org.biojava3.aaproperties.xml
Class ModifiedAminoAcidCompoundSet

java.lang.Object
  org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet

All Implemented Interfaces:

CompoundSet<AminoAcidCompound>

public class ModifiedAminoAcidCompoundSet
extends java.lang.Object
implements CompoundSet<AminoAcidCompound>

Constructor Summary

ModifiedAminoAcidCompoundSet(java.util.List<AminoAcidComposition> aaList, java.util.Map<java.lang.Character,java.lang.Double> aaSymbol2MolecularWeight)

Method Summary

boolean	compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)
java.util.List<AminoAcidCompound>	getAllCompounds()
AminoAcidCompound	getCompoundForString(java.lang.String string) Return null if not recognised.
java.util.Set<AminoAcidCompound>	getEquivalentCompounds(AminoAcidCompound compound)
int	getMaxSingleCompoundStringLength() Returns the maximum size of a compound String this set holds
java.lang.String	getStringForCompound(AminoAcidCompound compound)
boolean	hasCompound(AminoAcidCompound compound)
boolean	isComplementable()
boolean	isCompoundStringLengthEqual() Returns true if all String representations of Compounds are of the same length.
void	verifySequence(Sequence<AminoAcidCompound> sequence)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ModifiedAminoAcidCompoundSet

public ModifiedAminoAcidCompoundSet(java.util.List<AminoAcidComposition> aaList,
                                    java.util.Map<java.lang.Character,java.lang.Double> aaSymbol2MolecularWeight)

Method Detail

getMaxSingleCompoundStringLength

public int getMaxSingleCompoundStringLength()

Description copied from interface: CompoundSet

Returns the maximum size of a compound String this set holds

Specified by:

getMaxSingleCompoundStringLength in interface CompoundSet<AminoAcidCompound>

isCompoundStringLengthEqual

public boolean isCompoundStringLengthEqual()

Description copied from interface: CompoundSet

Returns true if all String representations of Compounds are of the same length.

Specified by:

isCompoundStringLengthEqual in interface CompoundSet<AminoAcidCompound>

getCompoundForString

public AminoAcidCompound getCompoundForString(java.lang.String string)

Description copied from interface: CompoundSet

Return null if not recognised. Throw IllegalArgumentException if string is longer than maximum allowed by CompoundSet.getStringForCompound(Compound).

Specified by:

getCompoundForString in interface CompoundSet<AminoAcidCompound>

getStringForCompound

public java.lang.String getStringForCompound(AminoAcidCompound compound)

Specified by:

getStringForCompound in interface CompoundSet<AminoAcidCompound>

compoundsEquivalent

public boolean compoundsEquivalent(AminoAcidCompound compoundOne,
                                   AminoAcidCompound compoundTwo)

Specified by:

compoundsEquivalent in interface CompoundSet<AminoAcidCompound>

verifySequence

public void verifySequence(Sequence<AminoAcidCompound> sequence)
                    throws CompoundNotFoundError

Specified by:

verifySequence in interface CompoundSet<AminoAcidCompound>

Throws:

CompoundNotFoundError

getEquivalentCompounds

public java.util.Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)

Specified by:

getEquivalentCompounds in interface CompoundSet<AminoAcidCompound>

hasCompound

public boolean hasCompound(AminoAcidCompound compound)

Specified by:

hasCompound in interface CompoundSet<AminoAcidCompound>

getAllCompounds

public java.util.List<AminoAcidCompound> getAllCompounds()

Specified by:

getAllCompounds in interface CompoundSet<AminoAcidCompound>

isComplementable

public boolean isComplementable()

Specified by:

isComplementable in interface CompoundSet<AminoAcidCompound>