Package sc.fiji.snt.analysis.graph

Class AnnotationGraph

java.lang.Object

org.jgrapht.graph.AbstractGraph<BrainAnnotation,AnnotationWeightedEdge>

org.jgrapht.graph.AbstractBaseGraph<BrainAnnotation,AnnotationWeightedEdge>

sc.fiji.snt.analysis.graph.SNTGraph<BrainAnnotation,AnnotationWeightedEdge>

sc.fiji.snt.analysis.graph.AnnotationGraph

All Implemented Interfaces:

Serializable, Cloneable, org.jgrapht.Graph<BrainAnnotation,AnnotationWeightedEdge>

public class AnnotationGraph
extends SNTGraph<BrainAnnotation,AnnotationWeightedEdge>

A specialized graph implementation for brain annotations that extends SNTGraph. This class provides functionality to create and analyze graphs based on brain annotations and their relationships, using different metrics for edge weighting.

The graph can be constructed using various metrics such as:

• Number of tips (TIPS)
• Total length (LENGTH)
• Number of branch points (BRANCH_POINTS)
• Edge count (EDGES)

See Also:

• SNTGraph
• BrainAnnotation
• AnnotationWeightedEdge
• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BRANCH_POINTS
static final String	EDGES
static final String	LENGTH
static final String	TIPS

Fields inherited from interface org.jgrapht.Graph

DEFAULT_EDGE_WEIGHT

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AnnotationGraph()	Protected default constructor for internal use.
	AnnotationGraph(Collection<Tree> trees, String metric, double threshold, int maxOntologyDepth)	Constructs an annotation graph from a collection of trees using specified parameters.
	AnnotationGraph(Collection<Tree> trees, Collection<BrainAnnotation> annotations, String metric)	Constructs an annotation graph from trees and annotations using a specified metric.
	AnnotationGraph(Collection<Tree> trees, Collection<BrainAnnotation> annotations, String metric, double threshold)	Constructs an annotation graph from trees and annotations with specified parameters.

Method Summary

Modifier and Type	Method	Description
void	filterEdgesByWeight(int minWeight)
int	getMaxOntologyDepth()
String	getMetric()
static String[]	getMetrics()
double	getThreshold()
List<Tree>	getTrees()
static void	main(String[] args)
Set<BrainAnnotation>	removeOrphans()
protected void	show()	Displays this graph in a new instance of SNT's "Dendrogram Viewer".
double	sumEdgeWeights()	Gets the sum of all edge weights.

Methods inherited from class sc.fiji.snt.analysis.graph.SNTGraph

applyEdges, applyVertices, filterEdges, filterVertices, getEdgeColor, getEdgeColorRGBMap, getVertexColor, getVertexColorRGBMap, getVertexValue, getVertexValueMap, setEdgeColor, setVertexColor, setVertexValue

Methods inherited from class org.jgrapht.graph.AbstractBaseGraph

addEdge, addEdge, addVertex, addVertex, clone, containsEdge, containsVertex, degreeOf, edgeSet, edgesOf, getAllEdges, getEdge, getEdgeSource, getEdgeSupplier, getEdgeTarget, getEdgeWeight, getType, getVertexSupplier, incomingEdgesOf, inDegreeOf, iterables, outDegreeOf, outgoingEdgesOf, removeEdge, removeEdge, removeVertex, setEdgeSupplier, setEdgeWeight, setVertexSupplier, vertexSet

Methods inherited from class org.jgrapht.graph.AbstractGraph

assertVertexExist, containsEdge, equals, hashCode, removeAllEdges, removeAllEdges, removeAllEdges, removeAllVertices, toString, toStringFromSets

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.jgrapht.Graph

containsEdge, removeAllEdges, removeAllEdges, removeAllVertices, setEdgeWeight

Field Details

TIPS

public static final String TIPS

See Also:

• Constant Field Values

LENGTH

public static final String LENGTH

See Also:

• Constant Field Values

BRANCH_POINTS

public static final String BRANCH_POINTS

See Also:

• Constant Field Values

EDGES

public static final String EDGES

See Also:

• Constant Field Values

Constructor Details

AnnotationGraph

protected AnnotationGraph()

Protected default constructor for internal use.

AnnotationGraph

public AnnotationGraph(Collection<Tree> trees,
 String metric,
 double threshold,
 int maxOntologyDepth)

Constructs an annotation graph from a collection of trees using specified parameters.

Parameters:

trees - The collection of trees to analyze

metric - The metric to use for graph construction (one of getMetrics())

threshold - The threshold value for filtering connections

maxOntologyDepth - The maximum depth to consider in the ontology hierarchy

AnnotationGraph

public AnnotationGraph(Collection<Tree> trees,
 Collection<BrainAnnotation> annotations,
 String metric,
 double threshold)

Constructs an annotation graph from trees and annotations with specified parameters.

Parameters:

trees - The collection of input trees to analyze

annotations - The collection of brain annotations. Used as nodes

metric - The metric to use for graph construction (one of getMetrics()). Used as edges

threshold - The threshold value for filtering connections

AnnotationGraph

public AnnotationGraph(Collection<Tree> trees,
 Collection<BrainAnnotation> annotations,
 String metric)

Constructs an annotation graph from trees and annotations using a specified metric.

Parameters:

trees - The collection of trees to analyze

annotations - The collection of brain annotations to consider

metric - The metric to use for graph construction (one of getMetrics())

Method Details

getMetrics

public static String[] getMetrics()

filterEdgesByWeight

public void filterEdgesByWeight(int minWeight)

removeOrphans

public Set<BrainAnnotation> removeOrphans()

sumEdgeWeights

public double sumEdgeWeights()

Gets the sum of all edge weights.

Returns:

the sum of all edge weights

getTrees

public List<Tree> getTrees()

show

protected void show()

Displays this graph in a new instance of SNT's "Dendrogram Viewer".

getMaxOntologyDepth

public int getMaxOntologyDepth()

getThreshold

public double getThreshold()

getMetric

public String getMetric()

main

public static void main(String[] args)