com.compomics.util.protein
Class AASequenceImpl

java.lang.Object
  extended by com.compomics.util.protein.AASequenceImpl
All Implemented Interfaces:
Sequence

public class AASequenceImpl
extends Object
implements Sequence

This class represents a sequence for a protein or peptide.

Author:
Lennart Martens
See Also:
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<P>FVATER-COOH' or 'Ace-MATHM<Mox>PIR-COOH').
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

AASequenceImpl

public AASequenceImpl(String aSequence)
Constructor that allows the initialization of the sequence with a String variable representing that sequence.

Parameters:
aSequence - String with the sequence.

AASequenceImpl

public 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.

Parameters:
aSequence - String with the sequence.
aMods - Vector with Modification instances.
Method Detail

setSequence

public void setSequence(String aSequence)
Simple setter for the sequence. It also clears the mass cache.

Specified by:
setSequence in interface Sequence
Parameters:
aSequence - String with the sequence to be set.

getSequence

public String getSequence()
Simple getter for the sequence.

Specified by:
getSequence in interface Sequence
Returns:
String the sequence.

setModifications

public void setModifications(Vector aMods)
Simple setter for the modifications.

Parameters:
aMods - Vector with the modifications.

getModifications

public Vector getModifications()
Simple getter for the modifications.

Returns:
Vector with the modifications.

getMz

public double getMz(int charge)
This method calculates the mass over charge ratio for a given charge for the current sequence. Returns -1, if the mass could not be calculated.

Parameters:
charge - the charge to use for the m/z ratio calculation
Returns:
double with the m/z ratio for this sequence with the given charge, -1 if the mass could not be calculated.

getMass

public double getMass()
This method calculates the mass for the current sequence.
Mass cached lazily, so after the first calculation it comes from memory.

Specified by:
getMass in interface Sequence
Returns:
double with the mass for this sequence.

parsePeptideFromAnnotatedSequence

public 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').

Parameters:
aAnnotatedSequence - String with the annotated sequence (eg., something like: 'NH2-YS<P>FVATER-COOH' or 'Ace-MATHM<Mox>PIR-COOH')
Returns:
AASequenceImpl with the sequence and annotated modifications.

parseSequenceAndModificationsFromString

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.
Typically, the String parsed should be derived from the 'String getModifiedSequence()' method (see documentation there).

Parameters:
aStringWithModificiations - String with annotated modifications.
See Also:
Modification

getLength

public int getLength()
This method reports on the length of the current sequence.

Specified by:
getLength in interface Sequence
Returns:
int with the length of the sequence.

getGravy

public double getGravy()
This method gets the GRAVY score (Kyte&Doolittle) from the cache, or, if it isn't cached, reconstructs it.

Returns:
double with the GRAVY coefficient.

getMeek

public 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.

Returns:
double with the 'net' HPLC retention time as calculated from Meek's table.

getModifiedSequence

public String getModifiedSequence()
This method will return the sequence with annotated modifications. For this annotation the key of the modifications will be used. If the key is a formula, it will be enclosed in '<>' as well.

Returns:
String with the annotated sequence (i.e.: containing the modifications.

getNTermTruncatedSequence

public AASequenceImpl getNTermTruncatedSequence(int aTruncationSize)
This method will return an AASequenceImpl that represents an N-terminal truncation of the current sequence.
Note that the applicable modifications (those within the truncation size) are also represented in the truncated sequence!

Parameters:
aTruncationSize - int with the amount of N-terminal residus the truncated sequence should have.
Returns:
AASEquenceImpl with the N-terminal truncated sequence (including modifications).

getCTermTruncatedSequence

public AASequenceImpl getCTermTruncatedSequence(int aTruncationSize)
This method will return an AASequenceImpl that represents a C-terminal truncation of the current sequence.
Note that the applicable modifications (those within the truncation size) are also represented in the truncated sequence!

Parameters:
aTruncationSize - int with the amount of C-terminal residus the truncated sequence should have.
Returns:
AASEquenceImpl with the C-terminal truncated sequence (including modifications).

getTruncatedSequence

public AASequenceImpl getTruncatedSequence(int aStart,
                                           int aEnd)
This method will return an AASequenceImpl that represents an internal truncation of the current sequence.
Note that the applicable modifications (those within the truncation size) are also represented in the resulting truncated sequence!

Parameters:
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.
Returns:
AASEquenceImpl with the C-terminal truncated sequence (including modifications).

contains

public boolean contains(String aSequence)
This method reports whether a certain residu (or fixed sequence String) is found in the current sequence.

Parameters:
aSequence - with the residu (or fixed sequence of residus) to find in the current sequence.
Returns:
boolean that indicates whether the sequence contains the indicated residu (or sequence).

addModification

public void addModification(Modification aModification)
This method adds a modification to the list of modifications.

Parameters:
aModification - Modification instance to add to the modifications list.

getMolecularFormula

public MolecularFormula getMolecularFormula()
This method calculates the molecular formula based on the sequence

Returns:
MolecularFormula

getIsotopicDistribution

public IsotopicDistribution getIsotopicDistribution()
This method gives the IsotopicDistribution for the sequence

Returns:
IsotopicDistribution


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