public class NeutralLossesMap extends Object implements Serializable
Constructor and Description |
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NeutralLossesMap()
Constructor.
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Modifier and Type | Method and Description |
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void |
addNeutralLoss(NeutralLoss neutralLoss,
int bStart,
int yStart)
Adds a new neutral loss to the map.
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void |
clearNeutralLosses()
Clears the mapping.
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boolean |
containsLoss(NeutralLoss neutralLoss)
Returns a boolean indicating whether a loss is implemented in the
mapping.
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ArrayList<NeutralLoss> |
getAccountedNeutralLosses()
Returns an arraylist of implemented neutral losses.
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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).
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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).
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boolean |
isEmpty()
Returns a boolean indicating if the mapping is empty.
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void |
makeSequenceIndependant()
Makes the neutral losses sequence independant.
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public void addNeutralLoss(NeutralLoss neutralLoss, int bStart, int yStart)
neutralLoss
- the new neutral lossbStart
- 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)public void clearNeutralLosses()
public void makeSequenceIndependant()
public boolean isEmpty()
public ArrayList<NeutralLoss> getAccountedNeutralLosses()
public int getBStart(NeutralLoss neutralLoss)
neutralLoss
- the neutral loss of interestpublic int getYStart(NeutralLoss neutralLoss)
neutralLoss
- the neutral loss of interestpublic boolean containsLoss(NeutralLoss neutralLoss)
neutralLoss
- the neutral loss of interestCopyright © 2013. All Rights Reserved.