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