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java.lang.Objectorg.biojava3.core.sequence.compound.AminoAcidCompoundSet
public class AminoAcidCompoundSet
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
Constructor Summary | |
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AminoAcidCompoundSet()
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Method Summary | |
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boolean |
compoundsEquivalent(AminoAcidCompound compoundOne,
AminoAcidCompound compoundTwo)
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List<AminoAcidCompound> |
getAllCompounds()
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static AminoAcidCompoundSet |
getAminoAcidCompoundSet()
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AminoAcidCompound |
getCompoundForString(String string)
Return null if not recognised. |
Set<AminoAcidCompound> |
getEquivalentCompounds(AminoAcidCompound compound)
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int |
getMaxSingleCompoundStringLength()
Returns the maximum size of a compound String this set holds |
String |
getStringForCompound(AminoAcidCompound compound)
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boolean |
hasCompound(AminoAcidCompound compound)
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boolean |
isComplementable()
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boolean |
isCompoundStringLengthEqual()
Returns true if all String representations of Compounds are of the same length. |
void |
verifySequence(Sequence<AminoAcidCompound> sequence)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public AminoAcidCompoundSet()
Method Detail |
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public String getStringForCompound(AminoAcidCompound compound)
getStringForCompound
in interface CompoundSet<AminoAcidCompound>
public AminoAcidCompound getCompoundForString(String string)
CompoundSet
CompoundSet.getStringForCompound(Compound)
.
getCompoundForString
in interface CompoundSet<AminoAcidCompound>
public int getMaxSingleCompoundStringLength()
CompoundSet
getMaxSingleCompoundStringLength
in interface CompoundSet<AminoAcidCompound>
public boolean isCompoundStringLengthEqual()
CompoundSet
isCompoundStringLengthEqual
in interface CompoundSet<AminoAcidCompound>
public static AminoAcidCompoundSet getAminoAcidCompoundSet()
public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)
compoundsEquivalent
in interface CompoundSet<AminoAcidCompound>
public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
getEquivalentCompounds
in interface CompoundSet<AminoAcidCompound>
public boolean hasCompound(AminoAcidCompound compound)
hasCompound
in interface CompoundSet<AminoAcidCompound>
public void verifySequence(Sequence<AminoAcidCompound> sequence) throws CompoundNotFoundError
verifySequence
in interface CompoundSet<AminoAcidCompound>
CompoundNotFoundError
public List<AminoAcidCompound> getAllCompounds()
getAllCompounds
in interface CompoundSet<AminoAcidCompound>
public boolean isComplementable()
isComplementable
in interface CompoundSet<AminoAcidCompound>
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