org.biojava3.core.sequence.template
Class AbstractCompoundSet<C extends Compound>
java.lang.Object
org.biojava3.core.sequence.template.AbstractCompoundSet<C>
- Type Parameters:
C
- The compound this set will contain
- All Implemented Interfaces:
- CompoundSet<C>
- Direct Known Subclasses:
- AbstractNucleotideCompoundSet
public abstract class AbstractCompoundSet<C extends Compound>
- extends Object
- implements CompoundSet<C>
- Author:
- Andy Yates
AbstractCompoundSet
public AbstractCompoundSet()
addCompound
protected void addCompound(C compound,
C lowerCasedCompound,
Iterable<C> equivalents)
addCompound
protected void addCompound(C compound,
C lowerCasedCompound,
C... equivalents)
addEquivalent
protected void addEquivalent(C compound,
C equivalent)
addCompound
protected void addCompound(C compound)
getStringForCompound
public String getStringForCompound(C compound)
- Specified by:
getStringForCompound
in interface CompoundSet<C extends Compound>
getCompoundForString
public C 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<C extends Compound>
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<C extends Compound>
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<C extends Compound>
hasCompound
public boolean hasCompound(C compound)
- Specified by:
hasCompound
in interface CompoundSet<C extends Compound>
compoundsEquivalent
public boolean compoundsEquivalent(C compoundOne,
C compoundTwo)
- Specified by:
compoundsEquivalent
in interface CompoundSet<C extends Compound>
getEquivalentCompounds
public Set<C> getEquivalentCompounds(C compound)
- Specified by:
getEquivalentCompounds
in interface CompoundSet<C extends Compound>
compoundsEqual
public boolean compoundsEqual(C compoundOne,
C compoundTwo)
verifySequence
public void verifySequence(Sequence<C> sequence)
throws CompoundNotFoundError
- Specified by:
verifySequence
in interface CompoundSet<C extends Compound>
- Throws:
CompoundNotFoundError
getAllCompounds
public List<C> getAllCompounds()
- Specified by:
getAllCompounds
in interface CompoundSet<C extends Compound>
isComplementable
public boolean isComplementable()
- Specified by:
isComplementable
in interface CompoundSet<C extends Compound>
hashCode
public int hashCode()
- Overrides:
hashCode
in class Object
equals
public boolean equals(Object o)
- Overrides:
equals
in class Object