Class AminoAcidCompoundSet
java.lang.Object
org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
- All Implemented Interfaces:
Serializable,CompoundSet<AminoAcidCompound>
public class AminoAcidCompoundSet
extends Object
implements CompoundSet<AminoAcidCompound>, Serializable
Set of proteinogenic amino acids. Molecular weights are recorded in daltons (Da) as residues of a chain; monomers
outside of a chain would likely have an additional mass of 18.01524 Da contributed by an associated water molecule.
Currently we have different symbols to handle inserts so not as clean as it should be
- Author:
- Richard Holland, Scooter Willis, Mark Chapman
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionbooleancompoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo) static AminoAcidCompoundSetgetCompoundForString(String string) Return null if not recognised.getEquivalentCompounds(AminoAcidCompound compound) intReturns the maximum size of a compound String this set holdsgetStringForCompound(AminoAcidCompound compound) booleanhasCompound(AminoAcidCompound compound) booleanbooleanReturns true if all String representations of Compounds are of the same length.booleanisValidSequence(Sequence<AminoAcidCompound> sequence)
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Constructor Details
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AminoAcidCompoundSet
public AminoAcidCompoundSet()
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Method Details
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getStringForCompound
- Specified by:
getStringForCompoundin interfaceCompoundSet<AminoAcidCompound>
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getCompoundForString
Description copied from interface:CompoundSetReturn null if not recognised. Throw IllegalArgumentException if string is longer than maximum allowed byCompoundSet.getStringForCompound(Compound).- Specified by:
getCompoundForStringin interfaceCompoundSet<AminoAcidCompound>
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getMaxSingleCompoundStringLength
public int getMaxSingleCompoundStringLength()Description copied from interface:CompoundSetReturns the maximum size of a compound String this set holds- Specified by:
getMaxSingleCompoundStringLengthin interfaceCompoundSet<AminoAcidCompound>
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isCompoundStringLengthEqual
public boolean isCompoundStringLengthEqual()Description copied from interface:CompoundSetReturns true if all String representations of Compounds are of the same length.- Specified by:
isCompoundStringLengthEqualin interfaceCompoundSet<AminoAcidCompound>
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getAminoAcidCompoundSet
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compoundsEquivalent
- Specified by:
compoundsEquivalentin interfaceCompoundSet<AminoAcidCompound>
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getEquivalentCompounds
- Specified by:
getEquivalentCompoundsin interfaceCompoundSet<AminoAcidCompound>
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hasCompound
- Specified by:
hasCompoundin interfaceCompoundSet<AminoAcidCompound>
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isValidSequence
- Specified by:
isValidSequencein interfaceCompoundSet<AminoAcidCompound>
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getAllCompounds
- Specified by:
getAllCompoundsin interfaceCompoundSet<AminoAcidCompound>
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isComplementable
public boolean isComplementable()- Specified by:
isComplementablein interfaceCompoundSet<AminoAcidCompound>
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