com.compomics.util.experiment.identification.amino_acid_tags

Class SequenceSegment

java.lang.Object

com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment

public class SequenceSegment
extends Object

Segment of sequence indexed on a protein sequence.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
boolean	nTerminus Boolean indicating whether the segment is sequencing from the N (true) or the C (false) terminus.

Constructor Summary

Constructors

Constructor and Description
SequenceSegment(int terminalIndex, boolean nTerminus) Constructor.
SequenceSegment(SequenceSegment sequenceSegment) Constructor.

Method Summary

Modifier and Type	Method and Description
void	addMass(double mass) Adds a mass to the segment.
void	addModificationTerminus(String modification) Adds a modification to the terminus of sequencing.
void	addModificationTerminus(String modification, double modificationMass) Adds a modification to the terminus of sequencing.
void	addMutation(Integer index, Character aa) Adds a mutation to the segment.
void	appendTerminus(AminoAcid aminoAcid) Appends an amino acid to the terminus of sequencing.
void	appendTerminus(AminoAcidPattern aminoAcidPattern) Appends an amino acid pattern to the terminus of sequencing.
void	appendTerminus(AminoAcidSequence aminoAcidSequence) Appends an amino acid sequence to the terminus of sequencing.
void	appendTerminus(SequenceSegment sequenceSegment) Appends a sequence segment to the terminus of sequencing.
int	getIndexOnProtein() Returns the starting index of the segment on the protein.
double	getMass() Returns the mass of the segment.
HashMap<Integer,String>	getModificationMatches() Returns a map of modifications on that segment: index on the segment - modification name.
Character	getMutation() Returns the mutated amino acid, null if none.
Integer	getMutationIndex() Returns the mutation index, null if none.
HashMap<Integer,Character>	getMutations() Returns a map of mutations on that segment: index on the segment - mutated character.
int	getnMutations() Returns the number of mutations.
String	getSegmentSequence(String sequence) Returns the sequence of this segment.
int	getTerminalIndex() Returns the index of the terminal on the protein sequence.
int	length() Returns the length of the segment.

Methods inherited from class java.lang.Object

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

Field Detail

nTerminus

public final boolean nTerminus

Boolean indicating whether the segment is sequencing from the N (true) or the C (false) terminus.

Constructor Detail

SequenceSegment

public SequenceSegment(int terminalIndex,
                       boolean nTerminus)

Constructor.

Parameters:

terminalIndex - the index of the segment on the protein

nTerminus - indicates whether the segment is indexed to the N (true) or C (false) terminus

SequenceSegment

public SequenceSegment(SequenceSegment sequenceSegment)

Constructor.

Parameters:

sequenceSegment - another sequence segment

Method Detail

length

public int length()

Returns the length of the segment.

Returns:

the length of the segment

getMutations

public HashMap<Integer,Character> getMutations()

Returns a map of mutations on that segment: index on the segment - mutated character.

Returns:

a map of mutations on that segment

getModificationMatches

public HashMap<Integer,String> getModificationMatches()

Returns a map of modifications on that segment: index on the segment - modification name.

Returns:

a map of modifications on that segment

getTerminalIndex

public int getTerminalIndex()

Returns the index of the terminal on the protein sequence.

Returns:

the index of the terminal on the protein sequence

getIndexOnProtein

public int getIndexOnProtein()

Returns the starting index of the segment on the protein.

Returns:

the starting index of the segment on the protein

getMutationIndex

public Integer getMutationIndex()

Returns the mutation index, null if none.

Returns:

the mutation index

getMutation

public Character getMutation()

Returns the mutated amino acid, null if none.

Returns:

the amino acid at the terminus if mutated

getMass

public double getMass()

Returns the mass of the segment.

Returns:

the mass of the segment

addMass

public void addMass(double mass)

Adds a mass to the segment.

Parameters:

mass - the mass to add

appendTerminus

public void appendTerminus(SequenceSegment sequenceSegment)

Appends a sequence segment to the terminus of sequencing.

Parameters:

sequenceSegment - a sequence segment

appendTerminus

public void appendTerminus(AminoAcidSequence aminoAcidSequence)

Appends an amino acid sequence to the terminus of sequencing.

Parameters:

aminoAcidSequence - an amino acid sequence

appendTerminus

public void appendTerminus(AminoAcidPattern aminoAcidPattern)

Appends an amino acid pattern to the terminus of sequencing.

Parameters:

aminoAcidPattern - an amino acid pattern

appendTerminus

public void appendTerminus(AminoAcid aminoAcid)

Appends an amino acid to the terminus of sequencing.

Parameters:

aminoAcid - an amino acid

addModificationTerminus

public void addModificationTerminus(String modification)

Adds a modification to the terminus of sequencing.

Parameters:

modification - the modification

addModificationTerminus

public void addModificationTerminus(String modification,
                                    double modificationMass)

Adds a modification to the terminus of sequencing.

Parameters:

modification - the name of the modification

modificationMass - the mass of the modification

addMutation

public void addMutation(Integer index,
                        Character aa)

Adds a mutation to the segment.

Parameters:

index - the index of the mutated amino acid

aa - the mutated amino acid

getnMutations

public int getnMutations()

Returns the number of mutations.

Returns:

the number of mutations

getSegmentSequence

public String getSegmentSequence(String sequence)

Returns the sequence of this segment.

Parameters:

sequence - the protein sequence

Returns:

the sequence of this segment