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public interface Modification
This interface describes the behaviour for a modification on a peptide or aminoacid sequence.
Field Summary | |
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static int |
AVERAGE
Constant to indicate the position of the average mass in the mass array. |
static java.lang.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 java.lang.String |
NTERMINUS
The residue code for the N-terminus. |
Method Summary | |
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double |
getAverageMassDelta(java.lang.String aResidue)
This method returns a double with the average mass difference conferred on the sequence by this modification for the specified residue. |
java.lang.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(java.lang.String aResidue)
This method returns a double with the monoisotopic mass difference conferred on the sequence by this modification for the specified residue. |
java.util.Collection |
getResidues()
This method reports on all the residues that can be modified by this Modification. |
java.lang.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. |
java.lang.String |
toString()
This method returns a String representation of the Modification. |
Methods inherited from interface java.lang.Comparable |
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compareTo |
Field Detail |
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static final int MONOISOTOPIC
static final int AVERAGE
static final java.lang.String NTERMINUS
static final java.lang.String CTERMINUS
Method Detail |
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int getLocation()
boolean isArtifact()
java.lang.String getCode()
java.lang.String getTitle()
double getMonoisotopicMassDelta(java.lang.String aResidue)
aResidue
- String with the residue for which the mass delta needs to be calculated.
double getAverageMassDelta(java.lang.String aResidue)
aResidue
- String with the residue for which the mass delta needs to be calculated.
void setLocation(int aLocation)
aLocation
- int with the location for this modification within the parent sequence.java.util.Collection getResidues()
java.lang.String toString()
toString
in class java.lang.Object
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