PtmSettings (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.identification.identification_parameters.PtmSettings

All Implemented Interfaces:

Serializable
```
public class PtmSettings
extends Object
implements Serializable
```
This class stores the information about the modification preferences (colors, names) used for the selected project.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

PtmSettings()
Constructor.

PtmSettings(PtmSettings modificationProfile)
Constructor creating a new Modification profile based on the given one.

Constructors
Constructor and Description
`PtmSettings()` Constructor.
`PtmSettings(PtmSettings modificationProfile)` Constructor creating a new Modification profile based on the given one.

Method Summary

All Methods Instance Methods Concrete Methods
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`	`clearFixedModifications()` Clears fixed modifications.
`void`	`clearRefinementModifications()` Clears refinement modifications.
`void`	`clearVariableModifications()` Clears variable modifications.
`boolean`	`contains(String modificationName)` Indicates whether the modification is contained in the profile, looking into all modifications (fixed, variable and refinement)
`boolean`	`equals(PtmSettings 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.
`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.
`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`	`setColor(String expectedModification, Color color)` Sets a new color for the given expected modification.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - PtmSettings
```
public PtmSettings()
```
    Constructor.
  - PtmSettings
```
public PtmSettings(PtmSettings modificationProfile)
```
    Constructor creating a new Modification profile based on the given one.
    
    Parameters:
    
    modificationProfile - the modification profile
- Method Detail
  - getVariableModifications
```
public ArrayList<String> getVariableModifications()
```
    Returns the expected variable modification names included in this profile.
    
    Returns:
    
    the expected variable modification names included in this profile
  - getFixedModifications
```
public ArrayList<String> getFixedModifications()
```
    Returns the searched fixed modifications names.
    
    Returns:
    
    the searched fixed modifications names
  - getRefinementVariableModifications
```
public ArrayList<String> getRefinementVariableModifications()
```
    Return the refinement variable modifications used for the second pass search.
    
    Returns:
    
    the refinement variable modifications
  - clearVariableModifications
```
public void clearVariableModifications()
```
    Clears variable modifications.
  - clearFixedModifications
```
public void clearFixedModifications()
```
    Clears fixed modifications.
  - clearRefinementModifications
```
public void clearRefinementModifications()
```
    Clears refinement modifications.
  - getRefinementFixedModifications
```
public ArrayList<String> getRefinementFixedModifications()
```
    Return the refinement fixed modifications used for the second pass search.
    
    Returns:
    
    the refinement fixed modifications
  - getAllModifications
```
public ArrayList<String> getAllModifications()
```
    Returns a list of all searched modifications.
    
    Returns:
    
    a list of all searched modifications
  - getAllNotFixedModifications
```
public ArrayList<String> getAllNotFixedModifications()
```
    Returns a list of all searched modifications but the fixed ones. Note: to be fixed a modification must be fixed during the first and second pass searches.
    
    Returns:
    
    a list of all searched modifications but the fixed ones
  - addVariableModification
```
public void addVariableModification(PTM modification)
```
    Adds a variable modification. The modification name is added in the variable modifications names list and the modification is saved in the back-up. In case a modification with the same name was already used it will be silently overwritten.
    
    Parameters:
    
    modification - The modification to add
  - addRefinementVariableModification
```
public void addRefinementVariableModification(PTM modification)
```
    Adds a variable refinement modification. The modification name is added in the refinement modifications names list and the modification is saved in the back-up. In case a modification with the same name was already used it will be silently overwritten.
    
    Parameters:
    
    modification - The modification to add
  - addRefinementFixedModification
```
public void addRefinementFixedModification(PTM modification)
```
    Adds a fixed refinement modification. The modification name is added in the refinement modifications names list and the modification is saved in the back-up. In case a modification with the same name was already used it will be silently overwritten.
    
    Parameters:
    
    modification - The modification to add
  - addFixedModification
```
public void addFixedModification(PTM modification)
```
    Adds a fixed modification. The modification name is added in the fixed modifications names list and the modification is saved in the back-up. In case a modification with the same name was already used it will be silently overwritten.
    
    Parameters:
    
    modification - The modification to add
  - setColor
```
public void setColor(String expectedModification,
                     Color color)
```
    Sets a new color for the given expected modification.
    
    Parameters:
    
    expectedModification - the name of the expected modification
    
    color - the new color
  - getColor
```
public Color getColor(String modification)
```
    Returns the color used to code the given modification.
    
    Parameters:
    
    modification - the name of the given expected modification
    
    Returns:
    
    the corresponding color
  - getColors
```
public HashMap<String,Color> getColors()
```
    Returns the modification colors as a map.
    
    Returns:
    
    the modifications colors as a map
  - getBackedUpPtms
```
public Set<String> getBackedUpPtms()
```
    Returns the names of the backed-up PTMs.
    
    Returns:
    
    the names of the backed-up PTMs
  - getPtm
```
public PTM getPtm(String modName)
```
    Returns the back-ed up PTM with the given name.
    
    Parameters:
    
    modName - the name of the PTM of interest
    
    Returns:
    
    the corresponding PTM. Null if not found.
  - getBackedUpPtmsMap
```
public HashMap<String,PTM> getBackedUpPtmsMap()
```
    Returns the PTMs backed-up as a map. PTM name > PTM.
    
    Returns:
    
    the PTMs backed-up as a map
  - removeVariableModification
```
public void removeVariableModification(String modificationName)
```
    Removes a modification from the list of variable modifications.
    
    Parameters:
    
    modificationName - the name of the modification
  - removeFixedModification
```
public void removeFixedModification(String modificationName)
```
    Removes a modification from the list of fixed modifications.
    
    Parameters:
    
    modificationName - the name of the modification
  - removeRefinementVariableModification
```
public void removeRefinementVariableModification(String modificationName)
```
    Removes a variable modification from the list of refinement modifications.
    
    Parameters:
    
    modificationName - the name of the modification
  - removeRefinementFixedModification
```
public void removeRefinementFixedModification(String modificationName)
```
    Removes a fixed modification from the list of refinement modifications.
    
    Parameters:
    
    modificationName - the name of the modification
  - contains
```
public boolean contains(String modificationName)
```
    Indicates whether the modification is contained in the profile, looking into all modifications (fixed, variable and refinement)
    
    Parameters:
    
    modificationName - the name of the modification
    
    Returns:
    
    a boolean indicating whether the modification is contained in the mapping
  - getSimilarNotFixedModifications
```
public ArrayList<String> getSimilarNotFixedModifications(Double ptmMass)
```
    Returns a list containing all not fixed modifications with the same mass. Warning: all modifications of the profile must be loaded in the PTM factory.
    
    Parameters:
    
    ptmMass - the mass
    
    Returns:
    
    a list of all not fixed modifications with the same mass
  - equals
```
public boolean equals(PtmSettings otherProfile)
```
    Returns true of the two profiles are identical.
    
    Parameters:
    
    otherProfile - the profile to compare against
    
    Returns:
    
    true of the two profiles are identical

Class PtmSettings

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PtmSettings

PtmSettings

Method Detail

getVariableModifications

getFixedModifications

getRefinementVariableModifications

clearVariableModifications

clearFixedModifications

clearRefinementModifications

getRefinementFixedModifications

getAllModifications

getAllNotFixedModifications

addVariableModification

addRefinementVariableModification

addRefinementFixedModification

addFixedModification

setColor

getColor

getColors

getBackedUpPtms

getPtm

getBackedUpPtmsMap

removeVariableModification

removeFixedModification

removeRefinementVariableModification

removeRefinementFixedModification

contains

getSimilarNotFixedModifications

equals