org.forester.sequence
Class BasicSequence

java.lang.Object
  org.forester.sequence.BasicSequence

All Implemented Interfaces:

Sequence

public class BasicSequence
extends java.lang.Object
implements Sequence

Nested Class Summary

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

Sequence.TYPE

Field Summary

Fields inherited from interface org.forester.sequence.Sequence

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

Constructor Summary

BasicSequence(java.lang.Object identifier, char[] mol_sequence, Sequence.TYPE type)

Method Summary

static Sequence	createAaSequence(java.lang.Object identifier, java.lang.String mol_sequence)
static Sequence	createDnaSequence(java.lang.Object identifier, java.lang.String mol_sequence)
static Sequence	createRnaSequence(java.lang.Object identifier, java.lang.String mol_sequence)
java.lang.Object	getIdentifier()
int	getLength()
char[]	getMolecularSequence()
int	getNumberOfGapResidues()
char	getResidueAt(int position)
Sequence.TYPE	getType()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicSequence

public BasicSequence(java.lang.Object identifier,
                     char[] mol_sequence,
                     Sequence.TYPE type)

Method Detail

getIdentifier

public java.lang.Object getIdentifier()

Specified by:

getIdentifier in interface Sequence

getLength

public int getLength()

Specified by:

getLength in interface Sequence

getMolecularSequence

public char[] getMolecularSequence()

Specified by:

getMolecularSequence in interface Sequence

getResidueAt

public char getResidueAt(int position)

Specified by:

getResidueAt in interface Sequence

getType

public Sequence.TYPE getType()

Specified by:

getType in interface Sequence

getNumberOfGapResidues

public int getNumberOfGapResidues()

Specified by:

getNumberOfGapResidues in interface Sequence

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

createAaSequence

public static Sequence createAaSequence(java.lang.Object identifier,
                                        java.lang.String mol_sequence)

createDnaSequence

public static Sequence createDnaSequence(java.lang.Object identifier,
                                         java.lang.String mol_sequence)

createRnaSequence

public static Sequence createRnaSequence(java.lang.Object identifier,
                                         java.lang.String mol_sequence)