org.biojava3.aaproperties.xml
Class ModifiedAminoAcidCompoundSet

java.lang.Object
  extended by org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet
All Implemented Interfaces:
CompoundSet<AminoAcidCompound>

public class ModifiedAminoAcidCompoundSet
extends Object
implements CompoundSet<AminoAcidCompound>


Constructor Summary
ModifiedAminoAcidCompoundSet(List<AminoAcidComposition> aaList, Map<Character,Double> aaSymbol2MolecularWeight)
           
 
Method Summary
 boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo)
           
 List<AminoAcidCompound> getAllCompounds()
           
 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

ModifiedAminoAcidCompoundSet

public ModifiedAminoAcidCompoundSet(List<AminoAcidComposition> aaList,
                                    Map<Character,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(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 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 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 List<AminoAcidCompound> getAllCompounds()
Specified by:
getAllCompounds in interface CompoundSet<AminoAcidCompound>

isComplementable

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