Package org.forester.sequence
Interface MolecularSequence
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- All Known Implementing Classes:
BasicSequence
public interface MolecularSequence
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
MolecularSequence.TYPE
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
AA_REGEXP
static java.lang.String
DNA_REGEXP
static char
GAP
static java.lang.String
GAP_STR
static java.lang.String
RNA_REGEXP
static char
TERMINATE
static char
UNSPECIFIED_AA
static char
UNSPECIFIED_NUC
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.String
getIdentifier()
int
getLength()
char[]
getMolecularSequence()
java.lang.String
getMolecularSequenceAsString()
int
getNumberOfGapResidues()
char
getResidueAt(int position)
MolecularSequence.TYPE
getType()
boolean
isGapAt(int position)
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Field Detail
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UNSPECIFIED_AA
static final char UNSPECIFIED_AA
- See Also:
- Constant Field Values
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UNSPECIFIED_NUC
static final char UNSPECIFIED_NUC
- See Also:
- Constant Field Values
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GAP
static final char GAP
- See Also:
- Constant Field Values
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GAP_STR
static final java.lang.String GAP_STR
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TERMINATE
static final char TERMINATE
- See Also:
- Constant Field Values
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AA_REGEXP
static final java.lang.String AA_REGEXP
- See Also:
- Constant Field Values
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DNA_REGEXP
static final java.lang.String DNA_REGEXP
- See Also:
- Constant Field Values
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RNA_REGEXP
static final java.lang.String RNA_REGEXP
- See Also:
- Constant Field Values
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Method Detail
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getIdentifier
java.lang.String getIdentifier()
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getLength
int getLength()
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getNumberOfGapResidues
int getNumberOfGapResidues()
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getMolecularSequence
char[] getMolecularSequence()
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getMolecularSequenceAsString
java.lang.String getMolecularSequenceAsString()
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getResidueAt
char getResidueAt(int position)
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isGapAt
boolean isGapAt(int position)
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getType
MolecularSequence.TYPE getType()
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