org.forester.sequence

Interface MolecularSequence

All Known Implementing Classes:

BasicSequence

public interface MolecularSequence

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	MolecularSequence.TYPE

Field Summary

Fields

Modifier and Type	Field and Description
static String	AA_REGEXP
static String	DNA_REGEXP
static char	GAP
static String	GAP_STR
static String	RNA_REGEXP
static char	TERMINATE
static char	UNSPECIFIED_AA
static char	UNSPECIFIED_NUC

Method Summary

Modifier and Type	Method and Description
String	getIdentifier()
int	getLength()
char[]	getMolecularSequence()
String	getMolecularSequenceAsString()
int	getNumberOfGapResidues()
char	getResidueAt(int position)
MolecularSequence.TYPE	getType()
boolean	isGapAt(int position)

Field Detail

UNSPECIFIED_AA

static final char UNSPECIFIED_AA

See Also:

Constant Field Values

UNSPECIFIED_NUC

static final char UNSPECIFIED_NUC

See Also:

Constant Field Values

GAP

static final char GAP

See Also:

Constant Field Values

GAP_STR

static final String GAP_STR

TERMINATE

static final char TERMINATE

See Also:

Constant Field Values

AA_REGEXP

static final String AA_REGEXP

See Also:

Constant Field Values

DNA_REGEXP

static final String DNA_REGEXP

See Also:

Constant Field Values

RNA_REGEXP

static final String RNA_REGEXP

See Also:

Constant Field Values

Method Detail

getIdentifier

String getIdentifier()

getLength

int getLength()

getNumberOfGapResidues

int getNumberOfGapResidues()

getMolecularSequence

char[] getMolecularSequence()

getMolecularSequenceAsString

String getMolecularSequenceAsString()

getResidueAt

char getResidueAt(int position)

isGapAt

boolean isGapAt(int position)

getType

MolecularSequence.TYPE getType()