Constructor and Description |
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AASequenceImpl(String aSequence)
Constructor that allows the initialization of the sequence
with a String variable representing that sequence.
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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.
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Modifier and Type | Method and Description |
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void |
addModification(Modification aModification)
This method adds a modification to the list of modifications.
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boolean |
contains(String aSequence)
This method reports whether a certain residu (or fixed sequence
String) is found in the current sequence.
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AASequenceImpl |
getCTermTruncatedSequence(int aTruncationSize)
This method will return an AASequenceImpl that represents
a C-terminal truncation of the current sequence.
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double |
getGravy()
This method gets the GRAVY score (Kyte & Doolittle) from
the cache, or, if it isn't cached, reconstructs it.
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IsotopicDistribution |
getIsotopicDistribution()
This method gives the IsotopicDistribution for the sequence
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int |
getLength()
This method reports on the length of the current sequence.
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double |
getMass()
This method calculates the mass for the current sequence.
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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.
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String |
getModifiedSequence()
This method will return the sequence with annotated modifications.
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MolecularFormula |
getMolecularFormula()
This method calculates the molecular formula based on the sequence
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double |
getMz(int charge)
This method calculates the mass over charge ratio for a given charge
for the current sequence.
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AASequenceImpl |
getNTermTruncatedSequence(int aTruncationSize)
This method will return an AASequenceImpl that represents
an N-terminal truncation of the current sequence.
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String |
getSequence()
Simple getter for the sequence.
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AASequenceImpl |
getTruncatedSequence(int aStart,
int aEnd)
This method will return an AASequenceImpl that represents
an internal truncation of the current sequence.
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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<P>FVATER-COOH' or 'Ace-MATHM<Mox>PIR-COOH').
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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.
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void |
setModifications(Vector aMods)
Simple setter for the modifications.
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void |
setSequence(String aSequence)
Simple setter for the sequence.
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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.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 calculationpublic double getMass()
public static AASequenceImpl parsePeptideFromAnnotatedSequence(String aAnnotatedSequence)
aAnnotatedSequence
- String with the annotated sequence (eg., something like:
'NH2-YS<P>FVATER-COOH' or 'Ace-MATHM<Mox>PIR-COOH')protected void parseSequenceAndModificationsFromString(String aStringWithModificiations)
aStringWithModificiations
- String with annotated modifications.Modification
public int getLength()
public double getGravy()
public double getMeek()
public String getModifiedSequence()
public AASequenceImpl getNTermTruncatedSequence(int aTruncationSize)
aTruncationSize
- int with the amount of N-terminal residues the
truncated sequence should have.public AASequenceImpl getCTermTruncatedSequence(int aTruncationSize)
aTruncationSize
- int with the amount of C-terminal residues the
truncated sequence should have.public AASequenceImpl getTruncatedSequence(int aStart, int aEnd)
aStart
- int with the start (N-terminal) residue for the
truncation. The first residue is number '1'.aEnd
- int with the end residue (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()
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