org.forester.sequence

Class BasicSequence

java.lang.Object

org.forester.sequence.BasicSequence

All Implemented Interfaces:

MolecularSequence

public class BasicSequence
extends Object
implements MolecularSequence

Nested Class Summary

Nested classes/interfaces inherited from interface org.forester.sequence.MolecularSequence

MolecularSequence.TYPE

Field Summary

Fields inherited from interface org.forester.sequence.MolecularSequence

AA_REGEXP, DNA_REGEXP, GAP, GAP_STR, RNA_REGEXP, TERMINATE, UNSPECIFIED_AA, UNSPECIFIED_NUC

Constructor Summary

Constructors

Constructor and Description
BasicSequence(String identifier, char[] mol_sequence, MolecularSequence.TYPE type) Only use if you know what you are doing!
BasicSequence(String identifier, String mol_sequence, MolecularSequence.TYPE type) Only use if you know what you are doing!

Method Summary

Modifier and Type	Method and Description
static MolecularSequence	copySequence(MolecularSequence seq)
static MolecularSequence	createAaSequence(String identifier, String mol_sequence)
static MolecularSequence	createDnaSequence(String identifier, String mol_sequence)
static MolecularSequence	createRnaSequence(String identifier, String mol_sequence)
boolean	equals(Object obj)
String	getIdentifier()
int	getLength()
char[]	getMolecularSequence()
String	getMolecularSequenceAsString()
int	getNumberOfGapResidues()
char	getResidueAt(int position)
MolecularSequence.TYPE	getType()
int	hashCode()
boolean	isGapAt(int position)
void	setIdentifier(String id)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

BasicSequence

public BasicSequence(String identifier,
                     String mol_sequence,
                     MolecularSequence.TYPE type)

Only use if you know what you are doing!

BasicSequence

public BasicSequence(String identifier,
                     char[] mol_sequence,
                     MolecularSequence.TYPE type)

Only use if you know what you are doing!

Method Detail

setIdentifier

public void setIdentifier(String id)

getIdentifier

public String getIdentifier()

Specified by:

getIdentifier in interface MolecularSequence

getLength

public int getLength()

Specified by:

getLength in interface MolecularSequence

getMolecularSequence

public char[] getMolecularSequence()

Specified by:

getMolecularSequence in interface MolecularSequence

getResidueAt

public char getResidueAt(int position)

Specified by:

getResidueAt in interface MolecularSequence

getType

public MolecularSequence.TYPE getType()

Specified by:

getType in interface MolecularSequence

getNumberOfGapResidues

public int getNumberOfGapResidues()

Specified by:

getNumberOfGapResidues in interface MolecularSequence

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

copySequence

public static MolecularSequence copySequence(MolecularSequence seq)

createAaSequence

public static MolecularSequence createAaSequence(String identifier,
                                                 String mol_sequence)

createDnaSequence

public static MolecularSequence createDnaSequence(String identifier,
                                                  String mol_sequence)

createRnaSequence

public static MolecularSequence createRnaSequence(String identifier,
                                                  String mol_sequence)

getMolecularSequenceAsString

public String getMolecularSequenceAsString()

Specified by:

getMolecularSequenceAsString in interface MolecularSequence

isGapAt

public boolean isGapAt(int position)

Specified by:

isGapAt in interface MolecularSequence