Class AASequenceImpl

java.lang.Object
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

    Constructors 
    Constructor Description
    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

    Modifier and Type Method Description
    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 Details

    • 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 Details

    • 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 residues 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 residues 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) residue for the truncation. The first residue is number '1'.
      aEnd - int with the end residue (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