Msa

All Known Implementing Classes:: BasicMsa, DeleteableMsa, ResampleableMsa

public interface Msa

Nested Class Summary

Nested Classes

Modifier and Type

Interface

Description

static enum

Msa.MSA_FORMAT
Method Summary

Modifier and Type

Method

Description

List<MolecularSequence>

asSequenceList()

List<Character>

getColumnAt(int col)

String

getIdentifier(int row)

int

getLength()

int

getNumberOfSequences()

char

getResidueAt(int row, int col)

MolecularSequence

getSequence(int row)

MolecularSequence

getSequence(String id)

StringBuffer

getSequenceAsString(int row)

MolecularSequence.TYPE

getType()

boolean

isGapAt(int row, int col)

void

setIdentifier(int row, String identifier)

void

setResidueAt(int row, int col, char residue)

void

write(Writer w, Msa.MSA_FORMAT format)

Method Details
- getIdentifier
  
  String getIdentifier(int row)
- setIdentifier
  
  void setIdentifier(int row, String identifier)
- getLength
  
  int getLength()
- getNumberOfSequences
  
  int getNumberOfSequences()
- getResidueAt
  
  char getResidueAt(int row, int col)
- isGapAt
  
  boolean isGapAt(int row, int col)
- getColumnAt
  
  List<Character> getColumnAt(int col)
- getSequence
  
  MolecularSequence getSequence(String id)
- getSequence
  
  MolecularSequence getSequence(int row)
- asSequenceList
  
  List<MolecularSequence> asSequenceList()
- getSequenceAsString
  
  StringBuffer getSequenceAsString(int row)
- getType
  
  MolecularSequence.TYPE getType()
- setResidueAt
  
  void setResidueAt(int row, int col, char residue)
- write
  
  void write(Writer w, Msa.MSA_FORMAT format) throws IOException
  
  Throws:
  
  IOException