|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectcom.compomics.util.protein.AASequenceImpl
public class AASequenceImpl
This class represents a sequence for a protein or peptide.
Sequence
Constructor Summary | |
---|---|
AASequenceImpl(String aSequence)
Constructor that allows the initialization of the sequence with a String variable representing that sequence. |
|
AASequenceImpl(String aSequence,
Vector aMods)
Constructor that allows the initialization of the sequence with a String variable representing that sequence and a Vector of Modification instances. |
Method Summary | |
---|---|
void |
addModification(Modification aModification)
This method adds a modification to the list of modifications. |
boolean |
contains(String aSequence)
This method reports whether a certain residu (or fixed sequence String) is found in the current sequence. |
AASequenceImpl |
getCTermTruncatedSequence(int aTruncationSize)
This method will return an AASequenceImpl that represents a C-terminal truncation of the current sequence. |
double |
getGravy()
This method gets the GRAVY score (Kyte&Doolittle) from the cache, or, if it isn't cached, reconstructs it. |
IsotopicDistribution |
getIsotopicDistribution()
This method gives the IsotopicDistribution for the sequence |
int |
getLength()
This method reports on the length of the current sequence. |
double |
getMass()
This method calculates the mass for the current sequence. |
double |
getMeek()
This method will return an estimated 'net' HPLC retention time for the sequence based on the table by Meek. It does NOT take a t0 value, specific to a setup, into account. |
Vector |
getModifications()
Simple getter for the modifications. |
String |
getModifiedSequence()
This method will return the sequence with annotated modifications. |
MolecularFormula |
getMolecularFormula()
This method calculates the molecular formula based on the sequence |
double |
getMz(int charge)
This method calculates the mass over charge ratio for a given charge for the current sequence. |
AASequenceImpl |
getNTermTruncatedSequence(int aTruncationSize)
This method will return an AASequenceImpl that represents an N-terminal truncation of the current sequence. |
String |
getSequence()
Simple getter for the sequence. |
AASequenceImpl |
getTruncatedSequence(int aStart,
int aEnd)
This method will return an AASequenceImpl that represents an internal truncation of the current sequence. |
static AASequenceImpl |
parsePeptideFromAnnotatedSequence(String aAnnotatedSequence)
This method allows the construction of an AASequenceImpl object, complete with modifications from an annotated sequence String (eg., something like: 'NH2-YS |
protected void |
parseSequenceAndModificationsFromString(String aStringWithModificiations)
This method is designed to load a sequence and it's set of modifications from a String which holds the sequence, annotated with all the modifications applied to it. |
void |
setModifications(Vector aMods)
Simple setter for the modifications. |
void |
setSequence(String aSequence)
Simple setter for the sequence. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public AASequenceImpl(String aSequence)
aSequence
- String with the sequence.public AASequenceImpl(String aSequence, Vector aMods)
aSequence
- String with the sequence.aMods
- Vector with Modification instances.Method Detail |
---|
public void setSequence(String aSequence)
setSequence
in interface Sequence
aSequence
- String with the sequence to be set.public String getSequence()
getSequence
in interface Sequence
public void setModifications(Vector aMods)
aMods
- Vector with the modifications.public Vector getModifications()
public double getMz(int charge)
charge
- the charge to use for the m/z ratio calculation
public double getMass()
getMass
in interface Sequence
public static AASequenceImpl parsePeptideFromAnnotatedSequence(String aAnnotatedSequence)
FVATER-COOH' or 'Ace-MATHM
FVATER-COOH' or 'Ace-MATHM
aAnnotatedSequence
- String with the annotated sequence (eg., something like:
'NH2-YS
protected void parseSequenceAndModificationsFromString(String aStringWithModificiations)
aStringWithModificiations
- String with annotated modifications.Modification
public int getLength()
getLength
in interface Sequence
public double getGravy()
public double getMeek()
public String getModifiedSequence()
public AASequenceImpl getNTermTruncatedSequence(int aTruncationSize)
aTruncationSize
- int with the amount of N-terminal residus the
truncated sequence should have.
public AASequenceImpl getCTermTruncatedSequence(int aTruncationSize)
aTruncationSize
- int with the amount of C-terminal residus the
truncated sequence should have.
public AASequenceImpl getTruncatedSequence(int aStart, int aEnd)
aStart
- int with the start (N-terminal) residu for the
truncation. The first residu is number '1'.aEnd
- int with the end residu (C-terminal; NOT included) for the truncation.
public boolean contains(String aSequence)
aSequence
- with the residu (or fixed sequence of residus)
to find in the current sequence.
public void addModification(Modification aModification)
aModification
- Modification instance to add to the modifications list.public MolecularFormula getMolecularFormula()
public IsotopicDistribution getIsotopicDistribution()
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |