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,
Integer bStart,
Integer yStart)
Adds a new neutral loss to the map.
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void |
addNeutralLoss(String neutralLossName,
Integer bStart,
Integer yStart)
Adds a new neutral loss to the map.
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void |
backwardCompatibilityFix()
Backward compatibility fix for objects of utilities version older than
4.2.16.
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void |
clearNeutralLosses()
Clears the mapping.
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NeutralLossesMap |
clone() |
boolean |
containsLoss(String neutralLossName)
Returns a boolean indicating whether a loss is implemented in the
mapping.
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ArrayList<String> |
getAccountedNeutralLosses()
Returns an arraylist of the names of the implemented neutral losses.
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Integer |
getForwardStart(String neutralLossName)
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 |
getRewindStart(String neutralLossName)
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 independent.
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public void backwardCompatibilityFix()
public void addNeutralLoss(NeutralLoss neutralLoss, Integer bStart, Integer 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 addNeutralLoss(String neutralLossName, Integer bStart, Integer yStart)
neutralLossName
- the new neutral loss namebStart
- 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<String> getAccountedNeutralLosses()
public Integer getForwardStart(String neutralLossName)
neutralLossName
- the name of the neutral loss of interestpublic int getRewindStart(String neutralLossName)
neutralLossName
- the name of the neutral loss of interestpublic boolean containsLoss(String neutralLossName)
neutralLossName
- the name of the neutral loss of interestpublic NeutralLossesMap clone()
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