Package com.compomics.util.interfaces
Interface Modification
- All Superinterfaces:
Comparable
- All Known Implementing Classes:
ModificationImplementation
public interface Modification extends Comparable
This interface describes the behaviour for a modification on a peptide or aminoacid sequence.
- Author:
- Lennart Martens
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Field Summary
Fields Modifier and Type Field Description static int
AVERAGE
Constant to indicate the position of the average mass in the mass array.static String
CTERMINUS
The residue code for the C-terminus.static int
MONOISOTOPIC
Constant to indicate the position of the monoisotopic mass in the mass array.static String
NTERMINUS
The residue code for the N-terminus. -
Method Summary
Modifier and Type Method Description double
getAverageMassDelta(String aResidue)
This method returns a double with the average mass difference conferred on the sequence by this modification for the specified residue.String
getCode()
This method returns the short code for the modification, eg.int
getLocation()
This method returns the location of the modification in the sequence.double
getMonoisotopicMassDelta(String aResidue)
This method returns a double with the monoisotopic mass difference conferred on the sequence by this modification for the specified residue.Collection
getResidues()
This method reports on all the residues that can be modified by this Modification.String
getTitle()
This method returns the title of the modification, eg.boolean
isArtifact()
This method indicates whether this modification is considered an artifact.void
setLocation(int aLocation)
This method allows the setting of the location for this modification.String
toString()
This method returns a String representation of the Modification.
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Field Details
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MONOISOTOPIC
static final int MONOISOTOPICConstant to indicate the position of the monoisotopic mass in the mass array.- See Also:
- Constant Field Values
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AVERAGE
static final int AVERAGEConstant to indicate the position of the average mass in the mass array.- See Also:
- Constant Field Values
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NTERMINUS
The residue code for the N-terminus.- See Also:
- Constant Field Values
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CTERMINUS
The residue code for the C-terminus.- See Also:
- Constant Field Values
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Method Details
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getLocation
int getLocation()This method returns the location of the modification in the sequence. Note that the N-terminus is 0, and the C-terminus is (sequence_length)+1.- Returns:
- int with the location for the modification.
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isArtifact
boolean isArtifact()This method indicates whether this modification is considered an artifact.- Returns:
- boolean that indicates whether this modification is an artifact.
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getCode
String getCode()This method returns the short code for the modification, eg. 'Mox'.- Returns:
- String with the short code for the modification. Can be used to annotate a sequence.
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getTitle
String getTitle()This method returns the title of the modification, eg. 'Oxidation Met'.- Returns:
- String with the title for the modification.
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getMonoisotopicMassDelta
This method returns a double with the monoisotopic mass difference conferred on the sequence by this modification for the specified residue. This mass delta can be negative!- Parameters:
aResidue
- String with the residue for which the mass delta needs to be calculated.- Returns:
- double with the monoisotopic mass difference.
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getAverageMassDelta
This method returns a double with the average mass difference conferred on the sequence by this modification for the specified residue. This mass delta can be negative!- Parameters:
aResidue
- String with the residue for which the mass delta needs to be calculated.- Returns:
- double with the average mass difference.
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setLocation
void setLocation(int aLocation)This method allows the setting of the location for this modification. The specified integer should be calculated from the start of the parent sequence, where the N-terminus is 0, and the C-terminus is (sequence_length)+1.- Parameters:
aLocation
- int with the location for this modification within the parent sequence.
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getResidues
Collection getResidues()This method reports on all the residues that can be modified by this Modification.- Returns:
- Collection with the residues that can be modified by this modification.
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toString
String toString()This method returns a String representation of the Modification.
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