Returns an arraylist of implemented neutral losses
 int getBStart(NeutralLoss neutralLoss)
          Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1)
 int getYStart(NeutralLoss neutralLoss)
          Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1)
 boolean isEmpty()
          Returns a boolean indicating if the mapping is empty
 void makeSequenceIndependant()
          Makes the neutral losses sequence independant
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

NeutralLossesMap

public NeutralLossesMap()
Constructor

Method Detail

addNeutralLoss

public void addNeutralLoss(NeutralLoss neutralLoss,
                           int bStart,
                           int yStart)
Adds a new neutral loss to the map

Parameters:
neutralLoss - the new neutral loss
bStart - the amino acid position where the neutral loss should start being accounted starting from the N-terminus (first is 1)
yStart - the amino acid position where the neutral loss should start being accounted starting from the C-terminus (first is 1)

clearNeutralLosses

public void clearNeutralLosses()
Clears the mapping


makeSequenceIndependant

public void makeSequenceIndependant()
Makes the neutral losses sequence independant


isEmpty

public boolean isEmpty()
Returns a boolean indicating if the mapping is empty

Returns:
a boolean indicating if the mapping is empty

getAccountedNeutralLosses

public java.util.ArrayList<NeutralLoss> getAccountedNeutralLosses()
Returns an arraylist of implemented neutral losses

Returns:
an arraylist of implemented neutral losses

getBStart

public int getBStart(NeutralLoss neutralLoss)
Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1)

Parameters:
neutralLoss - the neutral loss of interest
Returns:
the first amino acid where to account for the neutral loss

getYStart

public int getYStart(NeutralLoss neutralLoss)
Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1)

Parameters:
neutralLoss - the neutral loss of interest
Returns:
the first amino acid where to account for the neutral loss

containsLoss

public boolean containsLoss(NeutralLoss neutralLoss)
Returns a boolean indicating whether a loss is implemented in the mapping

Parameters:
neutralLoss - the neutral loss of interest
Returns:
a boolean indicating whether a loss is implemented in the mapping


Copyright © 2012. All Rights Reserved.