public class ModificationProfile extends Object implements Serializable
Constructor and Description |
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ModificationProfile()
Constructor.
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Modifier and Type | Method and Description |
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void |
addFixedModification(PTM modification)
Adds a fixed modification.
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void |
addRefinementModification(PTM modification)
Adds a refinement modification.
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void |
addVariableModification(PTM modification)
Adds a variable modification.
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void |
compatibilityCheck()
Checks the compatibility with older versions of the class and makes the
necessary changes.
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boolean |
contains(String modificationName)
Indicates whether the modification is contained in the profile, looking
into all modifications (fixed, variable and refinement)
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boolean |
equals(ModificationProfile otherProfile)
Returns true of the two profiles are identical.
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ArrayList<String> |
getAllModifications()
Returns a list of all searched modifications.
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ArrayList<String> |
getAllNotFixedModifications()
Returns a list of all searched modifications but the fixed ones.
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Set<String> |
getBackedUpPtms()
Returns the names of the backed-up PTMs.
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Color |
getColor(String modification)
Returns the color used to code the given modification.
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ArrayList<String> |
getFixedModifications()
Returns the searched fixed modifications names.
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String |
getModification(int omssaIndex)
Returns the name of the modification indexed by the given OMSSA index.
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Integer |
getOmssaIndex(String modificationName)
Returns the OMSSA index of a given modification, null if not found.
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PTM |
getPtm(String modName)
Returns the back-ed up PTM with the given name.
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ArrayList<String> |
getRefinementModifications()
Return the refinement modifications used for the second pass search.
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ArrayList<String> |
getSimilarNotFixedModifications(Double ptmMass)
Returns a list containing all not fixed modifications with the same mass.
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ArrayList<String> |
getVariableModifications()
Returns the expected variable modification names included in this
profile.
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void |
removeFixedModification(String modificationName)
Removes a modification from the list of fixed modifications.
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void |
removeRefinementModification(String modificationName)
Removes a modification from the list of refinement modifications
modifications.
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void |
removeVariableModification(String modificationName)
Removes a modification from the list of variable modifications.
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void |
repair()
Sets empty lists and maps to the values lost due to backward
compatability issues.
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void |
setColor(String expectedModification,
Color color)
Sets a new color for the given expected modification.
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void |
setOmssaIndex(String modificationName,
int omssaIndex)
Sets the OMSSA index for a given modification.
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public ArrayList<String> getVariableModifications()
public ArrayList<String> getFixedModifications()
public ArrayList<String> getRefinementModifications()
public ArrayList<String> getAllModifications()
public ArrayList<String> getAllNotFixedModifications()
public void addVariableModification(PTM modification)
modification
- The modification to addpublic void addRefinementModification(PTM modification)
modification
- The modification to addpublic void addFixedModification(PTM modification)
modification
- The modification to addpublic void setColor(String expectedModification, Color color)
expectedModification
- the name of the expected modificationcolor
- the new colorpublic Color getColor(String modification)
modification
- the name of the given expected modificationpublic void compatibilityCheck()
public Set<String> getBackedUpPtms()
public PTM getPtm(String modName)
modName
- the name of the PTM of interestpublic void removeVariableModification(String modificationName)
modificationName
- the name of the modificationpublic void removeFixedModification(String modificationName)
modificationName
- the name of the modificationpublic void removeRefinementModification(String modificationName)
modificationName
- the name of the modificationpublic void setOmssaIndex(String modificationName, int omssaIndex)
modificationName
- the name of the modificationomssaIndex
- the OMSSA index of the modificationpublic String getModification(int omssaIndex)
omssaIndex
- the OMSSA index of the modification to look forpublic Integer getOmssaIndex(String modificationName)
modificationName
- the name of the modificationpublic boolean contains(String modificationName)
modificationName
- the name of the modificationpublic ArrayList<String> getSimilarNotFixedModifications(Double ptmMass)
ptmMass
- the masspublic boolean equals(ModificationProfile otherProfile)
otherProfile
- the profile to compare againstpublic void repair()
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