| org.colomoto.biolqm |
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| org.colomoto.biolqm.io.avatar |
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| org.ginsim |
The base package for GINsim, with launcher classes.
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| org.ginsim.common.application |
Some system or application level helpers: detect OS, manage options, translate messages...
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| org.ginsim.common.callable |
API for processes which can run in background, based on callable and threads.
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| org.ginsim.common.document |
API to write reports and other simple documents in HTML, OpenDocument, or LaTeX.
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| org.ginsim.common.utils |
This package hosts a collection of miscellaneous utilities.
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| org.ginsim.common.xml |
This package contains helpers to write and parse XML files.
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| org.ginsim.commongui |
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| org.ginsim.commongui.dialog |
Help to create GUI dialogs, for data and messages.
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| org.ginsim.commongui.utils |
Collection of GUI helpers and widgets.
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| org.ginsim.core.annotation |
Manage annotations: bibliography, Database entries and links.
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| org.ginsim.core.graph |
Define the main Graph interfaces, and a GraphManager to handle graph types
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| org.ginsim.core.graph.backend |
Implementation of the graph backend.
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| org.ginsim.core.graph.dynamicgraph |
State Transition Graphs, representing dynamical behaviours.
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| org.ginsim.core.graph.hierarchicaltransitiongraph |
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| org.ginsim.core.graph.objectassociation |
Handling objects associated to Graphs.
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| org.ginsim.core.graph.reducedgraph |
Loop-free graphs where each node represents a strongly connected component of the original graph.
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| org.ginsim.core.graph.regulatorygraph |
The regulatory graph is the main graph, it represents the model.
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| org.ginsim.core.graph.regulatorygraph.logicalfunction |
Logical functions associated to nodes of the regulatory graph define their dynamical behaviour.
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| org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree |
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| org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function |
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| org.ginsim.core.graph.regulatorygraph.logicalfunction.parser |
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| org.ginsim.core.graph.regulatorygraph.namedstates |
Define states of a regulatory graph, which can be named and
used as starting point for simulations.
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| org.ginsim.core.graph.regulatorygraph.perturbation |
Perturbations to modify some parts of a model before analysis.
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| org.ginsim.core.graph.trapspacetree |
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| org.ginsim.core.graph.tree |
The Tree graph is a representation of a logical functions, allowing a graphical representation.
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| org.ginsim.core.graph.view |
Define the layout and appearance of graph elements.
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| org.ginsim.core.graph.view.css |
Customise Graph views through CSS-like commands.
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| org.ginsim.core.graph.view.shapes |
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| org.ginsim.core.graph.view.style |
Styles define visual properties for graph elements.
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| org.ginsim.core.io.parser |
Some tools to build parsers and writers for xml and text formats
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| org.ginsim.core.notification |
API for notifications: notifications, listener and a global manager to connect them
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| org.ginsim.core.notification.detailed |
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| org.ginsim.core.notification.resolvable |
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| org.ginsim.core.service |
Manage Services to extend the core features.
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| org.ginsim.core.utils.data |
Some simple data structures and collections
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| org.ginsim.gui |
Definition of the GUIManager: provide access to all opened windows
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| org.ginsim.gui.annotation |
Shared GUI to edit annotations
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| org.ginsim.gui.graph |
Common GUI for all graphs, and definition of hooks for specialised parts.
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| org.ginsim.gui.graph.canvas |
Custom implementation of the interactive view
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| org.ginsim.gui.graph.canvas.events |
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| org.ginsim.gui.graph.dynamicgraph |
Specialised GUI for the State Transition Graphs
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| org.ginsim.gui.graph.hierarchicaltransitiongraph |
Specialised GUI for the Hierarchical Transition Graphs
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| org.ginsim.gui.graph.reducedgraph |
Specialised GUI for the Reduced Graphs (Graph of the SCC)
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| org.ginsim.gui.graph.regulatorygraph |
Specialised GUI for the Regulatory graphs
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| org.ginsim.gui.graph.regulatorygraph.initialstate |
GUI for the definition and selection of states.
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| org.ginsim.gui.graph.regulatorygraph.logicalfunction |
GUI to view and edit logical functions associated to Regulatory Nodes
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| org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree |
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| org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd |
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| org.ginsim.gui.graph.regulatorygraph.perturbation |
GUI for the definition and selection of perturbations applied to a Regulatory Graph
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| org.ginsim.gui.graph.trapspacetree |
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| org.ginsim.gui.graph.tree |
Specialised GUI for the graphs representing logical functions.
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| org.ginsim.gui.graph.view.style |
GUI for the definition of styles associated to graph elements.
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| org.ginsim.gui.guihelpers |
API for GUI helpers: they provide specialised GUI to show/edit specific data types.
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| org.ginsim.gui.notifications |
GUI to present notifications, and propose related actions when needed.
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| org.ginsim.gui.service |
API for GUI services, and a manager to load them and integrate them in the shell.
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| org.ginsim.gui.shell |
Define the main shell: graph windows and common dialogs
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| org.ginsim.gui.shell.actions |
Define types of actions, which will be integrated in different parts of the shell.
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| org.ginsim.gui.shell.callbacks |
Define the Actions behind the menu entries
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| org.ginsim.gui.shell.editpanel |
Define edit panels: panels which follow graph selection events.
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| org.ginsim.gui.utils.data |
Widgets and panels to handle datasets: mostly list edition/selection panels.
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| org.ginsim.gui.utils.data.models |
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| org.ginsim.gui.utils.dialog.stackdialog |
Definition of StackDialog: a run dialog where the main panel can be changed.
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| org.ginsim.gui.utils.widgets |
Some common widgets
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| org.ginsim.gui.utils.widgets.treetable |
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| org.ginsim.johnsonCycles |
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| org.ginsim.service.export.cadp |
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| org.ginsim.service.export.documentation |
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| org.ginsim.service.export.image |
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| org.ginsim.service.export.nusmv |
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| org.ginsim.service.export.prism |
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| org.ginsim.service.export.reggraph |
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| org.ginsim.service.export.sat |
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| org.ginsim.service.export.struct |
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| org.ginsim.service.format |
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| org.ginsim.service.format.ginml |
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| org.ginsim.service.format.sbml |
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| org.ginsim.service.layout |
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| org.ginsim.service.tool.avatar.domain |
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| org.ginsim.service.tool.avatar.params |
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| org.ginsim.service.tool.avatar.service |
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| org.ginsim.service.tool.avatar.simulation |
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| org.ginsim.service.tool.avatar.simulation.others |
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| org.ginsim.service.tool.avatar.utils |
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| org.ginsim.service.tool.circuit |
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| org.ginsim.service.tool.composition |
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| org.ginsim.service.tool.graphcomparator |
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| org.ginsim.service.tool.interactionanalysis |
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| org.ginsim.service.tool.localgraph |
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| org.ginsim.service.tool.modelbooleanizer |
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| org.ginsim.service.tool.modelreduction |
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| org.ginsim.service.tool.modelreversion |
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| org.ginsim.service.tool.polytopesViz |
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| org.ginsim.service.tool.reg2dyn |
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| org.ginsim.service.tool.reg2dyn.helpers |
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| org.ginsim.service.tool.reg2dyn.htg |
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| org.ginsim.service.tool.reg2dyn.limitedsimulation |
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| org.ginsim.service.tool.reg2dyn.priorityclass |
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| org.ginsim.service.tool.reg2dyn.updater |
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| org.ginsim.service.tool.scc |
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| org.ginsim.service.tool.simulation |
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| org.ginsim.service.tool.stableregions |
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| org.ginsim.service.tool.stablestates |
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| org.ginsim.service.tool.trapspace |
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| org.ginsim.servicegui.export.cadp |
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| org.ginsim.servicegui.export.documentation |
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| org.ginsim.servicegui.export.image |
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| org.ginsim.servicegui.export.maboss |
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| org.ginsim.servicegui.export.nusmv |
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| org.ginsim.servicegui.export.petrinet |
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| org.ginsim.servicegui.export.prism |
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| org.ginsim.servicegui.export.reggraph |
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| org.ginsim.servicegui.export.sat |
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| org.ginsim.servicegui.export.struct |
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| org.ginsim.servicegui.format |
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| org.ginsim.servicegui.format.ginml |
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| org.ginsim.servicegui.format.sbml |
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| org.ginsim.servicegui.layout |
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| org.ginsim.servicegui.tool.avatar |
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| org.ginsim.servicegui.tool.avatar.algopanels |
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| org.ginsim.servicegui.tool.avatar.others |
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| org.ginsim.servicegui.tool.avatar.parameters |
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| org.ginsim.servicegui.tool.circuit |
search circuits in the regulatory graph.
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| org.ginsim.servicegui.tool.composition |
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| org.ginsim.servicegui.tool.composition.integrationgrammar |
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| org.ginsim.servicegui.tool.dataviewer |
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| org.ginsim.servicegui.tool.decisionanalysis |
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| org.ginsim.servicegui.tool.dynamicanalyser |
the state transition graph
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| org.ginsim.servicegui.tool.graphcomparator |
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| org.ginsim.servicegui.tool.interactionanalysis |
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| org.ginsim.servicegui.tool.localgraph |
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| org.ginsim.servicegui.tool.lrgcolorizer |
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| org.ginsim.servicegui.tool.modelbooleanizer |
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| org.ginsim.servicegui.tool.modelreduction |
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| org.ginsim.servicegui.tool.modelreversion |
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| org.ginsim.servicegui.tool.omddViz |
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| org.ginsim.servicegui.tool.pathfinding |
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| org.ginsim.servicegui.tool.polytopesViz |
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| org.ginsim.servicegui.tool.reg2dyn |
find the state transition graph from the regulatory one
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| org.ginsim.servicegui.tool.reg2dyn.limitedSimulation |
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| org.ginsim.servicegui.tool.reg2dyn.priorityclass |
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| org.ginsim.servicegui.tool.regulatorygraphanimation |
animate the regulatory graph (by simply changing nodes and edge's colors)
according to a path/state in the state transition graph.
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| org.ginsim.servicegui.tool.regulatorytreefunction |
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| org.ginsim.servicegui.tool.scc |
colorize the strongly connected components in a graph
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| org.ginsim.servicegui.tool.stableregions |
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| org.ginsim.servicegui.tool.stablestates |
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| org.ginsim.servicegui.tool.stateinregulatorygraph |
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| org.ginsim.servicegui.tool.trapspace |
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