ClosableChain represents a chain of fragments (chain links) that is closable (or candidate closable). More...

Inheritance diagram for denoptim.graph.rings.ClosableChain:

Collaboration diagram for denoptim.graph.rings.ClosableChain:

Public Member Functions
	ClosableChain ()
	Constructs an empty ClosableChain. More...

	ClosableChain (String str)
	Constructs a ClosableChain from the string representation. More...

void	appendLink (ChainLink l)
	Append a link to this chain. More...

void	setTurningPoint (int tp)
	Defined the turning point in the list of links. More...

ArrayList< ChainLink >	getLinks ()
	Get the list of `ChainLink`s. More...

ChainLink	getLink (int i)
	Get a specific `ChainLink` More...

int	getSize ()
	Get length of chain. More...

int	getTurningPointIdx ()
	Get the vertex ID of the turning point.Note that since the chain is a path in a graph the relative direction of the edges spanned can display an inversion point (i.e., the turning point). More...

int	involvesVertex (Vertex vert)
	Check whether a given vertex is involved in this chain. More...

int	involvesVertexAndAP (Vertex vert, int apIDA, int apIDB)
	Check whether a combination of vertex and attachment points ID is involved in this chain. More...

ClosableChain	clone ()
	Returns a deep-copy. More...

String	toString ()

Private Attributes
ArrayList< ChainLink >	links
	List of `ChainLink`s in this chain. More...

int	tuningPoint
	The position of the scaffold vertex: turning point for the direction of the chain. More...

Detailed Description

ClosableChain represents a chain of fragments (chain links) that is closable (or candidate closable).

Author: Marco Foscato

Definition at line 34 of file ClosableChain.java.

Constructor & Destructor Documentation

◆ ClosableChain() [1/2]

denoptim.graph.rings.ClosableChain.ClosableChain ( )

Constructs an empty ClosableChain.

Definition at line 53 of file ClosableChain.java.

Referenced by denoptim.graph.rings.ClosableChain.clone().

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◆ ClosableChain() [2/2]

denoptim.graph.rings.ClosableChain.ClosableChain ( String str )

Constructs a ClosableChain from the string representation.

Definition at line 64 of file ClosableChain.java.

References denoptim.graph.rings.ClosableChain.links, denoptim.graph.Vertex.BBType.parseInt(), and denoptim.graph.rings.ClosableChain.tuningPoint.

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Member Function Documentation

◆ appendLink()

void denoptim.graph.rings.ClosableChain.appendLink ( ChainLink l )

Append a link to this chain.

Parameters

link	the link to be appended

Definition at line 92 of file ClosableChain.java.

References denoptim.graph.rings.ClosableChain.links.

Referenced by denoptim.graph.rings.ClosableChain.clone().

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◆ clone()

ClosableChain denoptim.graph.rings.ClosableChain.clone ( )

Returns a deep-copy.

Returns: a deep copy

Definition at line 232 of file ClosableChain.java.

References denoptim.graph.rings.ClosableChain.appendLink(), denoptim.graph.rings.ClosableChain.ClosableChain(), denoptim.graph.rings.ClosableChain.links, denoptim.graph.rings.ClosableChain.setTurningPoint(), and denoptim.graph.rings.ClosableChain.tuningPoint.

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◆ getLink()

ChainLink denoptim.graph.rings.ClosableChain.getLink ( int i )

Get a specific ChainLink

Parameters

i	the index of the `ChainLink` in the list

Returns: the ChainLink in the given position of the chain

Definition at line 127 of file ClosableChain.java.

References denoptim.graph.rings.ClosableChain.links.

Referenced by denoptim.graph.rings.ClosableChain.getTurningPointIdx().

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◆ getLinks()

ArrayList< ChainLink > denoptim.graph.rings.ClosableChain.getLinks ( )

Get the list of ChainLinks.

Definition at line 114 of file ClosableChain.java.

References denoptim.graph.rings.ClosableChain.links.

◆ getSize()

int denoptim.graph.rings.ClosableChain.getSize ( )

Get length of chain.

Returns: the size of the list if ChainLinks

Definition at line 139 of file ClosableChain.java.

References denoptim.graph.rings.ClosableChain.links.

◆ getTurningPointIdx()

int denoptim.graph.rings.ClosableChain.getTurningPointIdx ( )

Get the vertex ID of the turning point.Note that since the chain is a path in a graph the relative direction of the edges spanned can display an inversion point (i.e., the turning point).

Returns: the ID of the DENOPTIMVertex corresponding to the turning point.

Definition at line 154 of file ClosableChain.java.

References denoptim.graph.rings.ChainLink.getIdx(), denoptim.graph.rings.ClosableChain.getLink(), and denoptim.graph.rings.ClosableChain.tuningPoint.

Referenced by denoptim.graph.rings.RingClosuresArchive.addRecord().

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◆ involvesVertex()

int denoptim.graph.rings.ClosableChain.involvesVertex ( Vertex vert )

Check whether a given vertex is involved in this chain.

Parameters

vert	the candidate vertex

Returns: the poisiton of the related chain link or -1 if the vertex is not part of this chain.

Definition at line 168 of file ClosableChain.java.

References denoptim.graph.rings.ChainLink.getFragType(), denoptim.graph.rings.ChainLink.getIdx(), and denoptim.graph.rings.ClosableChain.links.

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◆ involvesVertexAndAP()

int denoptim.graph.rings.ClosableChain.involvesVertexAndAP	(	Vertex	vert,
		int	apIDA,
		int	apIDB
	)

Check whether a combination of vertex and attachment points ID is involved in this chain.

Parameters

vert	the candidate vertex
apIDA	the index of the `DENOPTIMAttachmentPoint` on the left/rigth hand side of the vertex
apIDB	the index of the `DENOPTIMAttachmentPoint` on the right/left hand side of the vertex

Returns: the poisiton of the related chain link or -1 if the vertex is not part of this chain.

Definition at line 203 of file ClosableChain.java.

References denoptim.graph.rings.ChainLink.getApIdToLeft(), denoptim.graph.rings.ChainLink.getApIdToRight(), denoptim.graph.rings.ChainLink.getFragType(), denoptim.graph.rings.ChainLink.getIdx(), and denoptim.graph.rings.ClosableChain.links.

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◆ setTurningPoint()

void denoptim.graph.rings.ClosableChain.setTurningPoint ( int tp )

Defined the turning point in the list of links.

Parameters

tp	the index of the turning point

Definition at line 103 of file ClosableChain.java.

Referenced by denoptim.graph.rings.ClosableChain.clone().

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◆ toString()

String denoptim.graph.rings.ClosableChain.toString ( )

Returns: the string representation of this ClosableChain

Definition at line 249 of file ClosableChain.java.

References denoptim.graph.rings.ClosableChain.links.

Member Data Documentation

◆ links

ArrayList<ChainLink> denoptim.graph.rings.ClosableChain.links

private

List of ChainLinks in this chain.

Definition at line 39 of file ClosableChain.java.

Referenced by denoptim.graph.rings.ClosableChain.appendLink(), denoptim.graph.rings.ClosableChain.clone(), denoptim.graph.rings.ClosableChain.ClosableChain(), denoptim.graph.rings.ClosableChain.getLink(), denoptim.graph.rings.ClosableChain.getLinks(), denoptim.graph.rings.ClosableChain.getSize(), denoptim.graph.rings.ClosableChain.involvesVertex(), denoptim.graph.rings.ClosableChain.involvesVertexAndAP(), and denoptim.graph.rings.ClosableChain.toString().

◆ tuningPoint

int denoptim.graph.rings.ClosableChain.tuningPoint

private

The position of the scaffold vertex: turning point for the direction of the chain.

Definition at line 45 of file ClosableChain.java.

Referenced by denoptim.graph.rings.ClosableChain.clone(), denoptim.graph.rings.ClosableChain.ClosableChain(), and denoptim.graph.rings.ClosableChain.getTurningPointIdx().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/graph/rings/ClosableChain.java

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ClosableChain() [1/2]

◆ ClosableChain() [2/2]

Member Function Documentation

◆ appendLink()

◆ clone()

◆ getLink()

◆ getLinks()

◆ getSize()

◆ getTurningPointIdx()

◆ involvesVertex()

◆ involvesVertexAndAP()

◆ setTurningPoint()

◆ toString()

Member Data Documentation

◆ links

◆ tuningPoint