Package org.forester.msa
Interface Msa
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- All Known Implementing Classes:
BasicMsa
,DeleteableMsa
,ResampleableMsa
public interface Msa
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
Msa.MSA_FORMAT
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.util.List<MolecularSequence>
asSequenceList()
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 identifier)
void
setResidueAt(int row, int col, char residue)
void
write(java.io.Writer w, Msa.MSA_FORMAT format)
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Method Detail
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getIdentifier
java.lang.String getIdentifier(int row)
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setIdentifier
void setIdentifier(int row, java.lang.String identifier)
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getLength
int getLength()
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getNumberOfSequences
int getNumberOfSequences()
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getResidueAt
char getResidueAt(int row, int col)
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isGapAt
boolean isGapAt(int row, int col)
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getColumnAt
java.util.List<java.lang.Character> getColumnAt(int col)
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getSequence
MolecularSequence getSequence(java.lang.String id)
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getSequence
MolecularSequence getSequence(int row)
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asSequenceList
java.util.List<MolecularSequence> asSequenceList()
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getSequenceAsString
java.lang.StringBuffer getSequenceAsString(int row)
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getType
MolecularSequence.TYPE getType()
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setResidueAt
void setResidueAt(int row, int col, char residue)
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write
void write(java.io.Writer w, Msa.MSA_FORMAT format) throws java.io.IOException
- Throws:
java.io.IOException
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