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java.lang.Objectcom.compomics.util.preferences.ModificationProfile
public class ModificationProfile
This class stores the information about the modification preferences (colors, names) used for the selected project.
Constructor Summary | |
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ModificationProfile()
Constructor. |
Method Summary | |
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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(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. |
Color |
getColor(String modification)
Returns the color used to code the given modification. |
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. |
PTM |
getPtm(String modName)
Returns the back-ed up PTM with the given name. |
ArrayList<String> |
getRefinementModifications()
Return the refinement 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 |
removeRefinementModification(String modificationName)
Removes a modification from the list of refinement modifications 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. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ModificationProfile()
Method Detail |
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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 modification
public void compatibilityCheck()
public Set<String> getBackedUpPtms()
public PTM getPtm(String modName)
modName
- the name of the PTM of interest
public 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 for
public boolean hasOMSSAIndexes()
public Integer getOmssaIndex(String modificationName)
modificationName
- the name of the modification
public boolean contains(String modificationName)
modificationName
- the name of the modification
public ArrayList<String> getSimilarNotFixedModifications(Double ptmMass)
ptmMass
- the mass
public boolean equals(ModificationProfile otherProfile)
otherProfile
- the profile to compare against
public void repair()
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