public class ModificationProfile extends Object implements Serializable
Constructor and Description |
---|
ModificationProfile()
Constructor.
|
ModificationProfile(ModificationProfile modificationProfile)
Constructor creating a new Modification profile based on the given one.
|
Modifier and Type | Method and Description |
---|---|
void |
addFixedModification(PTM modification)
Adds a fixed modification.
|
void |
addRefinementFixedModification(PTM modification)
Adds a fixed refinement modification.
|
void |
addRefinementVariableModification(PTM modification)
Adds a variable 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(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.
|
ArrayList<String> |
getAllModifications()
Returns a list of all searched modifications.
|
ArrayList<String> |
getAllNotFixedModifications()
Returns a list of all searched modifications but the fixed ones.
|
Set<String> |
getBackedUpPtms()
Returns the names of the backed-up PTMs.
|
HashMap<String,PTM> |
getBackedUpPtmsMap()
Returns the PTMs backed-up as a map.
|
Color |
getColor(String modification)
Returns the color used to code the given modification.
|
HashMap<String,Color> |
getColors()
Returns the modification colors as a map.
|
ArrayList<String> |
getFixedModifications()
Returns the searched fixed modifications names.
|
String |
getModification(int omssaIndex)
Returns the name of the modification indexed by the given OMSSA index.
|
Integer |
getOmssaIndex(String modificationName)
Returns the OMSSA index of a given modification, null if not found.
|
HashMap<Integer,String> |
getOmssaIndexes()
Returns the OMSSA indexes as a map.
|
PTM |
getPtm(String modName)
Returns the back-ed up PTM with the given name.
|
ArrayList<String> |
getRefinementFixedModifications()
Return the refinement fixed modifications used for the second pass
search.
|
ArrayList<String> |
getRefinementVariableModifications()
Return the refinement variable modifications used for the second pass
search.
|
ArrayList<String> |
getSimilarNotFixedModifications(Double ptmMass)
Returns a list containing all not fixed modifications with the same mass.
|
ArrayList<String> |
getVariableModifications()
Returns the expected variable modification names included in this
profile.
|
boolean |
hasOMSSAIndexes()
Indicates whether the modification profile has OMSSA indexes.
|
void |
removeFixedModification(String modificationName)
Removes a modification from the list of fixed modifications.
|
void |
removeRefinementFixedModification(String modificationName)
Removes a fixed modification from the list of refinement modifications.
|
void |
removeRefinementVariableModification(String modificationName)
Removes a variable modification from the list of refinement
modifications.
|
void |
removeVariableModification(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.
|
void |
setColor(String expectedModification,
Color color)
Sets a new color for the given expected modification.
|
void |
setOmssaIndex(String modificationName,
int omssaIndex)
Sets the OMSSA index for a given modification.
|
public ModificationProfile()
public ModificationProfile(ModificationProfile modificationProfile)
modificationProfile
- the modification profilepublic ArrayList<String> getVariableModifications()
public ArrayList<String> getFixedModifications()
public ArrayList<String> getRefinementVariableModifications()
public ArrayList<String> getRefinementFixedModifications()
public ArrayList<String> getAllModifications()
public ArrayList<String> getAllNotFixedModifications()
public void addVariableModification(PTM modification)
modification
- The modification to addpublic void addRefinementVariableModification(PTM modification)
modification
- The modification to addpublic void addRefinementFixedModification(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 HashMap<String,Color> getColors()
public void compatibilityCheck()
public Set<String> getBackedUpPtms()
public PTM getPtm(String modName)
modName
- the name of the PTM of interestpublic HashMap<String,PTM> getBackedUpPtmsMap()
public void removeVariableModification(String modificationName)
modificationName
- the name of the modificationpublic void removeFixedModification(String modificationName)
modificationName
- the name of the modificationpublic void removeRefinementVariableModification(String modificationName)
modificationName
- the name of the modificationpublic void removeRefinementFixedModification(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 boolean hasOMSSAIndexes()
public Integer getOmssaIndex(String modificationName)
modificationName
- the name of the modificationpublic HashMap<Integer,String> getOmssaIndexes()
public 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()
Copyright © 2014. All rights reserved.