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Packages |
| cytoscape |
Core Cytoscape Classes. |
| cytoscape.actions |
UI classes that are attached to menu items in the menu or tool bar
of the window. |
| cytoscape.bookmarks |
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| cytoscape.command |
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| cytoscape.cruft.obo |
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| cytoscape.cruft.obo.test |
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| cytoscape.data |
Basic data classes used by Cytoscape. |
| cytoscape.data.annotation |
Classes used to represent generic annotation data in Cytoscape. |
| cytoscape.data.annotation.readers |
Reader classes for generic annotation data. |
| cytoscape.data.attr |
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| cytoscape.data.attr.util |
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| cytoscape.data.ontology |
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| cytoscape.data.ontology.readers |
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| cytoscape.data.readers |
Reader classes for the basic data types in cytoscape.data. |
| cytoscape.data.servers |
An interface for annotation data providers and various implementations
of that interface, including both remote and in-process implementations. |
| cytoscape.data.synonyms |
Classes providing synonym funcationality, that is identifying multiple
names that refer to the same entity. |
| cytoscape.data.synonyms.readers |
Readers for classes in the cytoscape.data.synonyms package. |
| cytoscape.data.webservice |
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| cytoscape.data.webservice.ui |
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| cytoscape.data.webservice.util |
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| cytoscape.data.writers |
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| cytoscape.dialogs |
UI classes for performing some action, generally more complicated than
those contained in the cytoscape.actions package. |
| cytoscape.dialogs.logger |
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| cytoscape.dialogs.plugins |
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| cytoscape.dialogs.preferences |
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| cytoscape.ding |
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| cytoscape.generated |
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| cytoscape.geom.rtree |
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| cytoscape.geom.rtree.test |
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| cytoscape.geom.spacial |
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| cytoscape.giny |
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| cytoscape.graph.dynamic |
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| cytoscape.graph.dynamic.util |
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| cytoscape.graph.fixed |
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| cytoscape.groups |
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| cytoscape.init |
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| cytoscape.layout |
Classes providing some kind of graph layout functionality. |
| cytoscape.layout.algorithms |
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| cytoscape.layout.ui |
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| cytoscape.logger |
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| cytoscape.plugin |
Classes related to Cytoscape plugins. |
| cytoscape.render.export |
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| cytoscape.render.immed |
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| cytoscape.render.immed.arrow |
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| cytoscape.render.immed.nodeshape |
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| cytoscape.render.stateful |
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| cytoscape.task |
Cytoscape Task Framework. |
| cytoscape.task.sample |
Sample task, used to illustrate the Task framework. |
| cytoscape.task.ui |
UI code related to task control. |
| cytoscape.task.util |
Utility manager for executing tasks. |
| cytoscape.util |
This package contains utility classes which are deemed generally useful,
but which do not clearly belong to any other package. |
| cytoscape.util.export |
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| cytoscape.util.intr |
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| cytoscape.util.intr.test |
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| cytoscape.util.shadegrown |
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| cytoscape.util.swing |
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| cytoscape.util.undo |
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| cytoscape.view |
Classes that provide a window to display a graph and UI components
connected to that window, such as the menus. |
| cytoscape.view.cytopanels |
CytoPanels Framework. |
| cytoscape.visual |
Framework for generalized mappings from graph attributes
to visual attributes. |
| cytoscape.visual.calculators |
Objects that calculate from the data attributes the value for one
visual attribute, such as color, shape, or size. |
| cytoscape.visual.converter |
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| cytoscape.visual.customgraphic |
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| cytoscape.visual.customgraphic.impl |
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| cytoscape.visual.customgraphic.impl.bitmap |
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| cytoscape.visual.customgraphic.impl.vector |
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| cytoscape.visual.customgraphic.paint |
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| cytoscape.visual.customgraphic.ui |
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| cytoscape.visual.mappings |
The Mappings are used by Calculators to map graph attributes
to visual attribute values. |
| cytoscape.visual.mappings.continuous |
Mappings from a continuous numerical input to a particular visual attribute. |
| cytoscape.visual.mappings.discrete |
Mappings from a discrete-valued input to a particular visual attribute. |
| cytoscape.visual.mappings.rangecalculators |
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| cytoscape.visual.parsers |
Translates visual attribute values to and from their String representation. |
| cytoscape.visual.properties |
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| cytoscape.visual.strokes |
The WidthStroke objects in this package should NOT be used directly by anyone other
than the LineStyle enum!!!! Seriously, DON'T USE THESE CLASSES!!! |
| cytoscape.visual.ui |
Top-level UI components for the cytoscape.visual package. |
| cytoscape.visual.ui.editors.continuous |
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| cytoscape.visual.ui.editors.discrete |
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| cytoscape.visual.ui.icon |
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| ding.view |
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| ding.view.test |
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| fing.model |
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| fing.model.test |
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| giny.filter |
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| giny.model |
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| giny.view |
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| org.apache.commons.cli |
Commons CLI 1.0 |
| org.apache.commons.cli.avalon |
Utility code for parsing command-line options. |
| org.cytoscape.equations |
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| org.cytoscape.equations.builtins |
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| org.cytoscape.equations.interpreter |
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| org.cytoscape.equations.parse_tree |
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| phoebe |
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| undo |
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