TableOfContents

1. Overview of the CytoscapeData Classes

CytoscapeData is the primary class that Cytoscape uses for its attribute storage and access. CytoscapeData is an interface that provides a tiered API that allows for more advanced use as the user becomes more familiar with the class. The primary class, CytoscapeData, is an interface located at cytoscape.data.CytoscapeData. It extends the old data class, GraphObjAttributes, to support legacy code. CytoscapeData also extends the classes, CyData and CyDataDefinition, these classes provide the advanced functionality of CytoscapeData.

This document will deal primarily with the API offered by CytoscapeData, but more information is available for the support classes. The implementation and inheritance of CytoscapeData is shown here:

[ftp://baker.systemsbiology.net/pub/xmas/CytoscapeData_classes.png]

2. CytoscapeData Attribute Storage and Access

CytoscapeData stores values in a multi-dimensional way. Every object in Cytoscape that has values stored for it, has a getIdentifier() method that will return the unique identifier for that object. Currently this is restricted to Nodes and Edges. To store or access a value, the value must be stored under an attribute name. This means that many different values can be associated with a node, each identifiable by a specifi attribute.

The simplest case is one attribute, and one value:

[ftp://baker.systemsbiology.net/pub/xmas/CD_structure_1.png]

The methods that use this one attribute, one value are below:

As more attributes are added, more values are stored for a given identifier.

[ftp://baker.systemsbiology.net/pub/xmas/CD_structure_2.png]

[ftp://baker.systemsbiology.net/pub/xmas/CD_structure_3.png]

[ftp://baker.systemsbiology.net/pub/xmas/CD_structure_4.png]

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Don't Fuck Up.

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Will give you access to the new data API now provided by Cytoscape.

Some Features

• This
• That
• Other