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:

AASequenceImpl

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor and Description
Protein(AASequenceImpl aSequence) This constructor requires an AASequenceImpl as argument.
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(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

Methods

Modifier and Type	Method and 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 Detail

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:

Constant Field Values

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:

Constant Field Values

Constructor Detail

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 Detail

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