MolecularSequence
public class BasicSequence extends java.lang.Object implements MolecularSequence
MolecularSequence.TYPE
AA_REGEXP, DNA_REGEXP, GAP, GAP_STR, RNA_REGEXP, TERMINATE, UNSPECIFIED_AA, UNSPECIFIED_NUC
Constructor | Description |
---|---|
BasicSequence(java.lang.String identifier,
char[] mol_sequence,
MolecularSequence.TYPE type) |
Only use if you know what you are doing!
|
BasicSequence(java.lang.String identifier,
java.lang.String mol_sequence,
MolecularSequence.TYPE type) |
Only use if you know what you are doing!
|
Modifier and Type | Method | Description |
---|---|---|
static MolecularSequence |
copySequence(MolecularSequence seq) |
|
static MolecularSequence |
createAaSequence(java.lang.String identifier,
java.lang.String mol_sequence) |
|
static MolecularSequence |
createDnaSequence(java.lang.String identifier,
java.lang.String mol_sequence) |
|
static MolecularSequence |
createRnaSequence(java.lang.String identifier,
java.lang.String mol_sequence) |
|
boolean |
equals(java.lang.Object obj) |
|
java.lang.String |
getIdentifier() |
|
int |
getLength() |
|
char[] |
getMolecularSequence() |
|
java.lang.String |
getMolecularSequenceAsString() |
|
int |
getNumberOfGapResidues() |
|
char |
getResidueAt(int position) |
|
MolecularSequence.TYPE |
getType() |
|
int |
hashCode() |
|
boolean |
isGapAt(int position) |
|
void |
setIdentifier(java.lang.String id) |
|
java.lang.String |
toString() |
public BasicSequence(java.lang.String identifier, java.lang.String mol_sequence, MolecularSequence.TYPE type)
public BasicSequence(java.lang.String identifier, char[] mol_sequence, MolecularSequence.TYPE type)
public void setIdentifier(java.lang.String id)
public java.lang.String getIdentifier()
getIdentifier
in interface MolecularSequence
public int getLength()
getLength
in interface MolecularSequence
public char[] getMolecularSequence()
getMolecularSequence
in interface MolecularSequence
public char getResidueAt(int position)
getResidueAt
in interface MolecularSequence
public MolecularSequence.TYPE getType()
getType
in interface MolecularSequence
public int getNumberOfGapResidues()
getNumberOfGapResidues
in interface MolecularSequence
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
public java.lang.String toString()
toString
in class java.lang.Object
public static MolecularSequence copySequence(MolecularSequence seq)
public static MolecularSequence createAaSequence(java.lang.String identifier, java.lang.String mol_sequence)
public static MolecularSequence createDnaSequence(java.lang.String identifier, java.lang.String mol_sequence)
public static MolecularSequence createRnaSequence(java.lang.String identifier, java.lang.String mol_sequence)
public java.lang.String getMolecularSequenceAsString()
getMolecularSequenceAsString
in interface MolecularSequence
public boolean isGapAt(int position)
isGapAt
in interface MolecularSequence