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

Constructor Summary

AbstractCompoundSet()

Method Summary

protected void	addCompound(C compound)
protected void	addCompound(C compound, C lowerCasedCompound, C... equivalents)
protected void	addCompound(C compound, C lowerCasedCompound, Iterable<C> equivalents)
protected void	addEquivalent(C compound, C equivalent)
boolean	compoundsEqual(C compoundOne, C compoundTwo)
boolean	compoundsEquivalent(C compoundOne, C compoundTwo)
List<C>	getAllCompounds()
C	getCompoundForString(String string) Return null if not recognised.
Set<C>	getEquivalentCompounds(C compound)
int	getMaxSingleCompoundStringLength() Returns the maximum size of a compound String this set holds
String	getStringForCompound(C compound)
boolean	hasCompound(C compound)
boolean	isComplementable()
boolean	isCompoundStringLengthEqual() Returns true if all String representations of Compounds are of the same length.
void	verifySequence(Sequence<C> sequence)

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractCompoundSet

public AbstractCompoundSet()

Method Detail

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>