- get(int) - Method in class com.dpgil.pathlinker.path_linker.internal.util.Algorithms.PathWay
-
Returns the ith node in the path
- getComponent() - Method in class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel
-
- getComponent() - Method in class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerResultPanel
-
- getCyNodeToId() - Method in class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModelParams
-
Getter method of cyNodeToId
- getCytoPanelName() - Method in class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel
-
- getCytoPanelName() - Method in class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerResultPanel
-
- getEdge(CyNetwork, CyNode, CyNode) - Static method in class com.dpgil.pathlinker.path_linker.internal.util.Algorithms
-
Returns an edge that connects source to target if it exists, null
otherwise
- getIcon() - Method in class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel
-
- getIcon() - Method in class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerResultPanel
-
- getNodeList() - Method in class com.dpgil.pathlinker.path_linker.internal.util.Path
-
Getter method for the node list
- getOutputK() - Method in class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModel
-
Getter method of output k value
- getPathRankColumnName() - Method in class com.dpgil.pathlinker.path_linker.internal.rest.PathLinkerAppResponse
-
Getter method of the pathRankColumnName
- getPaths() - Method in class com.dpgil.pathlinker.path_linker.internal.rest.PathLinkerAppResponse
-
Getter method of the paths
- getRank() - Method in class com.dpgil.pathlinker.path_linker.internal.util.Path
-
Getter method for rank
- getResult() - Method in class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModel
-
Getter method of the result
- getResults(Class<? extends R>) - Method in class com.dpgil.pathlinker.path_linker.internal.task.CreateKSPViewTask
-
Used to access the ksp subgraph/view and path rank column name created by the task
- getResults(Class<? extends R>) - Method in class com.dpgil.pathlinker.path_linker.internal.task.CreateResultPanelTask
-
Get Result method
returns PathLinkerResultPanel instance created by the task
- getResults(Class<? extends R>) - Method in class com.dpgil.pathlinker.path_linker.internal.task.RunKSPTask
-
Get Result method
returns PathLinkerModel used by the RunKSPTask
the model consist of error lists and results from running the ksp algorithm
- getScore() - Method in class com.dpgil.pathlinker.path_linker.internal.util.Path
-
Getter method for score
- getSourceNames() - Method in class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModelParams
-
Getter method of sourceNames
- getSourcesList() - Method in class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModelParams
-
Getter method of sourcesList
- getSubgraphSources() - Method in class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModel
-
Getter method of the subgraph sources
- getSubgraphTargets() - Method in class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModel
-
Getter method of the subgraph targets
- getSubnetworkSUID() - Method in class com.dpgil.pathlinker.path_linker.internal.rest.PathLinkerAppResponse
-
Getter method of the subnetworkSUID
- getSubnetworkViewSUID() - Method in class com.dpgil.pathlinker.path_linker.internal.rest.PathLinkerAppResponse
-
Getter method of the subnetworkViewSUID
- getTargetNames() - Method in class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModelParams
-
Getter method of targetNames
- getTargetsList() - Method in class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModelParams
-
Getter method of targetsList
- getTitle() - Method in class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel
-
- getTitle() - Method in class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerResultPanel
-
- getWeight(CyNetwork, CyEdge) - Static method in class com.dpgil.pathlinker.path_linker.internal.util.Algorithms
-
Returns the weight of an edge in the network
- Path - Class in com.dpgil.pathlinker.path_linker.internal.util
-
Path class that represents the path generated by PathLinker
Each path contains a path rank in the corresponding network,
the total path weight
an array list of nodes names that is included in the path
- Path(int, double, ArrayList<String>) - Constructor for class com.dpgil.pathlinker.path_linker.internal.util.Path
-
Default constructor
- PATH_NOT_FOUND_CODE - Static variable in class com.dpgil.pathlinker.path_linker.internal.util.PathLinkerError
-
Error code for path not found
- PATH_NOT_FOUND_ERROR - Static variable in class com.dpgil.pathlinker.path_linker.internal.util.PathLinkerError
-
Error message for path not found
- PathLinkerAboutMenuDialog - Class in com.dpgil.pathlinker.path_linker.internal.view
-
About dialog box for PathLinker
- PathLinkerAboutMenuDialog(CySwingApplication, String, String) - Constructor for class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerAboutMenuDialog
-
Constructor for the dialog box
- PathLinkerAppResponse - Class in com.dpgil.pathlinker.path_linker.internal.rest
-
Class handles PathLinker API function response
- PathLinkerAppResponse() - Constructor for class com.dpgil.pathlinker.path_linker.internal.rest.PathLinkerAppResponse
-
- PathLinkerColumnUpdateListener - Class in com.dpgil.pathlinker.path_linker.internal.event
-
Listener class for _edgeWeightColumnBox in PathLinkerPanel class
Updates the _suidToPathIndexMap and _pathIndexToSuidMap
Can be use by more GUI objects in the future
- PathLinkerColumnUpdateListener(PathLinkerControlPanel) - Constructor for class com.dpgil.pathlinker.path_linker.internal.event.PathLinkerColumnUpdateListener
-
Default constructor to gain access of the control panel
- PathLinkerControlPanel - Class in com.dpgil.pathlinker.path_linker.internal.view
-
Panel for the PathLinker plugin
- PathLinkerControlPanel() - Constructor for class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel
-
- PathLinkerControlPanel.PanelState - Enum in com.dpgil.pathlinker.path_linker.internal.view
-
The state of the panel
- PathLinkerDocumentation - Class in com.dpgil.pathlinker.path_linker.internal
-
- PathLinkerDocumentation() - Constructor for class com.dpgil.pathlinker.path_linker.internal.PathLinkerDocumentation
-
- PathLinkerError - Class in com.dpgil.pathlinker.path_linker.internal.util
-
Class extending CIError which stores and represents errors generate by user inputs in PathLinker
- PathLinkerError(Integer, String, String, String) - Constructor for class com.dpgil.pathlinker.path_linker.internal.util.PathLinkerError
-
Default constructor
- PathLinkerImpl - Class in com.dpgil.pathlinker.path_linker.internal.rest
-
Implementation of the PathLinkerResource interface
- PathLinkerImpl(PathLinkerControlPanel, CyApplicationManager, CyNetworkManager, CyAppAdapter, CyServiceRegistrar, CySwingApplication, CIExceptionFactory) - Constructor for class com.dpgil.pathlinker.path_linker.internal.rest.PathLinkerImpl
-
Default constructor
- PathLinkerMenuAction - Class in com.dpgil.pathlinker.path_linker.internal
-
// -------------------------------------------------------------------------
/** Menu option to open the PathLinker plugin
- PathLinkerMenuAction(PathLinkerControlPanel, CyApplicationManager) - Constructor for class com.dpgil.pathlinker.path_linker.internal.PathLinkerMenuAction
-
Constructor for the menu option
- PathLinkerModel - Class in com.dpgil.pathlinker.path_linker.internal.model
-
Back end model for the PathLinker plugin
- PathLinkerModel(CyNetwork, boolean, boolean, Set<String>, Set<String>, List<CyNode>, List<CyNode>, String, int, EdgeWeightType, Double, Map<CyNode, String>) - Constructor for class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModel
-
Constructor of the model
- PathLinkerModelParams - Class in com.dpgil.pathlinker.path_linker.internal.model
-
The Class that holds and validates all the required parameters for PathLinkerModel
in order to run ksp algorithm in CyRest
- PathLinkerModelParams() - Constructor for class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModelParams
-
- PathLinkerNetworkEventListener - Class in com.dpgil.pathlinker.path_linker.internal.event
-
Listener class for _edgeWeightColumnBox
_networkCmb
Can be use by more GUI objects in the future
- PathLinkerNetworkEventListener(PathLinkerControlPanel) - Constructor for class com.dpgil.pathlinker.path_linker.internal.event.PathLinkerNetworkEventListener
-
Default constructor to gain access to the control panel
- PathLinkerNodeSelectionListener - Class in com.dpgil.pathlinker.path_linker.internal.event
-
Listener class for _loadNodeToSourceButton and _loadNodeToTargetButton in PathLinkerPanel class
- PathLinkerNodeSelectionListener(PathLinkerControlPanel, CyApplicationManager) - Constructor for class com.dpgil.pathlinker.path_linker.internal.event.PathLinkerNodeSelectionListener
-
Default constructor
- PathLinkerResource - Interface in com.dpgil.pathlinker.path_linker.internal.rest
-
Interface for PathLinker CytoScape CyRest Service
- PathLinkerResultPanel - Class in com.dpgil.pathlinker.path_linker.internal.view
-
// -------------------------------------------------------------------------
/** Panel that displays the results for the PathLinker CytoScape plugin
- PathLinkerResultPanel(PathLinkerControlPanel, String, CyNetworkManager, CyNetwork, List<Algorithms.PathWay>) - Constructor for class com.dpgil.pathlinker.path_linker.internal.view.PathLinkerResultPanel
-
Constructor for the result frame class
- PathWay(ArrayList<CyNode>, Map<CyNode, String>, double) - Constructor for class com.dpgil.pathlinker.path_linker.internal.util.Algorithms.PathWay
-
Constructor for the path class
- RESOURCE_ERROR_ROOT - Static variable in class com.dpgil.pathlinker.path_linker.internal.util.PathLinkerError
-
Response String for error origin
- reverseSingleSourceDijkstra(CyNetwork, CyNode) - Static method in class com.dpgil.pathlinker.path_linker.internal.util.Algorithms
-
Computes the shortest distance from a source to every node in the graph
- run(long, PathLinkerModelParams) - Method in class com.dpgil.pathlinker.path_linker.internal.rest.PathLinkerImpl
-
Implementation of run method from PathLinkerResource
Runs algorithm on the input network SUID and user parameters
- run(PathLinkerModelParams) - Method in class com.dpgil.pathlinker.path_linker.internal.rest.PathLinkerImpl
-
Implementation of run method from PathLinkerResource
Runs algorithm on the currently selected network and user parameters
- run(long, PathLinkerModelParams) - Method in interface com.dpgil.pathlinker.path_linker.internal.rest.PathLinkerResource
-
Post Function that takes user input, and runs PathLinker on specific network;
generate new network/network view,
and return network/view SUIDs and k-number sorted path list
- run(PathLinkerModelParams) - Method in interface com.dpgil.pathlinker.path_linker.internal.rest.PathLinkerResource
-
Post Function that takes user input, and runs PathLinker on currently selected network;
generate new network/network view,
and return network/view SUIDs and k-number sorted path list
- run(TaskMonitor) - Method in class com.dpgil.pathlinker.path_linker.internal.task.CreateKSPViewTask
-
Runs the task to create the ksp subgraph, subgraphview, and path rank
- run(TaskMonitor) - Method in class com.dpgil.pathlinker.path_linker.internal.task.CreateResultPanelTask
-
Creates the Result Panel
- run(TaskMonitor) - Method in class com.dpgil.pathlinker.path_linker.internal.task.RunKSPTask
-
Runs the KSP algorithm
- RUN_CURRENT_NETWORK_SWAGGER_NOTES - Static variable in class com.dpgil.pathlinker.path_linker.internal.PathLinkerDocumentation
-
- RUN_SWAGGER_NOTES - Static variable in class com.dpgil.pathlinker.path_linker.internal.PathLinkerDocumentation
-
- runKSP() - Method in class com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModel
-
Runs all the necessary algorithms to calculate kth shortest path
If path exists, selects corresponding nodes and edges in the network
to prepare for the subnetwork creation
- RunKSPTask - Class in com.dpgil.pathlinker.path_linker.internal.task
-
Class which creates a task that runs the KSP algorithm
- RunKSPTask(CyNetwork, PathLinkerModelParams) - Constructor for class com.dpgil.pathlinker.path_linker.internal.task.RunKSPTask
-
Default constructor