AbstractNode (Graph-Theoretic Querying 5.0.0 API)

java.lang.Object
- org.biopax.paxtools.query.model.AbstractNode

All Implemented Interfaces:

GraphObject, Node

Direct Known Subclasses:

ControlWrapper, ControlWrapper, EventWrapper, EventWrapper, PhysicalEntityWrapper, PhysicalEntityWrapper
```
public abstract class AbstractNode
extends Object
implements Node
```
Author:

Ozgun Babur

Field Summary

Fields
Modifier and Type	Field and Description
`protected Set<Node>`	`banned` For saying: "If the algorithm traverses this node, it cannot traverse those others".
`protected Set<Edge>`	`downstream` Set of downstream edges.
`protected boolean`	`downstreamInited` Flag to remember if downstream links were created.
`protected Graph`	`graph` Owner graph.
`protected Set<Node>`	`lowerEquivalent` If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node and members, then this set is for the child equivalents of this node.
`protected int`	`pathSign` This variable can be used by algorithms that need to label nodes with a path sign (typically the current path).
`protected Set<Node>`	`upperEquivalent` If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node and members, then this set is for the parent equivalents of this node.
`protected Set<Edge>`	`upstream` Set of upstream edges.
`protected boolean`	`upstreamInited` Flag to remember if upstream links were created.

Fields inherited from interface org.biopax.paxtools.query.model.Node
NEGATIVE, NEUTRAL, POSITIVE

Constructor Summary

Constructors
Modifier Constructor and Description

protected AbstractNode(Graph graph)
Constructor with the owner graph.

Constructors
Modifier	Constructor and Description
`protected`	`AbstractNode(Graph graph)` Constructor with the owner graph.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`clear()` Resets the path sign.
`Set<Node>`	`getBanned()`
`Collection<Edge>`	`getDownstream()` Gets the downstream edges.
`Collection<Edge>`	`getDownstreamNoInit()` This class gets the downstream links but does not initialize.
`Graph`	`getGraph()` Every graph object should have an owner graph.
`Collection<Node>`	`getLowerEquivalent()`
`int`	`getPathSign()`
`Collection<Node>`	`getUpperEquivalent()`
`Collection<Edge>`	`getUpstream()` Gets the upstream edges.
`Collection<Edge>`	`getUpstreamNoInit()` This class gets the upstream links but does not initialize.
`void`	`init()` Does nothing yet.
`void`	`initBanned()` Initializes the set of banned nodes.
`void`	`initDownstream()` Initializes the downstream connections.
`void`	`initUpstream()` Initializes the upstream connections.
`boolean`	`isTranscription()` Nodes are not transcription by default.
`void`	`setBanned(Set<Node> banned)`
`void`	`setPathSign(int pathSign)`

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

Methods inherited from interface org.biopax.paxtools.query.model.Node
getSign, isBreadthNode, isUbique

Methods inherited from interface org.biopax.paxtools.query.model.GraphObject
getKey

- Field Detail
  - graph
```
protected Graph graph
```
    Owner graph.
  - upstreamInited
```
protected boolean upstreamInited
```
    Flag to remember if upstream links were created.
  - downstreamInited
```
protected boolean downstreamInited
```
    Flag to remember if downstream links were created.
  - upperEquivalent
```
protected Set<Node> upperEquivalent
```
    If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node and members, then this set is for the parent equivalents of this node.
  - lowerEquivalent
```
protected Set<Node> lowerEquivalent
```
    If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node and members, then this set is for the child equivalents of this node.
  - upstream
```
protected Set<Edge> upstream
```
    Set of upstream edges.
  - downstream
```
protected Set<Edge> downstream
```
    Set of downstream edges.
  - pathSign
```
protected int pathSign
```
    This variable can be used by algorithms that need to label nodes with a path sign (typically the current path).
  - banned
```
protected Set<Node> banned
```
    For saying: "If the algorithm traverses this node, it cannot traverse those others". If this set will be used, then initBanned() should be called. Otherwise getBanned() will return an immutable empty set.
- Constructor Detail
  - AbstractNode
```
protected AbstractNode(Graph graph)
```
    Constructor with the owner graph.
    
    Parameters:
    
    graph - Owner graph
- Method Detail
  - getGraph
```
public Graph getGraph()
```
    Description copied from interface: GraphObject
    
    Every graph object should have an owner graph.
    
    Specified by:
    
    getGraph in interface GraphObject
    
    Returns:
    
    The owner graph
  - getBanned
```
public Set<Node> getBanned()
```
    Returns:
    
    Set of banned-to-traverse nodes if this node is traversed.
  - initBanned
```
public void initBanned()
```
    Initializes the set of banned nodes. If the algorithm will use this set, then this method or setBanned method should be called.
  - setBanned
```
public void setBanned(Set<Node> banned)
```
    Parameters:
    
    banned - Set of banned nodes
  - getUpstream
```
public Collection<Edge> getUpstream()
```
    Gets the upstream edges. Initializes if necessary.
    
    Specified by:
    
    getUpstream in interface Node
    
    Returns:
    
    upstream edges
  - getDownstream
```
public Collection<Edge> getDownstream()
```
    Gets the downstream edges. Initializes if necessary.
    
    Specified by:
    
    getDownstream in interface Node
    
    Returns:
    
    downstream edges
  - initUpstream
```
public void initUpstream()
```
    Initializes the upstream connections.
  - initDownstream
```
public void initDownstream()
```
    Initializes the downstream connections.
  - getUpstreamNoInit
```
public Collection<Edge> getUpstreamNoInit()
```
    This class gets the upstream links but does not initialize.
    
    Returns:
    
    Upstream links
  - getDownstreamNoInit
```
public Collection<Edge> getDownstreamNoInit()
```
    This class gets the downstream links but does not initialize.
    
    Returns:
    
    Downstream links
  - getUpperEquivalent
```
public Collection<Node> getUpperEquivalent()
```
    Specified by:
    
    getUpperEquivalent in interface Node
    
    Returns:
    
    Parent equivalent nodes.
  - getLowerEquivalent
```
public Collection<Node> getLowerEquivalent()
```
    Specified by:
    
    getLowerEquivalent in interface Node
    
    Returns:
    
    Child equivalent nodes
  - init
```
public void init()
```
    Does nothing yet.
    
    Specified by:
    
    init in interface Node
  - getPathSign
```
public int getPathSign()
```
    Returns:
    
    path sign
  - setPathSign
```
public void setPathSign(int pathSign)
```
    Parameters:
    
    pathSign - The path sign
  - clear
```
public void clear()
```
    Resets the path sign.
    
    Specified by:
    
    clear in interface GraphObject
  - isTranscription
```
public boolean isTranscription()
```
    Nodes are not transcription by default.
    
    Specified by:
    
    isTranscription in interface Node
    
    Returns:
    
    False

Class AbstractNode

Field Summary

Fields inherited from interface org.biopax.paxtools.query.model.Node

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface org.biopax.paxtools.query.model.Node

Methods inherited from interface org.biopax.paxtools.query.model.GraphObject

Field Detail

graph

upstreamInited

downstreamInited

upperEquivalent

lowerEquivalent

upstream

downstream

pathSign

banned

Constructor Detail

AbstractNode

Method Detail

getGraph

getBanned

initBanned

setBanned

getUpstream

getDownstream

initUpstream

initDownstream

getUpstreamNoInit

getDownstreamNoInit

getUpperEquivalent

getLowerEquivalent

init

getPathSign

setPathSign

clear

isTranscription