Package com.compomics.util.protein

Class Protein

java.lang.Object
com.compomics.util.protein.Protein
public class Protein extends Object
This class implements the behaviour for a Protein instance. A lot of functionality is borrowed from the AASequenceImpl class. The internal representation corresponds most closely to a FASTA entry.
Author:
Lennart Martens
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    CTERMTRUNC
    The code for an C-terminal truncation.
    static final int
    NTERMTRUNC
    The code for an N-terminal truncation.

  • Constructor Summary

    Constructors
    Constructor
    Description
    Protein()
    Empty default constructor
    Protein(Header aHeader, AASequenceImpl aSequence)
    This constructor allows the passing of a Header, as well as an AASequenceImpl for this Protein.
    Protein(Header aHeader, AASequenceImpl aSequence, boolean aTruncated, int aTruncationPosition)
    This constructor allows the passing of a Header, as well as an AASequenceImpl for this Protein.
    Protein(AASequenceImpl aSequence)
    This constructor requires an AASequenceImpl as argument.
    Protein(String aFASTAString)
    This constructor allows for the construction of a Protein instance by passing a FASTA entry.
    Protein(String aFASTAString, boolean aTruncated, int aTruncationPosition)
    This constructor allows for the construction of a Protein instance by passing a FASTA entry and boolean flag for truncation.
    Protein(String aHeader, String aSequence)
    This constructor allows for the construction of a Protein instance through the passing of a Header String and a Sequence String.
    Protein(String aHeader, String aSequence, boolean aTruncated, int aTruncationPosition)
    This constructor allows for the construction of a Protein instance through the passing of a Header String and a Sequence String.

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    equals(Object o)
    This method will check equality between this object and another Protein instance.
    Protein
    getCTermTruncatedProtein(int aSize)
    This method truncates the sequence for this protein on the C-terminus to the requested size.
    Header
    getHeader()
    This method reports on the header for the current protein.
    long
    getLength()
    This method reports on the length of the sequence for the current protein.
    double
    getMass()
    This method returns the protein weight in Da.
    Protein
    getNTermTruncatedProtein(int aSize)
    This method truncates the sequence for this protein on the N-terminus to the requested size.
    AASequenceImpl
    getSequence()
    This method reports on the sequence for the current protein.
    int
    getTruncationPosition()
    This method reports on the position of the truncation.
    boolean
    isTruncated()
    This method reports on the 'truncatedness' of the protein.
    void
    setHeader(Header aHeader)
    Simple setter for the header.
    void
    setSequence(AASequenceImpl aSequence)
    Simple setter for the sequence.
    void
    writeToFASTAFile(PrintWriter aOut)
    This method can be used to append this protein to the FASTA DB flatfile the PrintWriter points to.

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • NTERMTRUNC

      public static final int NTERMTRUNC
      The code for an N-terminal truncation. These variables can be compared to the result of the 'getTruncationPosition()' method, BUT ONLY when the 'isTruncated()' method returns true.
      See Also:

    • CTERMTRUNC

      public static final int CTERMTRUNC
      The code for an C-terminal truncation. These variables can be compared to the result of the 'getTruncationPosition()' method, BUT ONLY when the 'isTruncated()' method returns true.
      See Also:

  • Constructor Details

    • Protein

      public Protein()
      Empty default constructor

    • Protein

      public Protein(AASequenceImpl aSequence)
      This constructor requires an AASequenceImpl as argument. This will be the sequence around which the protein will be built.
      Parameters:
      aSequence - AASequenceImpl around which this protein will be built.

    • Protein

      public Protein(Header aHeader, AASequenceImpl aSequence)
      This constructor allows the passing of a Header, as well as an AASequenceImpl for this Protein.
      Parameters:
      aHeader - Header with the header information for this Protein.
      aSequence - AASequenceImpl with the sequence for this Protein.

    • Protein

      public Protein(Header aHeader, AASequenceImpl aSequence, boolean aTruncated, int aTruncationPosition)
      This constructor allows the passing of a Header, as well as an AASequenceImpl for this Protein. It also allows for the specification of the 'truncatedness' of the Protein.
      Parameters:
      aHeader - Header with the header information for this Protein.
      aSequence - AASequenceImpl with the sequence for this Protein.
      aTruncated - boolean that indicates whether this Protein has been truncated.
      aTruncationPosition - int with the coded position for the truncation (N-Term or C-Term).

    • Protein

      public Protein(String aFASTAString)
      This constructor allows for the construction of a Protein instance by passing a FASTA entry.
      Parameters:
      aFASTAString - String with the FASTA representation of the Protein.

    • Protein

      public Protein(String aFASTAString, boolean aTruncated, int aTruncationPosition)
      This constructor allows for the construction of a Protein instance by passing a FASTA entry and boolean flag for truncation.
      Parameters:
      aFASTAString - String with the FASTA representation of the Protein.
      aTruncated - boolean that indicates whether this Protein has been truncated.
      aTruncationPosition - int with the coded position for the truncation (N-Term or C-Term).

    • Protein

      public Protein(String aHeader, String aSequence)
      This constructor allows for the construction of a Protein instance through the passing of a Header String and a Sequence String. This is mainly useful to obtain a Protein instance without a Header.
      Parameters:
      aHeader - String with the header (can be 'null').
      aSequence - String with the sequence.

    • Protein

      public Protein(String aHeader, String aSequence, boolean aTruncated, int aTruncationPosition)
      This constructor allows for the construction of a Protein instance through the passing of a Header String and a Sequence String. This is mainly useful to obtain a Protein instance without a Header.
      Parameters:
      aHeader - String with the header (can be 'null').
      aSequence - String with the sequence.
      aTruncated - boolean that indicates whether this Protein has been truncated.
      aTruncationPosition - int with the coded position for the truncation (N-Term or C-Term).

  • Method Details

    • getHeader

      public Header getHeader()
      This method reports on the header for the current protein.
      Returns:
      Header with the current header for this protein.

    • getSequence

      public AASequenceImpl getSequence()
      This method reports on the sequence for the current protein.
      Returns:
      AASequenceImpl with the current sequence for this protein.

    • getNTermTruncatedProtein

      public Protein getNTermTruncatedProtein(int aSize)
      This method truncates the sequence for this protein on the N-terminus to the requested size.
      Parameters:
      aSize - int with the size of the resulting N-terminal sequence
      Returns:
      Protein with an N-terminal truncated sequence.

    • getCTermTruncatedProtein

      public Protein getCTermTruncatedProtein(int aSize)
      This method truncates the sequence for this protein on the C-terminus to the requested size.
      Parameters:
      aSize - int with the size of the resulting C-terminal sequence
      Returns:
      Protein with an C-terminal truncated sequence.

    • getLength

      public long getLength()
      This method reports on the length of the sequence for the current protein.
      Returns:
      long with the length of the sequence for the current protein.

    • getMass

      public double getMass()
      This method returns the protein weight in Da.
      Returns:
      double with the mass of the Protein in Da.

    • setHeader

      public void setHeader(Header aHeader)
      Simple setter for the header.
      Parameters:
      aHeader - the Header to set for this protein.

    • setSequence

      public void setSequence(AASequenceImpl aSequence)
      Simple setter for the sequence.
      Parameters:
      aSequence - the AASequenceImpl with the sequence to set for this protein.

    • writeToFASTAFile

      public void writeToFASTAFile(PrintWriter aOut) throws IOException
      This method can be used to append this protein to the FASTA DB flatfile the PrintWriter points to.
      Parameters:
      aOut - PrintWriter to write the file to.
      Throws:
      IOException - when the writing failed.

    • isTruncated

      public boolean isTruncated()
      This method reports on the 'truncatedness' of the protein.
      Returns:
      boolean whether this protein is the result of a truncation.

    • getTruncationPosition

      public int getTruncationPosition()
      This method reports on the position of the truncation. Note that the method can only be trusted when the 'isTruncated()' method returns 'true'.
      Returns:
      int with the code for the position (either N-term or C-term). This return code can be evaluated against the constants defined on this class.

    • equals

      public boolean equals(Object o)
      This method will check equality between this object and another Protein instance.
      Overrides:
      equals in class Object