org.biojava3.core.sequence.compound
Class AminoAcidCompoundSet

java.lang.Object
  extended by org.biojava3.core.sequence.compound.AminoAcidCompoundSet
All Implemented Interfaces:
CompoundSet<AminoAcidCompound>

public class AminoAcidCompoundSet
extends Object
implements CompoundSet<AminoAcidCompound>

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

Constructor Summary
AminoAcidCompoundSet()
           
 
Method Summary
 boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)
           
 List<AminoAcidCompound> getAllCompounds()
           
static AminoAcidCompoundSet getAminoAcidCompoundSet()
           
 AminoAcidCompound getCompoundForString(String string)
          Return null if not recognised.
 Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound)
           
 int getMaxSingleCompoundStringLength()
          Returns the maximum size of a compound String this set holds
 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

AminoAcidCompoundSet

public AminoAcidCompoundSet()
Method Detail

getStringForCompound

public String getStringForCompound(AminoAcidCompound compound)
Specified by:
getStringForCompound in interface CompoundSet<AminoAcidCompound>

getCompoundForString

public AminoAcidCompound getCompoundForString(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>

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>

getAminoAcidCompoundSet

public static AminoAcidCompoundSet getAminoAcidCompoundSet()

compoundsEquivalent

public boolean compoundsEquivalent(AminoAcidCompound compoundOne,
                                   AminoAcidCompound compoundTwo)
Specified by:
compoundsEquivalent in interface CompoundSet<AminoAcidCompound>

getEquivalentCompounds

public 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>

verifySequence

public void verifySequence(Sequence<AminoAcidCompound> sequence)
                    throws CompoundNotFoundError
Specified by:
verifySequence in interface CompoundSet<AminoAcidCompound>
Throws:
CompoundNotFoundError

getAllCompounds

public List<AminoAcidCompound> getAllCompounds()
Specified by:
getAllCompounds in interface CompoundSet<AminoAcidCompound>

isComplementable

public boolean isComplementable()
Specified by:
isComplementable in interface CompoundSet<AminoAcidCompound>