Package org.forester.sequence
Class BasicSequence
- java.lang.Object
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- org.forester.sequence.BasicSequence
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- All Implemented Interfaces:
MolecularSequence
public class BasicSequence extends java.lang.Object implements MolecularSequence
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.forester.sequence.MolecularSequence
MolecularSequence.TYPE
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Field Summary
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Fields inherited from interface org.forester.sequence.MolecularSequence
AA_REGEXP, DNA_REGEXP, GAP, GAP_STR, RNA_REGEXP, TERMINATE, UNSPECIFIED_AA, UNSPECIFIED_NUC
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Constructor Summary
Constructors 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!
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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()
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Constructor Detail
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BasicSequence
public BasicSequence(java.lang.String identifier, java.lang.String mol_sequence, MolecularSequence.TYPE type)
Only use if you know what you are doing!
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BasicSequence
public BasicSequence(java.lang.String identifier, char[] mol_sequence, MolecularSequence.TYPE type)
Only use if you know what you are doing!
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Method Detail
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setIdentifier
public void setIdentifier(java.lang.String id)
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getIdentifier
public java.lang.String getIdentifier()
- Specified by:
getIdentifier
in interfaceMolecularSequence
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getLength
public int getLength()
- Specified by:
getLength
in interfaceMolecularSequence
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getMolecularSequence
public char[] getMolecularSequence()
- Specified by:
getMolecularSequence
in interfaceMolecularSequence
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getResidueAt
public char getResidueAt(int position)
- Specified by:
getResidueAt
in interfaceMolecularSequence
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getType
public MolecularSequence.TYPE getType()
- Specified by:
getType
in interfaceMolecularSequence
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getNumberOfGapResidues
public int getNumberOfGapResidues()
- Specified by:
getNumberOfGapResidues
in interfaceMolecularSequence
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equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in classjava.lang.Object
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hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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copySequence
public static MolecularSequence copySequence(MolecularSequence seq)
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createAaSequence
public static MolecularSequence createAaSequence(java.lang.String identifier, java.lang.String mol_sequence)
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createDnaSequence
public static MolecularSequence createDnaSequence(java.lang.String identifier, java.lang.String mol_sequence)
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createRnaSequence
public static MolecularSequence createRnaSequence(java.lang.String identifier, java.lang.String mol_sequence)
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getMolecularSequenceAsString
public java.lang.String getMolecularSequenceAsString()
- Specified by:
getMolecularSequenceAsString
in interfaceMolecularSequence
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isGapAt
public boolean isGapAt(int position)
- Specified by:
isGapAt
in interfaceMolecularSequence
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