AbstractContinuousSet

java.lang.Object
- info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet<T>

Type Parameters:

T - the type of tokens represented by this set

All Implemented Interfaces:

TokenSet<ContinuousToken<T>>, java.lang.Cloneable, java.lang.Iterable<ContinuousToken<T>>, java.util.Collection<ContinuousToken<T>>, java.util.Set<ContinuousToken<T>>

Direct Known Subclasses:

DoubleTokenSet, FloatTokenSet
```
public abstract class AbstractContinuousSet<T extends java.lang.Number & java.lang.Comparable<T>>
extends java.lang.Object
implements TokenSet<ContinuousToken<T>>
```
Implements type independent functionality for continuous token sets.
This implementation does not support the optional add and remove operations. Because it represents non-discrete values the methods toArray(), toArray(Object[]) and iterator() cannot be implemented and return an empty array or iterator. size() always returns Integer.MAX_VALUE in accordance with the definition in Collection.size().

Since:

0.4.0

Author:

Ben Stöver

Constructor Summary

Constructors
Constructor and Description

AbstractContinuousSet()

Constructors
Constructor and Description
`AbstractContinuousSet()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`add(ContinuousToken<T> e)` This method is not supported by this implementation and will always throw an `UnsupportedOperationException`.
`boolean`	`addAll(java.util.Collection<? extends ContinuousToken<T>> c)` This method is not supported by this implementation and will always throw an `UnsupportedOperationException`.
`void`	`clear()` This method is not supported by this implementation and will always throw an `UnsupportedOperationException`.
`abstract AbstractContinuousSet<T>`	`clone()` Returns a deep copy of this instance.
`boolean`	`contains(java.lang.Object o)` This default implementation always returns `true`.
`boolean`	`containsAll(java.util.Collection<?> c)` This default implementation always returns `true`.
`java.lang.String`	`descriptionByToken(ContinuousToken<T> token)` An description of the specified token (e.g.
`ContinuousToken<T>`	`getGapToken()` Returns the default object that represents a gap in this token set.
`CharacterSymbolMeaning`	`getMeaning(ContinuousToken<T> token)` Returns the meaning of the specified symbol.
`ContinuousToken<T>`	`getMissingInformationToken()` Returns the default object that represents an unknown position in this token set.
`CharacterSymbolType`	`getSymbolType(ContinuousToken<T> token)` Returns the type of the specified token (symbol).
`CharacterStateSetType`	`getType()` Determines the type of tokens that are defined by this instance.
`boolean`	`isEmpty()` This default implementation always returns `false`.
`boolean`	`isGapToken(ContinuousToken<T> token)` Tests if the specified token represents a gap.
`boolean`	`isMissingInformationToken(ContinuousToken<T> token)` Tests if the specified token represents an unknown position (usually '?').
`boolean`	`isSpaceForGap()` Determines whether `TokenSet.tokenByKeyStroke(KeyStroke)` shall return the gap token, if the space bar is pressed, even if that key stroke is not associated with that token.
`java.util.Iterator<ContinuousToken<T>>`	`iterator()` Continuous sets cannot be iterated, therefore this method is not supported by this class.
`protected abstract ContinuousToken<T>`	`parseValue(java.lang.String value)`
`boolean`	`remove(java.lang.Object o)` This method is not supported by this implementation and will always throw an `UnsupportedOperationException`.
`boolean`	`removeAll(java.util.Collection<?> c)` This method is not supported by this implementation and will always throw an `UnsupportedOperationException`.
`java.lang.String`	`representationByToken(ContinuousToken<T> token)` Returns the representation string of the specified token that shall be displayed in an `AlignmentArea` or written into an alignment file.
`boolean`	`representationLengthEqual()` Checks if all representation strings returned by `TokenSet.representationByToken(Object)` have the same length.
`boolean`	`retainAll(java.util.Collection<?> c)` This method is not supported by this implementation and will always throw an `UnsupportedOperationException`.
`void`	`setSpaceForGap(boolean spaceForGap)` Allows to specify whether `TokenSet.tokenByKeyStroke(KeyStroke)` shall return the gap token, if the space bar is pressed, even if that key stroke is not associated with that token.
`int`	`size()` The number of elements in a continuous set is unlimited.
`java.lang.Object[]`	`toArray()` Continuous sets cannot be stored in arrays, therefore this method is not supported by this class.
`<E> E[]`	`toArray(E[] a)` Continuous sets cannot be stored in arrays, therefore this method is not supported by this class.
`ContinuousToken<T>`	`tokenByKeyStroke(javax.swing.KeyStroke key)` Returns the token from this set that is associated with the specified key stroke.
`ContinuousToken<T>`	`tokenByRepresentation(java.lang.String representation)` Returns the token associated with the specified string representation used to display the token in an `AlignmentArea` or an alignment file.

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface info.bioinfweb.libralign.model.tokenset.TokenSet
maxRepresentationLength

Methods inherited from interface java.util.Set
equals, hashCode, spliterator

Methods inherited from interface java.util.Collection
parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable
forEach

- Constructor Detail
  - AbstractContinuousSet
```
public AbstractContinuousSet()
```
- Method Detail
  - parseValue
```
protected abstract ContinuousToken<T> parseValue(java.lang.String value)
                                          throws java.lang.NumberFormatException
```
    Throws:
    
    java.lang.NumberFormatException
  - tokenByRepresentation
```
public ContinuousToken<T> tokenByRepresentation(java.lang.String representation)
```
    Description copied from interface: TokenSet
    
    Returns the token associated with the specified string representation used to display the token in an AlignmentArea or an alignment file.
    
    Specified by:
    
    tokenByRepresentation in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Parameters:
    
    representation - the string representation of the token
    
    Returns:
    
    the according token or null if none is defined
  - tokenByKeyStroke
```
public ContinuousToken<T> tokenByKeyStroke(javax.swing.KeyStroke key)
```
    Description copied from interface: TokenSet
    
    Returns the token from this set that is associated with the specified key stroke. This key can be pressed to insert the specified token into an AlignmentArea.
    Note that the key character is only used by AlignmentArea if it does not collide with a default keyboard action. (Usually the key character can be any lower or upper case letter or digit.)
    
    Specified by:
    
    tokenByKeyStroke in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Parameters:
    
    key - the key stroke (key code and shift mask) the user can press to insert the returned token into an AlignmentArea
    
    Returns:
    
    the associated token (sequence element) or null if none is defined
  - isGapToken
```
public boolean isGapToken(ContinuousToken<T> token)
```
    Description copied from interface: TokenSet
    
    Tests if the specified token represents a gap. This method is e.g. used by data areas to determine the positions of gaps.
    Note that it's legal to have multiple tokens to be considered as gaps, but one of them must be defined as the default gap tokens. When alignments are written to files (e.g. using JPhyloIO), some formats may accept only one of these tokens as a gap and the others may be represented as additional character states.
    
    Specified by:
    
    isGapToken in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Parameters:
    
    token - the token to be tested
    
    Returns:
    
    true if the specified token is recognized as a gap, false otherwise.
  - getGapToken
```
public ContinuousToken<T> getGapToken()
```
    Description copied from interface: TokenSet
    
    Returns the default object that represents a gap in this token set.
    
    Specified by:
    
    getGapToken in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    the according gap object (Implementations may create a new instance with every call of this method or always return the same instance. In general gap objects should not have any mutable object specific properties to avoid problems if the same instance if located at multiple positions in an alignment.)
  - isMissingInformationToken
```
public boolean isMissingInformationToken(ContinuousToken<T> token)
```
    Description copied from interface: TokenSet
    
    Tests if the specified token represents an unknown position (usually '?'). This method is e.g. used by data areas to determine the positions of gaps.
    Note that it's legal to have multiple tokens to be considered as unknown symbols, but one of them must be defined as the default. When alignments are written to files, some formats may accept only one
    
    Specified by:
    
    isMissingInformationToken in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Parameters:
    
    token - the token to be tested
    
    Returns:
    
    true if the specified token is recognized as an unknown position, false otherwise.
  - getMissingInformationToken
```
public ContinuousToken<T> getMissingInformationToken()
```
    Description copied from interface: TokenSet
    
    Returns the default object that represents an unknown position in this token set.
    
    Specified by:
    
    getMissingInformationToken in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    the according object (Implementations may create a new instance with every call of this method or always return the same instance. In general objects should not have any mutable object specific properties to avoid problems if the same instance if located at multiple positions in an alignment.)
  - getSymbolType
```
public CharacterSymbolType getSymbolType(ContinuousToken<T> token)
```
    Description copied from interface: TokenSet
    
    Returns the type of the specified token (symbol). Symbols can either represent an atomic token or a polymorphic state or a set of tokens, if the the position is uncertain.
    
    Specified by:
    
    getSymbolType in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Parameters:
    
    token - the symbol to be tested
    
    Returns:
    
    the type of the specified symbol
  - getMeaning
```
public CharacterSymbolMeaning getMeaning(ContinuousToken<T> token)
```
    Description copied from interface: TokenSet
    
    Returns the meaning of the specified symbol. (Note that LibrAlign models will usually not contain match tokens directly).
    
    Specified by:
    
    getMeaning in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Parameters:
    
    token - the token to determine the meaning from
    
    Returns:
    
    the meaning of the specified token
  - add
```
public boolean add(ContinuousToken<T> e)
```
    This method is not supported by this implementation and will always throw an UnsupportedOperationException.
    
    Specified by:
    
    add in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    add in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Throws:
    
    java.lang.UnsupportedOperationException - always
  - addAll
```
public boolean addAll(java.util.Collection<? extends ContinuousToken<T>> c)
```
    This method is not supported by this implementation and will always throw an UnsupportedOperationException.
    
    Specified by:
    
    addAll in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    addAll in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Throws:
    
    java.lang.UnsupportedOperationException - always
  - clear
```
public void clear()
```
    This method is not supported by this implementation and will always throw an UnsupportedOperationException.
    
    Specified by:
    
    clear in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    clear in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Throws:
    
    java.lang.UnsupportedOperationException - always
  - contains
```
public boolean contains(java.lang.Object o)
```
    This default implementation always returns true.
    
    Specified by:
    
    contains in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    contains in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    always true
  - containsAll
```
public boolean containsAll(java.util.Collection<?> c)
```
    This default implementation always returns true.
    
    Specified by:
    
    containsAll in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    containsAll in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    always true
  - isEmpty
```
public boolean isEmpty()
```
    This default implementation always returns false.
    
    Specified by:
    
    isEmpty in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    isEmpty in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    always false
  - iterator
```
public java.util.Iterator<ContinuousToken<T>> iterator()
```
    Continuous sets cannot be iterated, therefore this method is not supported by this class.
    
    Specified by:
    
    iterator in interface java.lang.Iterable<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    iterator in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    iterator in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    always an empty iterator
  - remove
```
public boolean remove(java.lang.Object o)
```
    This method is not supported by this implementation and will always throw an UnsupportedOperationException.
    
    Specified by:
    
    remove in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    remove in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Throws:
    
    java.lang.UnsupportedOperationException - always
  - removeAll
```
public boolean removeAll(java.util.Collection<?> c)
```
    This method is not supported by this implementation and will always throw an UnsupportedOperationException.
    
    Specified by:
    
    removeAll in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    removeAll in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Throws:
    
    java.lang.UnsupportedOperationException - always
  - retainAll
```
public boolean retainAll(java.util.Collection<?> c)
```
    This method is not supported by this implementation and will always throw an UnsupportedOperationException.
    
    Specified by:
    
    retainAll in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    retainAll in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Throws:
    
    java.lang.UnsupportedOperationException - always
  - size
```
public int size()
```
    The number of elements in a continuous set is unlimited.
    
    Specified by:
    
    size in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    size in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    always Integer.MAX_VALUE in accordance with the definition of Collection.size()
  - toArray
```
public java.lang.Object[] toArray()
```
    Continuous sets cannot be stored in arrays, therefore this method is not supported by this class.
    
    Specified by:
    
    toArray in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    toArray in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    always an empty array
  - toArray
```
public <E> E[] toArray(E[] a)
```
    Continuous sets cannot be stored in arrays, therefore this method is not supported by this class.
    
    Specified by:
    
    toArray in interface java.util.Collection<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Specified by:
    
    toArray in interface java.util.Set<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Parameters:
    
    a - the array into which the elements of this set would be stored, if it was not continuous
    
    Returns:
    
    a without any modifications
  - representationByToken
```
public java.lang.String representationByToken(ContinuousToken<T> token)
```
    Description copied from interface: TokenSet
    
    Returns the representation string of the specified token that shall be displayed in an AlignmentArea or written into an alignment file.
    Note that some CharSequenceAdapters and StringAdapters only use the first character of the returned string to represent a token.
    
    Specified by:
    
    representationByToken in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Parameters:
    
    token - the token associated with the representation
    
    Returns:
    
    a string which is at least one character long an empty string if no token in this set has the specified representation
  - representationLengthEqual
```
public boolean representationLengthEqual()
```
    Description copied from interface: TokenSet
    
    Checks if all representation strings returned by TokenSet.representationByToken(Object) have the same length.
    
    Specified by:
    
    representationLengthEqual in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    true if all lengths are equal, false otherwise
  - descriptionByToken
```
public java.lang.String descriptionByToken(ContinuousToken<T> token)
```
    Description copied from interface: TokenSet
    
    An description of the specified token (e.g. the full name of the compound like "Adenine").
    
    Specified by:
    
    descriptionByToken in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Parameters:
    
    token - the token that shall be described
    
    Returns:
    
    a string containing no line breaks
  - getType
```
public CharacterStateSetType getType()
```
    Description copied from interface: TokenSet
    
    Determines the type of tokens that are defined by this instance.
    
    Specified by:
    
    getType in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    the token set type
  - isSpaceForGap
```
public boolean isSpaceForGap()
```
    Description copied from interface: TokenSet
    
    Determines whether TokenSet.tokenByKeyStroke(KeyStroke) shall return the gap token, if the space bar is pressed, even if that key stroke is not associated with that token.
    
    Specified by:
    
    isSpaceForGap in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Returns:
    
    true if the gap token shall always be returned, false otherwise.
  - setSpaceForGap
```
public void setSpaceForGap(boolean spaceForGap)
```
    Description copied from interface: TokenSet
    
    Allows to specify whether TokenSet.tokenByKeyStroke(KeyStroke) shall return the gap token, if the space bar is pressed, even if that key stroke is not associated with that token.
    
    Specified by:
    
    setSpaceForGap in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Parameters:
    
    spaceForGap - Specify true here, if the gap token shall always be returned, false otherwise.
  - clone
```
public abstract AbstractContinuousSet<T> clone()
```
    Description copied from interface: TokenSet
    
    Returns a deep copy of this instance. Implementing this method is important when creating custom implementations of this interface, because other classes in LibrAlign use this method internally.
    
    Specified by:
    
    clone in interface TokenSet<ContinuousToken<T extends java.lang.Number & java.lang.Comparable<T>>>
    
    Overrides:
    
    clone in class java.lang.Object
    
    Returns:
    
    an identical token set

Class AbstractContinuousSet<T extends java.lang.Number & java.lang.Comparable<T>>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface info.bioinfweb.libralign.model.tokenset.TokenSet

Methods inherited from interface java.util.Set

Methods inherited from interface java.util.Collection

Methods inherited from interface java.lang.Iterable

Constructor Detail

AbstractContinuousSet

Method Detail

parseValue

tokenByRepresentation

tokenByKeyStroke

isGapToken

getGapToken

isMissingInformationToken

getMissingInformationToken

getSymbolType

getMeaning

add

addAll

clear

contains

containsAll

isEmpty

iterator

remove

removeAll

retainAll

size

toArray

toArray

representationByToken

representationLengthEqual

descriptionByToken

getType

isSpaceForGap

setSpaceForGap

clone