Package org.forester.msa
Class BasicMsa
- java.lang.Object
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- org.forester.msa.BasicMsa
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- All Implemented Interfaces:
Msa
- Direct Known Subclasses:
DeleteableMsa
,ResampleableMsa
public class BasicMsa extends java.lang.Object implements Msa
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.forester.msa.Msa
Msa.MSA_FORMAT
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Constructor Summary
Constructors Constructor Description BasicMsa(int rows, int columns, MolecularSequence.TYPE type)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.List<MolecularSequence>
asSequenceList()
static Msa
createInstance(java.util.List<MolecularSequence> seqs)
java.util.List<java.lang.Character>
getColumnAt(int col)
java.lang.String
getIdentifier(int row)
int
getLength()
int
getNumberOfSequences()
char
getResidueAt(int row, int col)
MolecularSequence
getSequence(int row)
MolecularSequence
getSequence(java.lang.String id)
java.lang.StringBuffer
getSequenceAsString(int row)
MolecularSequence.TYPE
getType()
boolean
isGapAt(int row, int col)
void
setIdentifier(int row, java.lang.String id)
void
setResidueAt(int row, int col, char residue)
java.lang.String
toString()
void
write(java.io.Writer w, Msa.MSA_FORMAT format)
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Constructor Detail
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BasicMsa
public BasicMsa(int rows, int columns, MolecularSequence.TYPE type)
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Method Detail
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asSequenceList
public java.util.List<MolecularSequence> asSequenceList()
- Specified by:
asSequenceList
in interfaceMsa
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getColumnAt
public java.util.List<java.lang.Character> getColumnAt(int col)
- Specified by:
getColumnAt
in interfaceMsa
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getIdentifier
public java.lang.String getIdentifier(int row)
- Specified by:
getIdentifier
in interfaceMsa
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getNumberOfSequences
public int getNumberOfSequences()
- Specified by:
getNumberOfSequences
in interfaceMsa
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getResidueAt
public char getResidueAt(int row, int col)
- Specified by:
getResidueAt
in interfaceMsa
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getSequence
public MolecularSequence getSequence(int row)
- Specified by:
getSequence
in interfaceMsa
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getSequence
public MolecularSequence getSequence(java.lang.String id)
- Specified by:
getSequence
in interfaceMsa
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getSequenceAsString
public java.lang.StringBuffer getSequenceAsString(int row)
- Specified by:
getSequenceAsString
in interfaceMsa
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getType
public MolecularSequence.TYPE getType()
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setIdentifier
public void setIdentifier(int row, java.lang.String id)
- Specified by:
setIdentifier
in interfaceMsa
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setResidueAt
public void setResidueAt(int row, int col, char residue)
- Specified by:
setResidueAt
in interfaceMsa
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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write
public void write(java.io.Writer w, Msa.MSA_FORMAT format) throws java.io.IOException
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createInstance
public static Msa createInstance(java.util.List<MolecularSequence> seqs)
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