com.compomics.util.experiment.identification
Class NeutralLossesMap

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

public class NeutralLossesMap
extends Object
implements 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.
 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 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


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