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

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

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 Details
- 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 Details
- 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

Class BasicSequence

Nested Class Summary

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

Field Summary

Fields inherited from interface org.forester.sequence.MolecularSequence

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

BasicSequence

BasicSequence

Method Details

setIdentifier

getIdentifier

getLength

getMolecularSequence

getResidueAt

getType

getNumberOfGapResidues

equals

hashCode

toString

copySequence

createAaSequence

createDnaSequence

createRnaSequence

getMolecularSequenceAsString

isGapAt