MolecularSequence

All Known Implementing Classes:: BasicSequence

public interface MolecularSequence

Nested Class Summary

Nested Classes

Modifier and Type

Interface

Description

static enum

MolecularSequence.TYPE
Field Summary

Fields

Modifier and Type

Field

Description

static final String

AA_REGEXP

static final String

DNA_REGEXP

static final char

GAP

static final String

GAP_STR

static final String

RNA_REGEXP

static final char

TERMINATE

static final char

UNSPECIFIED_AA

static final char

UNSPECIFIED_NUC
Method Summary

Modifier and Type

Method

Description

String

getIdentifier()

int

getLength()

char[]

getMolecularSequence()

String

getMolecularSequenceAsString()

int

getNumberOfGapResidues()

char

getResidueAt(int position)

MolecularSequence.TYPE

getType()

boolean

isGapAt(int position)

Field Details
- 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 Details
- 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()