Class ModifiedAminoAcidCompoundSet
- java.lang.Object
-
- org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- All Implemented Interfaces:
CompoundSet<AminoAcidCompound>
public class ModifiedAminoAcidCompoundSet extends java.lang.Object implements CompoundSet<AminoAcidCompound>
-
-
Constructor Summary
Constructors Constructor Description ModifiedAminoAcidCompoundSet(java.util.List<AminoAcidComposition> aaList, java.util.Map<java.lang.Character,java.lang.Double> aaSymbol2MolecularWeight)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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 holdsjava.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.boolean
isValidSequence(Sequence<AminoAcidCompound> sequence)
-
-
-
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 interfaceCompoundSet<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 interfaceCompoundSet<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 byCompoundSet.getStringForCompound(Compound)
.- Specified by:
getCompoundForString
in interfaceCompoundSet<AminoAcidCompound>
-
getStringForCompound
public java.lang.String getStringForCompound(AminoAcidCompound compound)
- Specified by:
getStringForCompound
in interfaceCompoundSet<AminoAcidCompound>
-
compoundsEquivalent
public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)
- Specified by:
compoundsEquivalent
in interfaceCompoundSet<AminoAcidCompound>
-
getEquivalentCompounds
public java.util.Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
- Specified by:
getEquivalentCompounds
in interfaceCompoundSet<AminoAcidCompound>
-
hasCompound
public boolean hasCompound(AminoAcidCompound compound)
- Specified by:
hasCompound
in interfaceCompoundSet<AminoAcidCompound>
-
getAllCompounds
public java.util.List<AminoAcidCompound> getAllCompounds()
- Specified by:
getAllCompounds
in interfaceCompoundSet<AminoAcidCompound>
-
isComplementable
public boolean isComplementable()
- Specified by:
isComplementable
in interfaceCompoundSet<AminoAcidCompound>
-
isValidSequence
public boolean isValidSequence(Sequence<AminoAcidCompound> sequence)
- Specified by:
isValidSequence
in interfaceCompoundSet<AminoAcidCompound>
-
-