A B C D E F G H I K L M N O P R S T U V W

A

AbstractGraph - Class in org.gersteinlab.tyna.core.graph
This class is the abstract parent class of all actual graph classes.
AbstractGraph() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractGraph
Default constructor: creates an empty graph.
AbstractGraph(Graph) - Constructor for class org.gersteinlab.tyna.core.graph.AbstractGraph
Copy constructor: creates a copy of an existing graph.
AbstractGraph.AbstractGraphEdgeIterator - Class in org.gersteinlab.tyna.core.graph
 
AbstractGraph.AbstractGraphEdgeIterator() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphEdgeIterator
 
AbstractGraph.AbstractGraphNodeIterator - Class in org.gersteinlab.tyna.core.graph
 
AbstractGraph.AbstractGraphNodeIterator() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphNodeIterator
Constructor: initialize the iteration state.
AbstractGraph.BetweennessNode - Class in org.gersteinlab.tyna.core.graph
A utility class for calculating betweenness.
AbstractGraph.BetweennessNode(Node, int) - Constructor for class org.gersteinlab.tyna.core.graph.AbstractGraph.BetweennessNode
 
AbstractGraph.DuplicateTree - Class in org.gersteinlab.tyna.core.graph
A utility class for removing duplicated chains/cycles.
AbstractGraph.DuplicateTree() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractGraph.DuplicateTree
 
AbstractGraph.HeadTailTree - Class in org.gersteinlab.tyna.core.graph
A utility class for computing minimal and maximal motifs.
AbstractGraph.HeadTailTree() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractGraph.HeadTailTree
 
AbstractGraph.HeadTree - Class in org.gersteinlab.tyna.core.graph
A utility class for computing minimal and maximal motifs.
AbstractGraph.HeadTree() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractGraph.HeadTree
 
AbstractGraph.TailTree - Class in org.gersteinlab.tyna.core.graph
A utility class for computing minimal and maximal motifs.
AbstractGraph.TailTree() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractGraph.TailTree
 
AbstractMultiGraph - Class in org.gersteinlab.tyna.core.graph
This class is the abstract parent class of all multigraph classes.
AbstractMultiGraph() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractMultiGraph
 
AbstractMultiGraph.AbstractMultiGraphEdgeIterator - Class in org.gersteinlab.tyna.core.graph
 
AbstractMultiGraph.AbstractMultiGraphEdgeIterator() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractMultiGraph.AbstractMultiGraphEdgeIterator
Constructor: initialize the iteration state.
AbstractSimpleGraph - Class in org.gersteinlab.tyna.core.graph
This class is the abstract parent class of all simple graph classes.
AbstractSimpleGraph() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph
 
AbstractSimpleGraph.AbstractSimpleGraphEdgeIterator - Class in org.gersteinlab.tyna.core.graph
 
AbstractSimpleGraph.AbstractSimpleGraphEdgeIterator() - Constructor for class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph.AbstractSimpleGraphEdgeIterator
Constructor: initialize the iteration state.
accumulateLocalBetweenness(AbstractGraph.BetweennessNode, Map) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
actionPerformed(ActionEvent) - Method in class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
 
actionPerformed(ActionEvent) - Method in class org.gersteinlab.tyna.cytoscape.TYNAPlugin
 
actionPerformed(ActionEvent) - Method in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
addChain(Node[]) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph.HeadTailTree
 
addChain(Node[]) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph.HeadTree
 
addChain(Node[]) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph.TailTree
 
addEdge(Edge, boolean) - Method in class org.gersteinlab.tyna.core.graph.AbstractMultiGraph
 
addEdge(Edge, boolean) - Method in class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph
 
addEdge(Edge, boolean) - Method in interface org.gersteinlab.tyna.core.graph.Graph
Add an edge to the graph.
addNode(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
addNode(Node) - Method in interface org.gersteinlab.tyna.core.graph.Graph
Add a node to the graph.
addValue(double) - Method in class org.gersteinlab.tyna.core.util.SimpleStats
Add a new value.
AdvancedDirectedGraph - Interface in org.gersteinlab.tyna.core.graph
This interface declares advanced methods for directed graphs such as motif mining that are not mandatory for basic implementations of DirectedGraph classes.
AdvancedGraph - Interface in org.gersteinlab.tyna.core.graph
This interface declares advanced methods such as graph statistics that are not mandatory for basic implementations of Graph classes.
AdvancedUndirectedGraph - Interface in org.gersteinlab.tyna.core.graph
This interface declares advanced methods for undirected graphs such as motif mining that are not mandatory for basic implementations of UndirectedGraph classes.
allInteractions - Variable in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
A Vector that holds all of the Interactions
associative() - Method in interface org.gersteinlab.tyna.core.operators.BinaryOperator
Whether the operator is associative, i.e., whether a op (b op c) equals (a op b) op c.
associative() - Method in class org.gersteinlab.tyna.core.operators.Difference
 
associative() - Method in class org.gersteinlab.tyna.core.operators.Intersection
 
associative() - Method in class org.gersteinlab.tyna.core.operators.Union
 
attrs - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph
The attributes of the graph.
attrs - Variable in class org.gersteinlab.tyna.core.graph.Edge
Other attributes of the edge (can be null).
attrs - Variable in class org.gersteinlab.tyna.core.graph.Node
The (possibly null) other attributes of the node.

B

BETWEENNESSES - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
BinaryOperator - Interface in org.gersteinlab.tyna.core.operators
This class defines the interface for binary graph operators, which take two graphs as input, and returns a single graph as output.

C

canonicalizeName(String) - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
categoriesToNodes - Variable in class org.gersteinlab.tyna.webapp.data.CategoryInfo
A map from the classes to the nodes
Category - Class in org.gersteinlab.tyna.webapp.data
This class contains the information of a category of the nodes.
Category() - Constructor for class org.gersteinlab.tyna.webapp.data.Category
Default constructor: creates an empty object.
Category(Integer, String, String, Integer, String, Timestamp, Boolean) - Constructor for class org.gersteinlab.tyna.webapp.data.Category
Creates a new object that stores the supplied information.
categoryDir - Variable in class org.gersteinlab.tyna.webapp.data.FileDataStore
The directory to store categories
CategoryInfo - Class in org.gersteinlab.tyna.webapp.data
This class reads some category information for query.
CategoryInfo(InputStream) - Constructor for class org.gersteinlab.tyna.webapp.data.CategoryInfo
Read the category information from a source.
CategoryInfo.CategoryInfoNodeIterator - Class in org.gersteinlab.tyna.webapp.data
 
CategoryInfo.CategoryInfoNodeIterator(Iterator) - Constructor for class org.gersteinlab.tyna.webapp.data.CategoryInfo.CategoryInfoNodeIterator
Constructor: initialize the iteration state.
ChainMotifMiner - Class in org.gersteinlab.tyna.core.operators
This class defines the chain motif miner.
ChainMotifMiner(String, int, int, String) - Constructor for class org.gersteinlab.tyna.core.operators.ChainMotifMiner
Create a new chain motif miner.
checkCategoryPermission(int, char) - Method in class org.gersteinlab.tyna.webapp.security.SecurityController
Check if the current user has the right to access a category.
checkEdge(Edge) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
Check if an edge is non null.
checkNetworkPermission(int, char) - Method in class org.gersteinlab.tyna.webapp.security.SecurityController
Check if the current user has the right to access a network.
checkNode(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
Check if a node is non null and is in the graph.
clear() - Static method in class org.gersteinlab.tyna.core.util.IntegerPool
Remove all the integers from the pool.
close() - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Close the connection.
CLUS_COEFS - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
columnNames - Variable in class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
 
commit() - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Commit the current transaction.
commutative() - Method in interface org.gersteinlab.tyna.core.operators.BinaryOperator
Whether the operator is commutative, i.e., whether a op b equals b op a.
commutative() - Method in class org.gersteinlab.tyna.core.operators.Difference
 
commutative() - Method in class org.gersteinlab.tyna.core.operators.Intersection
 
commutative() - Method in class org.gersteinlab.tyna.core.operators.Union
 
compareTo(Object) - Method in class org.gersteinlab.tyna.core.graph.Node
 
compareTo(Object) - Method in class org.gersteinlab.tyna.core.util.NodePair
 
CompleteTwoLayerMotifMiner - Class in org.gersteinlab.tyna.core.operators
This class defines the complete two layer motif miner.
CompleteTwoLayerMotifMiner(String, int, int, int) - Constructor for class org.gersteinlab.tyna.core.operators.CompleteTwoLayerMotifMiner
Create a new complete two layer motif miner.
computeLocalBetweenness(AbstractGraph.BetweennessNode) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
Config - Class in org.gersteinlab.tyna.webapp.config
This class provides methods for accessing the configuration settings stored in the default property file.
config - Static variable in class org.gersteinlab.tyna.webapp.config.Config
The singleton object.
ConfigException - Exception in org.gersteinlab.tyna.webapp.config
This class represents an exception due to a configuration problem.
ConfigException() - Constructor for exception org.gersteinlab.tyna.webapp.config.ConfigException
Default constructor: create a new object without an error message.
ConfigException(String) - Constructor for exception org.gersteinlab.tyna.webapp.config.ConfigException
Create a new object with an error message.
ConfigException(Throwable) - Constructor for exception org.gersteinlab.tyna.webapp.config.ConfigException
Create a new object with the cause of this exception.
ConfigException(String, Throwable) - Constructor for exception org.gersteinlab.tyna.webapp.config.ConfigException
Create a new object with an error message and the cause of this exception.
configFile - Static variable in class org.gersteinlab.tyna.webapp.config.Config
Name of the configuration file.
conn - Variable in class org.gersteinlab.tyna.webapp.data.RDBDataStore
The database connection.
containsEdge(Node, Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
containsEdge(Node, Node) - Method in interface org.gersteinlab.tyna.core.graph.Graph
Whether there is an edge between the two nodes.
containsNode(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
containsNode(Node) - Method in interface org.gersteinlab.tyna.core.graph.Graph
Whether a given node is in the graph.
context - Variable in class org.gersteinlab.tyna.webapp.data.FileDataStore
The servlet context
count - Variable in class org.gersteinlab.tyna.core.util.SimpleStats
Number of the values.
created - Variable in class org.gersteinlab.tyna.webapp.data.Category
Time of category creation.
created - Variable in class org.gersteinlab.tyna.webapp.data.Network
Time of network creation.
createNetwork(String, String) - Static method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
ImportGraphFileAction
createOutputGraph(Graph, Graph, Set, Map) - Static method in class org.gersteinlab.tyna.core.operators.MotifMiner
 
createRootGraphFromInteractionData(boolean) - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
creation - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphEdgeIterator
The creation time of the iterator.
creatorId - Variable in class org.gersteinlab.tyna.webapp.data.Category
ID of the category creator.
creatorId - Variable in class org.gersteinlab.tyna.webapp.data.Network
ID of the network creator.
creatorName - Variable in class org.gersteinlab.tyna.webapp.data.Category
Name of the category creator.
creatorName - Variable in class org.gersteinlab.tyna.webapp.data.Network
Name of the network creator.
CSVIO - Class in org.gersteinlab.tyna.core.io
This class represents the IO unit for a simple comma-delimited format that assumes a directed or undirected, simple or multi graph with no edge attributes.
CSVIO() - Constructor for class org.gersteinlab.tyna.core.io.CSVIO
 
currEdge - Variable in class org.gersteinlab.tyna.core.graph.AbstractMultiGraph.AbstractMultiGraphEdgeIterator
The current edge.
currNode1 - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphEdgeIterator
The current node 1.
currNode2 - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphEdgeIterator
The current node 2.
CycleMotifMiner - Class in org.gersteinlab.tyna.core.operators
This class defines the cycle motif miner.
CycleMotifMiner(String, int, int) - Constructor for class org.gersteinlab.tyna.core.operators.CycleMotifMiner
Create a new cycle motif miner.

D

DefectiveCliqueMotifMiner - Class in org.gersteinlab.tyna.core.operators
This class defines the defective clique motif miner.
DefectiveCliqueMotifMiner(String, int, int) - Constructor for class org.gersteinlab.tyna.core.operators.DefectiveCliqueMotifMiner
Create a new complete two layer motif miner.
DEGREES - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
deleteCategory(int) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Delete a category from the database.
deleteCategoryFile(int) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Delete a cateogry file.
deleteNetwork(int) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Delete a network from the database.
deleteNetworkByUser(int) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Delete a network from the database based on the current user's privilege.
deleteNetworkFile(int) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Delete a network file.
description - Variable in class org.gersteinlab.tyna.webapp.data.Category
Category description.
description - Variable in class org.gersteinlab.tyna.webapp.data.Network
Network description.
description - Variable in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Network format description.
destroy() - Method in class org.gersteinlab.tyna.webapp.util.HouseKeeper
 
Difference - Class in org.gersteinlab.tyna.core.operators
This class defines the set difference binary operator.
Difference() - Constructor for class org.gersteinlab.tyna.core.operators.Difference
 
directedCheckBox - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
DirectedGraph - Interface in org.gersteinlab.tyna.core.graph
This interface declares that each implemented class is a directed graph.
DirectedMultiGraph - Class in org.gersteinlab.tyna.core.graph
This class represents a directed multigraph.
DirectedMultiGraph() - Constructor for class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
Default constructor: creates an empty graph.
DirectedMultiGraph(Graph) - Constructor for class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
DirectedMultiGraph.DirectedMultiGraphEdgeIterator - Class in org.gersteinlab.tyna.core.graph
 
DirectedMultiGraph.DirectedMultiGraphEdgeIterator() - Constructor for class org.gersteinlab.tyna.core.graph.DirectedMultiGraph.DirectedMultiGraphEdgeIterator
Constructor: initialize the iteration state.
DirectedSimpleGraph - Class in org.gersteinlab.tyna.core.graph
This class represents a directed simple graph.
DirectedSimpleGraph() - Constructor for class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
Default constructor: creates an empty graph.
DirectedSimpleGraph(Graph) - Constructor for class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
DirectedSimpleGraph.DirectedSimpleGraphEdgeIterator - Class in org.gersteinlab.tyna.core.graph
 
DirectedSimpleGraph.DirectedSimpleGraphEdgeIterator() - Constructor for class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph.DirectedSimpleGraphEdgeIterator
Constructor: initialize the iteration state.
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.gersteinlab.tyna.webapp.util.FileDownload
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.gersteinlab.tyna.webapp.util.HouseKeeper
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.gersteinlab.tyna.webapp.util.FileDownload
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.gersteinlab.tyna.webapp.util.HouseKeeper
 
downloadItem - Variable in class org.gersteinlab.tyna.cytoscape.TYNAPlugin
 
downloadNetwork(String, String, int, int) - Method in interface org.gersteinlab.tyna.webservice.TYNA
Download a network from the tYNA database.
downloadNetwork(String, String, int, int) - Method in class org.gersteinlab.tyna.webservice.TYNASoapBindingImpl
 
downloadWin - Variable in class org.gersteinlab.tyna.cytoscape.TYNAPlugin
 

E

ECCENTRICITIES - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
Edge - Class in org.gersteinlab.tyna.core.graph
This class represents an edge in a graph.
Edge(Node, Node, double, Map) - Constructor for class org.gersteinlab.tyna.core.graph.Edge
Constructor: creates an edge between the two nodes, with the input attributes.
edgeCount - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph
The number of edges in the graph.
EdgeIterator - Interface in org.gersteinlab.tyna.core.graph
This interface declares that each implemented class is an iterator of a set of edges of a graph.
edges - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph
The edges of the graph.
edges12Iter - Variable in class org.gersteinlab.tyna.core.graph.AbstractMultiGraph.AbstractMultiGraphEdgeIterator
An iterator for edges between node 1 and node 2.
email - Variable in class org.gersteinlab.tyna.webapp.data.User
Email.
EQ - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
equals(Object) - Method in class org.gersteinlab.tyna.core.graph.Node
 
equals(Object) - Method in class org.gersteinlab.tyna.core.util.NodePair
 
EXACT - Static variable in class org.gersteinlab.tyna.core.operators.NodeIdFilter
 
existChain(Node[]) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph.DuplicateTree
 
existUser(String) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Check if a user name is already in use.

F

FeedforwardLoopMotifMiner - Class in org.gersteinlab.tyna.core.operators
This class defines the feedforward loop motif miner.
FeedforwardLoopMotifMiner(String, int, int) - Constructor for class org.gersteinlab.tyna.core.operators.FeedforwardLoopMotifMiner
Create a new feedforward loop motif miner.
FileDataStore - Class in org.gersteinlab.tyna.webapp.data
This class is the agent for accessing data files.
FileDataStore(ServletContext, HttpSession) - Constructor for class org.gersteinlab.tyna.webapp.data.FileDataStore
Default constructor.
FileDownload - Class in org.gersteinlab.tyna.webapp.util
This class is a servlet for downloading files.
FileDownload() - Constructor for class org.gersteinlab.tyna.webapp.util.FileDownload
 
filterName - Variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
The name of the filtering statistic
filterOp - Variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
The filtering operator
filterType - Variable in class org.gersteinlab.tyna.core.operators.NodeIdFilter
The filtering type
filterUnit - Variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
The filtering unit
filterValue - Variable in class org.gersteinlab.tyna.core.operators.NodeIdFilter
The filtering value
filterValue - Variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
The filtering value
finalize() - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Free unfreed resources.
formatId - Variable in class org.gersteinlab.tyna.webapp.data.Network
Id of network format.
formatName - Variable in class org.gersteinlab.tyna.webapp.data.Network
Name of network format.

G

GEQ - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
get(int) - Static method in class org.gersteinlab.tyna.core.util.IntegerPool
Get a pooled integer object.
getAdjacencyMatrix(List) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getAdjacencyMatrix(List) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the adjacency matrix of a subgraph according to a given node order.
getAllInteractions() - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
getAllUnweightedShortestPaths(Node, Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getAllUnweightedShortestPaths(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getAllUnweightedShortestPaths() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getAllUnweightedShortestPaths(Node, Node) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get all unweighted shortest paths from node1 to node2.
getAllUnweightedShortestPaths(Node) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get all unweighted shortest paths from a given node to every node.
getAllUnweightedShortestPaths() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get all unweighted shortest paths from every node to every node.
getAttr(Object) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getAttr(Object) - Method in class org.gersteinlab.tyna.core.graph.Edge
Get the (possibly null) value of an attribute of the edge.
getAttr(Object) - Method in interface org.gersteinlab.tyna.core.graph.Graph
Get the (possibly null) value of an attribute of the graph.
getAttr(Object) - Method in class org.gersteinlab.tyna.core.graph.Node
Get the (possibly null) value of an attribute of the node.
getAttribute(String) - Method in class org.gersteinlab.tyna.webapp.security.SecurityController
Get the value of an attribute from session.
getAttrs() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getAttrs() - Method in class org.gersteinlab.tyna.core.graph.Edge
Get the (possibly null) attribute map of the node.
getAttrs() - Method in interface org.gersteinlab.tyna.core.graph.Graph
Get the (possibly null) attribute map of the graph.
getAttrs() - Method in class org.gersteinlab.tyna.core.graph.Node
Get the (possibly null) attribute map of the node.
getBetweenness(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getBetweenness(Node) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the betweenness of a node n, which is defined as the number of node pairs (n1, n2) where the shortest path from n1 to n2 passes through n, with the following two requirements: .
getBetweennesses() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
A simple algorithm that involves two phases: a minimum spanning graph constructing phase and a depth-first computation phase.
getBetweennesses() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the betweenness of all nodes in the graph.
getCategory(int) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Get a category.
getCategoryFile(int) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get a File object of a category.
getCategoryInputStream(int) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get an input stream of a category.
getCategoryNames() - Method in class org.gersteinlab.tyna.webapp.data.CategoryInfo
Get an array of all the category names.
getCategoryReader(int) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get a reader of a category.
getClusCoef(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getClusCoef(Node) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the clustering coefficient of a node n, which is defined as follows: let E(n) be the set of nodes n'<>n such that (n, n1) is in the set of all edges of the graph, E.
getClusCoefs() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getClusCoefs() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the clustering coefficients of all nodes in the graph.
getConnectedComponentCount() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getConnectedComponentCount() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the number of connected components in the graph.
getConnectedComponents() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getConnectedComponents() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the connected components of the graph.
getCount() - Method in class org.gersteinlab.tyna.core.util.SimpleStats
Get the number of values added.
getCount() - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
getCreated() - Method in class org.gersteinlab.tyna.webapp.data.Category
Get the time of category creation.
getCreated() - Method in class org.gersteinlab.tyna.webapp.data.Network
Get the time of network creation.
getCreatorId() - Method in class org.gersteinlab.tyna.webapp.data.Category
Get the ID of the category creator.
getCreatorId() - Method in class org.gersteinlab.tyna.webapp.data.Network
Get the ID of the network creator.
getCreatorName() - Method in class org.gersteinlab.tyna.webapp.data.Category
Get the name of the category creator.
getCreatorName() - Method in class org.gersteinlab.tyna.webapp.data.Network
Get the name of the network creator.
getCycles(int, int) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getCycles(int, int, LinkedHashSet, Node, Set, List) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getCycles(int, int) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get all cycles of distinct nodes that .
getDefectiveCliquesMissingEdges(int, int) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getDefectiveCliquesMissingEdges(int, int) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedUndirectedGraph
Get the missing edges in defective cliques formed by two cliques with .
getDefectiveCliquesMissingEdges(int, int) - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getDefectiveCliquesMissingEdges(int, int) - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getDegree(Node) - Method in interface org.gersteinlab.tyna.core.graph.UndirectedGraph
Get the degree of a node.
getDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getDegrees() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getDegrees() - Method in interface org.gersteinlab.tyna.core.graph.UndirectedGraph
Get the degrees of all nodes in the graph.
getDegrees() - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getDegrees() - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getDescription() - Method in class org.gersteinlab.tyna.webapp.data.Category
Get the category description.
getDescription() - Method in class org.gersteinlab.tyna.webapp.data.Network
Get the network description.
getDescription() - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Get the network format description.
getDiffusionDistanceMatrix(double, List) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getDiffusionDistanceMatrix(double, int[][]) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getDiffusionDistanceMatrix(double, List) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedUndirectedGraph
Get the diffusion distance matrix of a subgraph according to a given node order.
getDiffusionDistanceMatrix(double, int[][]) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedUndirectedGraph
Get the diffusion distance matrix of a subgraph according to a given Laplacian matrix.
getDiffusionDistanceMatrix(double, List) - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getDiffusionDistanceMatrix(double, int[][]) - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getDiffusionDistanceMatrix(double, List) - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getDiffusionDistanceMatrix(double, int[][]) - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getEccentricities() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getEccentricities() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the eccentricities of all nodes in the graph.
getEccentricity(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getEccentricity(Node) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the eccentricity of a node n, which is deinfed as follows: A maximum shortest path of node n is a shortest path from n to a node reachable from it that has the largest length among all shortest paths from n to its reachable nodes.
getEdgeAttributes() - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
getEdgeBetweennesses() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
A simple algorithm that involves two phases: a minimum spanning graph constructing phase and a depth-first computation phase.
getEdgeBetweennesses() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the betweenness of all edges in the graph.
getEdgeCount() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getEdgeCount() - Method in interface org.gersteinlab.tyna.core.graph.Graph
Get the number of edges in the graph.
getEdgeIndicesArray() - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
getEdgeIterator() - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getEdgeIterator() - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getEdgeIterator() - Method in interface org.gersteinlab.tyna.core.graph.Graph
Return an iterator of the edges in the graph.
getEdgeIterator() - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getEdgeIterator() - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getEdgeNodePairs() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getEdgeNodePairs() - Method in interface org.gersteinlab.tyna.core.graph.Graph
Return a list of unique node pairs between which there is an edge from the first node to the second node.
getEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getEdges(Node) - Method in interface org.gersteinlab.tyna.core.graph.UndirectedGraph
Get the edges incident on a node.
getEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getEmail() - Method in class org.gersteinlab.tyna.webapp.data.User
Get the email.
getFeedforwardLoops(int, int) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getFeedforwardLoops(int, int, LinkedHashSet, Node, List) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getFeedforwardLoops(int, int) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedDirectedGraph
Get all chains of distinct nodes that .
getFeedforwardLoops(int, int) - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getFeedforwardLoops(int, int) - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getFormatId() - Method in class org.gersteinlab.tyna.webapp.data.Network
Get the ID of the network format.
getFormatName() - Method in class org.gersteinlab.tyna.webapp.data.Network
Get the name of the network format.
getId() - Method in class org.gersteinlab.tyna.core.graph.Node
Get the ID of the node.
getId() - Method in class org.gersteinlab.tyna.webapp.data.Category
Get the category ID.
getId() - Method in class org.gersteinlab.tyna.webapp.data.Network
Get the network ID.
getId() - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Get the network format ID.
getId() - Method in class org.gersteinlab.tyna.webapp.data.NetworkType
Get the network type ID.
getId() - Method in class org.gersteinlab.tyna.webapp.data.User
Get the user ID.
getInDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getInDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractMultiGraph
 
getInDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph
 
getInDegree(Node) - Method in interface org.gersteinlab.tyna.core.graph.DirectedGraph
Get the in-degree of a node.
getInDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getInDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getInDegrees() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getInDegrees() - Method in interface org.gersteinlab.tyna.core.graph.DirectedGraph
Get the in-degrees of all nodes in the graph.
getInDegrees() - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getInDegrees() - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getInEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getInEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractMultiGraph
 
getInEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph
 
getInEdges(Node) - Method in interface org.gersteinlab.tyna.core.graph.DirectedGraph
Get the in-edges of a node.
getInEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getInEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getInNeighbors(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getInNeighbors(Node) - Method in interface org.gersteinlab.tyna.core.graph.DirectedGraph
Get the in-neighbors of a node.
getInNeighbors(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getInNeighbors(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getInstitution() - Method in class org.gersteinlab.tyna.webapp.data.User
Get the institution.
getIsDirected() - Method in class org.gersteinlab.tyna.webapp.data.Network
Check if the network is directed.
getIsMultigraph() - Method in class org.gersteinlab.tyna.webapp.data.Network
Check if the network is a multigraph.
getIsPublic() - Method in class org.gersteinlab.tyna.webapp.data.Category
Check if the category is public.
getIsPublic() - Method in class org.gersteinlab.tyna.webapp.data.Network
Check if the network is public.
getLaplacianMatrix(List) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getLaplacianMatrix(int[][]) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getLaplacianMatrix(List) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedUndirectedGraph
Get the Laplacian matrix of a subgraph according to a given node order.
getLaplacianMatrix(int[][]) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedUndirectedGraph
Get the Laplacian matrix of a subgraph according to a given adjacency matrix.
getLaplacianMatrix(List) - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getLaplacianMatrix(int[][]) - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getLaplacianMatrix(List) - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getLaplacianMatrix(int[][]) - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getLeaf(Node[], int, int, boolean) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph.HeadTailTree
 
getMax() - Method in class org.gersteinlab.tyna.core.util.SimpleStats
Get the maximum of the values.
getMaximalChains(int, int) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getMaximalChains(int, int) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get all chains of distinct nodes that .
getMaximalCliques() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getMaximalCliques() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedUndirectedGraph
Get all maximal cliques
getMaximalCliques() - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getMaximalCliques() - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getMaximalCompleteTwoLayerSubgraphs(int, int, int) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getMaximalCompleteTwoLayerSubgraphs(int, int, int) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedDirectedGraph
Get all maximal motifs that contain two layers of nodes such that .
getMaximalCompleteTwoLayerSubgraphs(int, int, int) - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getMaximalCompleteTwoLayerSubgraphs(int, int, int) - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getMaximalIndependentSets() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getMaximalIndependentSets() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedUndirectedGraph
Get all maximal independent sets
getMaximalIndependentSets() - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getMaximalIndependentSets() - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getMean() - Method in class org.gersteinlab.tyna.core.util.SimpleStats
Get the mean of the values.
getMin() - Method in class org.gersteinlab.tyna.core.util.SimpleStats
Get the minimum of the values.
getMinimalChains(int) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getMinimalChains(int) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get all chains of distinct nodes that .
getName() - Method in class org.gersteinlab.tyna.webapp.data.Category
Get the category name.
getName() - Method in class org.gersteinlab.tyna.webapp.data.Network
Get the network name.
getName() - Method in class org.gersteinlab.tyna.webapp.data.NetworkAttr
Get the network attribute name.
getName() - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Get the network format name.
getName() - Method in class org.gersteinlab.tyna.webapp.data.NetworkType
Get the network type name.
getName() - Method in class org.gersteinlab.tyna.webapp.data.User
Get the login name.
getNeighbors(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getNeighbors(Node) - Method in interface org.gersteinlab.tyna.core.graph.UndirectedGraph
Get the neighbors of a node.
getNeighbors(Node) - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
getNeighbors(Node) - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
getNetwork(int) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Get a network.
getNetworkFile(int) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get a File object of a network.
getNetworkFormat(int) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Get a network format.
getNetworkId() - Method in class org.gersteinlab.tyna.webapp.data.NetworkAttr
Get the network ID.
getNetworkInputStream(int) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get an input stream of a network.
getNetworkName() - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
getNetworkReader(int) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get a reader of a network.
getNode(Object) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getNode(Object) - Method in interface org.gersteinlab.tyna.core.graph.Graph
Get the node that has the input node ID.
getNode1() - Method in class org.gersteinlab.tyna.core.graph.Edge
Get the first node of the edge.
getNode1() - Method in class org.gersteinlab.tyna.core.util.NodePair
 
getNode2() - Method in class org.gersteinlab.tyna.core.graph.Edge
Get the second node of the edge.
getNode2() - Method in class org.gersteinlab.tyna.core.util.NodePair
 
getNodeAttributes() - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
getNodeCount() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getNodeCount() - Method in interface org.gersteinlab.tyna.core.graph.Graph
Get the number of nodes in the graph.
getNodeCount(String) - Method in class org.gersteinlab.tyna.webapp.data.CategoryInfo
Get the number of nodes of a category.
getNodeIndicesArray() - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
getNodeIterator() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getNodeIterator() - Method in interface org.gersteinlab.tyna.core.graph.Graph
Return an iterator of the nodes in the graph.
getNodeIterator(String) - Method in class org.gersteinlab.tyna.webapp.data.CategoryInfo
Get an iterator of the nodes of a category.
getOutDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getOutDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractMultiGraph
 
getOutDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph
 
getOutDegree(Node) - Method in interface org.gersteinlab.tyna.core.graph.DirectedGraph
Get the out-degree of a node.
getOutDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getOutDegree(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getOutDegrees() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getOutDegrees() - Method in interface org.gersteinlab.tyna.core.graph.DirectedGraph
Get the out-degrees of all nodes in the graph.
getOutDegrees() - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getOutDegrees() - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getOutEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getOutEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractMultiGraph
 
getOutEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph
 
getOutEdges(Node) - Method in interface org.gersteinlab.tyna.core.graph.DirectedGraph
Get the out-edges of a node.
getOutEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getOutEdges(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getOutNeighbors(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getOutNeighbors(Node) - Method in interface org.gersteinlab.tyna.core.graph.DirectedGraph
Get the out-neighbors of a node.
getOutNeighbors(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph
 
getOutNeighbors(Node) - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph
 
getReaderClass() - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Get the reader class that reads data of this format.
getRootGraph() - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
getServletContext() - Method in class org.gersteinlab.tyna.webservice.TYNASoapBindingImpl
Get the servlet context for the operations.
getSession(String, String) - Method in class org.gersteinlab.tyna.webservice.TYNASoapBindingImpl
Get the servlet session for the operations, and login if username is not null.
getStdDev() - Method in class org.gersteinlab.tyna.core.util.SimpleStats
Get the standard deviation of the values.
getSuffix() - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Get the network format file suffix.
getTempFile(long, String) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get a File object of an existing temporary file.
getTempFileId(String) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get the file ID of a new temporary file.
getTempFileInputStream(long, String) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get an input stream of a temporarily stored file.
getTempFileOutputStream(long, String) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get an output stream of a temporarily stored file.
getTempFileReader(long, String) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get a reader of a temporarily stored file.
getTempFileWriter(long, String) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Get a writer of a temporarily stored file.
getType() - Method in class org.gersteinlab.tyna.webapp.data.Network
Get the network type.
getUnweightedShortestPath(Node, Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getUnweightedShortestPath(Node, Node) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get an unweighted shortest path from node1 to node2.
getUnweightedShortestPathLength(Node, Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getUnweightedShortestPathLength(Node, Node) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the unweighted shortest path length from node1 to node2.
getUnweightedShortestPathLengths(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getUnweightedShortestPathLengths() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getUnweightedShortestPathLengths(Node) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the unweighted shortest path lengths from every node to every node.
getUnweightedShortestPathLengths() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get the unweighted shortest path lengths from every node to every node.
getUnweightedShortestPaths(Node, Node, boolean) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getUnweightedShortestPaths(Node) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getUnweightedShortestPaths(Node, boolean) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getUnweightedShortestPaths() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
getUnweightedShortestPaths(Node) - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get an unweighted shortest path from a given node to every node.
getUnweightedShortestPaths() - Method in interface org.gersteinlab.tyna.core.graph.AdvancedGraph
Get an unweighted shortest path from every node to every node.
getUser(String, String) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Get the information of a user, based on the login name and password of the user.
getUser() - Method in class org.gersteinlab.tyna.webapp.security.SecurityController
Get the information of the current user.
getValue() - Method in class org.gersteinlab.tyna.webapp.data.NetworkAttr
Get the network attribute value.
getVariance() - Method in class org.gersteinlab.tyna.core.util.SimpleStats
Get the variance of the values.
getWeight() - Method in class org.gersteinlab.tyna.core.graph.Edge
Get the edge weight.
getWriterClass() - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Get the writer class that reads data of this format.
Graph - Interface in org.gersteinlab.tyna.core.graph
This interface declares that each implemented class is a graph.
GraphReader - Interface in org.gersteinlab.tyna.core.io
This interface declares that each implemented class is a graph reader that creates a graph from an input stream or a reader.
GraphTypeException - Exception in org.gersteinlab.tyna.core.graph
This class represents an exception due to incorrect graph type.
GraphTypeException() - Constructor for exception org.gersteinlab.tyna.core.graph.GraphTypeException
Default constructor: create a new object without an error message.
GraphTypeException(String) - Constructor for exception org.gersteinlab.tyna.core.graph.GraphTypeException
Create a new object with an error message.
GraphTypeException(Throwable) - Constructor for exception org.gersteinlab.tyna.core.graph.GraphTypeException
Create a new object with the cause of this exception.
GraphTypeException(String, Throwable) - Constructor for exception org.gersteinlab.tyna.core.graph.GraphTypeException
Create a new object with an error message and the cause of this exception.
GraphWriter - Interface in org.gersteinlab.tyna.core.io
This interface declares that each implemented class is a graph writer that outputs a graph to an output stream or a writer.
GT - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 

H

hashCode() - Method in class org.gersteinlab.tyna.core.graph.Node
 
hashCode() - Method in class org.gersteinlab.tyna.core.util.NodePair
 
hasNext - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphEdgeIterator
Whether there are more edges to be iterated.
hasNext() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphEdgeIterator
 
hasNext() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphNodeIterator
 
hasNext() - Method in interface org.gersteinlab.tyna.core.graph.EdgeIterator
Check whether there are still edges to be iterated.
hasNext() - Method in interface org.gersteinlab.tyna.core.graph.NodeIterator
Check whether there are still nodes to be iterated.
hasNext() - Method in class org.gersteinlab.tyna.webapp.data.CategoryInfo.CategoryInfoNodeIterator
 
HouseKeeper - Class in org.gersteinlab.tyna.webapp.util
This class performs the housekeeping job for the web application.
HouseKeeper() - Constructor for class org.gersteinlab.tyna.webapp.util.HouseKeeper
 

I

id - Variable in class org.gersteinlab.tyna.core.graph.Node
The ID of the node.
id - Variable in class org.gersteinlab.tyna.webapp.data.Category
Category ID.
id - Variable in class org.gersteinlab.tyna.webapp.data.Network
Network ID.
id - Variable in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Network format ID.
id - Variable in class org.gersteinlab.tyna.webapp.data.NetworkType
Network type ID.
id - Variable in class org.gersteinlab.tyna.webapp.data.User
User ID.
IN_DEGREES - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
includeNeighbors - Variable in class org.gersteinlab.tyna.core.operators.NodeIdFilter
Whether to include the neighbors of the nodes that pass the requirements
includeNeighbors - Variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
Whether to include the neighbors of the nodes that pass the requirements
init(ServletConfig) - Method in class org.gersteinlab.tyna.webapp.util.HouseKeeper
 
InputFormatException - Exception in org.gersteinlab.tyna.core.io
This class represents an exception due to invalid input file format.
InputFormatException() - Constructor for exception org.gersteinlab.tyna.core.io.InputFormatException
Default constructor: create a new object without an error message.
InputFormatException(String) - Constructor for exception org.gersteinlab.tyna.core.io.InputFormatException
Create a new object with an error message.
InputFormatException(Throwable) - Constructor for exception org.gersteinlab.tyna.core.io.InputFormatException
Create a new object with the cause of this exception.
InputFormatException(String, Throwable) - Constructor for exception org.gersteinlab.tyna.core.io.InputFormatException
Create a new object with an error message and the cause of this exception.
insertCategory(Category) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Insert a new category into the database.
insertNetwork(Network) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Insert a new network into the database.
insertNetworkAttr(NetworkAttr) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Insert a new network attribute into the database.
insertUser(User, String) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Insert a new user into the database.
institution - Variable in class org.gersteinlab.tyna.webapp.data.User
Institution.
IntegerPool - Class in org.gersteinlab.tyna.core.util
This class represents a pool of integer objects for reuse.
IntegerPool() - Constructor for class org.gersteinlab.tyna.core.util.IntegerPool
 
INTEGRATED - Static variable in class org.gersteinlab.tyna.core.operators.MotifMiner
 
InteractionsReader2 - Class in org.gersteinlab.tyna.cytoscape
 
InteractionsReader2(BioDataServer, String, String) - Constructor for class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
InteractionsSerializer2 - Class in org.gersteinlab.tyna.cytoscape
 
InteractionsSerializer2() - Constructor for class org.gersteinlab.tyna.cytoscape.InteractionsSerializer2
 
Intersection - Class in org.gersteinlab.tyna.core.operators
This class defines the intersection binary operator.
Intersection() - Constructor for class org.gersteinlab.tyna.core.operators.Intersection
 
isDirected - Variable in class org.gersteinlab.tyna.webapp.data.Network
Is the network directed.
isMultigraph - Variable in class org.gersteinlab.tyna.webapp.data.Network
Is the network a multigraph.
isPublic - Variable in class org.gersteinlab.tyna.webapp.data.Category
Is the category public.
isPublic - Variable in class org.gersteinlab.tyna.webapp.data.Network
Is the network public.
iter - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphNodeIterator
An iterator of the nodes.
iter - Variable in class org.gersteinlab.tyna.webapp.data.CategoryInfo.CategoryInfoNodeIterator
An iterator of the nodes.
iteratedNodes - Variable in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph.UndirectedMultiGraphEdgeIterator
 
iteratedNodes - Variable in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph.UndirectedSimpleGraphEdgeIterator
The nodes being iterated.

K

k - Variable in class org.gersteinlab.tyna.core.operators.DefectiveCliqueMotifMiner
The minimum size of the overlapped clique

L

l - Variable in class org.gersteinlab.tyna.core.operators.DefectiveCliqueMotifMiner
The maximum number of nodes not in the overlapping clique
lastModified - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph
The last modified time of the graph.
layout(GraphView) - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
leftPad(String, int, char) - Static method in class org.gersteinlab.tyna.webapp.util.TextUtil
Left-pad a string to a certain length by a character.
LEQ - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
listButton - Variable in class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
 
listCategories(String, String, String) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
List categories.
listNetworkAttrs(int, String) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
List network attributes of a network type.
listNetworkFormats() - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
List network formats.
listNetworkFormats() - Method in interface org.gersteinlab.tyna.webservice.TYNA
List the network formats supported by tYNA.
listNetworkFormats() - Method in class org.gersteinlab.tyna.webservice.TYNASoapBindingImpl
 
listNetworks(String, String, String, String, String, String) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
List networks.
listNetworks(String, String, String) - Method in interface org.gersteinlab.tyna.webservice.TYNA
List the metadata of the networks in the tYNA database.
listNetworks(String, String, String) - Method in class org.gersteinlab.tyna.webservice.TYNASoapBindingImpl
 
listNetworkTypes(String) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
List network types.
listNetworkTypes() - Method in interface org.gersteinlab.tyna.webservice.TYNA
List the network types supported by tYNA.
listNetworkTypes() - Method in class org.gersteinlab.tyna.webservice.TYNASoapBindingImpl
 
listTypeBox - Variable in class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
 
loadButton - Variable in class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
 
login(String, String) - Method in class org.gersteinlab.tyna.webapp.security.SecurityController
Login.
loginCheckBox - Variable in class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
 
loginCheckBox - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
logout() - Method in class org.gersteinlab.tyna.webapp.security.SecurityController
Logout.
LT - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 

M

map1 - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphEdgeIterator
The map of edges of node 1.
markModified() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
Mark the current object as modified.
max - Variable in class org.gersteinlab.tyna.core.util.SimpleStats
Maximum of the values.
MAXIMAL - Static variable in class org.gersteinlab.tyna.core.operators.MotifMiner
 
maxSize - Variable in class org.gersteinlab.tyna.core.operators.ChainMotifMiner
The maximum size
maxSize - Variable in class org.gersteinlab.tyna.core.operators.CycleMotifMiner
The maximum size
maxSize - Variable in class org.gersteinlab.tyna.core.operators.FeedforwardLoopMotifMiner
The maximum size
maxSize1 - Variable in class org.gersteinlab.tyna.core.operators.CompleteTwoLayerMotifMiner
The maximum size of the first layer
min - Variable in class org.gersteinlab.tyna.core.util.SimpleStats
Minimum of the values.
MINIMAL - Static variable in class org.gersteinlab.tyna.core.operators.MotifMiner
 
minSize - Variable in class org.gersteinlab.tyna.core.operators.ChainMotifMiner
The minimum size
minSize - Variable in class org.gersteinlab.tyna.core.operators.CycleMotifMiner
The minimum size
minSize - Variable in class org.gersteinlab.tyna.core.operators.FeedforwardLoopMotifMiner
The minimum size
minSize1 - Variable in class org.gersteinlab.tyna.core.operators.CompleteTwoLayerMotifMiner
The minimum size of the first layer
minSize2 - Variable in class org.gersteinlab.tyna.core.operators.CompleteTwoLayerMotifMiner
The minimum size of the second layer
MotifMiner - Class in org.gersteinlab.tyna.core.operators
This class defines the parent class of motif miners for, which are unary graph operators.
MotifMiner() - Constructor for class org.gersteinlab.tyna.core.operators.MotifMiner
 
motifType - Variable in class org.gersteinlab.tyna.core.operators.ChainMotifMiner
The motif type
MultiGraph - Interface in org.gersteinlab.tyna.core.graph
This interface declares that each implemented class is a graph that may contain multiple edges between a pair of nodes, and may contain self loops.
multigraphCheckBox - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
MutableDouble - Class in org.gersteinlab.tyna.core.util
This class represents a double of which the content can be changed.
MutableDouble(double) - Constructor for class org.gersteinlab.tyna.core.util.MutableDouble
 
MutableInteger - Class in org.gersteinlab.tyna.core.util
This class represents an integer of which the content can be changed.
MutableInteger(int) - Constructor for class org.gersteinlab.tyna.core.util.MutableInteger
 

N

name - Variable in class org.gersteinlab.tyna.webapp.data.Category
Category name.
name - Variable in class org.gersteinlab.tyna.webapp.data.Network
Network name.
name - Variable in class org.gersteinlab.tyna.webapp.data.NetworkAttr
Network attribute name.
name - Variable in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Network format name.
name - Variable in class org.gersteinlab.tyna.webapp.data.NetworkType
Network type name.
name - Variable in class org.gersteinlab.tyna.webapp.data.User
Login name.
Network - Class in org.gersteinlab.tyna.webapp.data
This class contains the information of a network.
Network() - Constructor for class org.gersteinlab.tyna.webapp.data.Network
Default constructor: creates an empty object.
Network(Integer, String, String, Integer, String, Boolean, Boolean, Integer, String, Timestamp, Boolean, Integer) - Constructor for class org.gersteinlab.tyna.webapp.data.Network
Creates a new object that stores the supplied information.
NetworkAttr - Class in org.gersteinlab.tyna.webapp.data
This class contains the information of a network attribute name and value pair.
NetworkAttr() - Constructor for class org.gersteinlab.tyna.webapp.data.NetworkAttr
Default constructor: creates an empty object.
NetworkAttr(String, String, Integer) - Constructor for class org.gersteinlab.tyna.webapp.data.NetworkAttr
Creates a new object that stores the supplied information.
networkDescArea - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
networkDir - Variable in class org.gersteinlab.tyna.webapp.data.FileDataStore
The directory to store networks
NetworkFormat - Class in org.gersteinlab.tyna.webapp.data
This class contains the information of a network format.
NetworkFormat() - Constructor for class org.gersteinlab.tyna.webapp.data.NetworkFormat
Default constructor: creates an empty object.
NetworkFormat(Integer, String, String, String, String, String) - Constructor for class org.gersteinlab.tyna.webapp.data.NetworkFormat
Creates a new object that stores the supplied information.
networkId - Variable in class org.gersteinlab.tyna.webapp.data.NetworkAttr
Network ID.
networkNameField - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
networks - Variable in class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
 
networksTable - Variable in class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
 
NetworkType - Class in org.gersteinlab.tyna.webapp.data
This class contains the information of a network type.
NetworkType() - Constructor for class org.gersteinlab.tyna.webapp.data.NetworkType
Default constructor: creates an empty object.
NetworkType(Integer, String) - Constructor for class org.gersteinlab.tyna.webapp.data.NetworkType
Creates a new object that stores the supplied information.
networkTypeBox - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
newInstance() - Static method in class org.gersteinlab.tyna.webapp.config.Config
Get an instance of the class.
next() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphNodeIterator
 
next() - Method in class org.gersteinlab.tyna.core.graph.AbstractMultiGraph.AbstractMultiGraphEdgeIterator
 
next() - Method in class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph.AbstractSimpleGraphEdgeIterator
 
next() - Method in interface org.gersteinlab.tyna.core.graph.EdgeIterator
Get the next edge of the graph.
next() - Method in interface org.gersteinlab.tyna.core.graph.NodeIterator
Get the next node of the graph.
next() - Method in class org.gersteinlab.tyna.webapp.data.CategoryInfo.CategoryInfoNodeIterator
 
Node - Class in org.gersteinlab.tyna.core.graph
This class represents a node in a graph.
Node() - Constructor for class org.gersteinlab.tyna.core.graph.Node
Default constructor: creates a node with no ID or attributes.
Node(Object, Map) - Constructor for class org.gersteinlab.tyna.core.graph.Node
Constructor: creates a node with an ID and/or attributes.
node1 - Variable in class org.gersteinlab.tyna.core.graph.Edge
The first node of the edge.
node1Iter - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphEdgeIterator
An iterator of the nodes that have edges.
node2 - Variable in class org.gersteinlab.tyna.core.graph.Edge
The second node of the edge.
node2Iter - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphEdgeIterator
An iterator of the nodes that node 1 has edges with.
NodeIdFilter - Class in org.gersteinlab.tyna.core.operators
This class defines the ID filter, which is a unary graph operator.
NodeIdFilter(String, String, boolean) - Constructor for class org.gersteinlab.tyna.core.operators.NodeIdFilter
Create a new node ID filter.
NodeIterator - Interface in org.gersteinlab.tyna.core.graph
This interface declares that each implemented class is an iterator of a set of nodes of a graph.
NodePair - Class in org.gersteinlab.tyna.core.util
This class is a utility class for working with node pairs.
NodePair(Node, Node) - Constructor for class org.gersteinlab.tyna.core.util.NodePair
 
nodes - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph
The nodes of the graph.
nodesToCategories - Variable in class org.gersteinlab.tyna.webapp.data.CategoryInfo
A map from the nodes to the categories

O

openWinCheckBox - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
operate(Graph, Graph) - Method in interface org.gersteinlab.tyna.core.operators.BinaryOperator
Perform the operation on two graphs.
operate(Graph) - Method in class org.gersteinlab.tyna.core.operators.ChainMotifMiner
 
operate(Graph) - Method in class org.gersteinlab.tyna.core.operators.CompleteTwoLayerMotifMiner
 
operate(Graph) - Method in class org.gersteinlab.tyna.core.operators.CycleMotifMiner
 
operate(Graph) - Method in class org.gersteinlab.tyna.core.operators.DefectiveCliqueMotifMiner
 
operate(Graph, Graph) - Method in class org.gersteinlab.tyna.core.operators.Difference
 
operate(Graph) - Method in class org.gersteinlab.tyna.core.operators.FeedforwardLoopMotifMiner
 
operate(Graph, Graph) - Method in class org.gersteinlab.tyna.core.operators.Intersection
 
operate(Graph) - Method in class org.gersteinlab.tyna.core.operators.NodeIdFilter
 
operate(Graph) - Method in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
operate(Graph) - Method in interface org.gersteinlab.tyna.core.operators.UnaryOperator
Perform the operation on a graph.
operate(Graph, Graph) - Method in class org.gersteinlab.tyna.core.operators.Union
 
org.gersteinlab.tyna.core.graph - package org.gersteinlab.tyna.core.graph
Contains basic definitions of graphs, nodes and edges.
org.gersteinlab.tyna.core.io - package org.gersteinlab.tyna.core.io
Contains graph readers and writers.
org.gersteinlab.tyna.core.operators - package org.gersteinlab.tyna.core.operators
Contains network operators.
org.gersteinlab.tyna.core.util - package org.gersteinlab.tyna.core.util
Contains utility classes useful for network analyses.
org.gersteinlab.tyna.cytoscape - package org.gersteinlab.tyna.cytoscape
Contains classes for the Cytoscape plugin.
org.gersteinlab.tyna.webapp.config - package org.gersteinlab.tyna.webapp.config
Contains classes for making system configurations.
org.gersteinlab.tyna.webapp.data - package org.gersteinlab.tyna.webapp.data
Contains classes for accessing data within the tYNA web application.
org.gersteinlab.tyna.webapp.security - package org.gersteinlab.tyna.webapp.security
Contains classes that deal with security issues, such as login and access permission.
org.gersteinlab.tyna.webapp.util - package org.gersteinlab.tyna.webapp.util
Contains utility classes useful for building the tYNA application.
org.gersteinlab.tyna.webservice - package org.gersteinlab.tyna.webservice
Contains classes for exposing tYNA as a webservice.
OUT_DEGREES - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
OutputFormatException - Exception in org.gersteinlab.tyna.core.io
This class represents an exception due to invalid output file format.
OutputFormatException() - Constructor for exception org.gersteinlab.tyna.core.io.OutputFormatException
Default constructor: create a new object without an error message.
OutputFormatException(String) - Constructor for exception org.gersteinlab.tyna.core.io.OutputFormatException
Create a new object with an error message.
OutputFormatException(Throwable) - Constructor for exception org.gersteinlab.tyna.core.io.OutputFormatException
Create a new object with the cause of this exception.
OutputFormatException(String, Throwable) - Constructor for exception org.gersteinlab.tyna.core.io.OutputFormatException
Create a new object with an error message and the cause of this exception.
outputType - Variable in class org.gersteinlab.tyna.core.operators.MotifMiner
 
OWNED - Variable in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Owned resource (networks/categories).

P

passwordField - Variable in class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
 
passwordField - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
PERCENTILE - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
pool - Static variable in class org.gersteinlab.tyna.core.util.IntegerPool
The pool of integers (each integer maps to itself)
prepareNext() - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph.AbstractGraphEdgeIterator
Prepare for the next node to be returned, to be called by next().
prepareNext() - Method in class org.gersteinlab.tyna.core.graph.DirectedMultiGraph.DirectedMultiGraphEdgeIterator
 
prepareNext() - Method in class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph.DirectedSimpleGraphEdgeIterator
 
prepareNext() - Method in class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph.UndirectedMultiGraphEdgeIterator
 
prepareNext() - Method in class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph.UndirectedSimpleGraphEdgeIterator
 
PRIVATE - Variable in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Private resource (networks/categories).
privateCheckBox - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
PUBLIC_OR_OWNED - Variable in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Public or owned resource (networks/categories).

R

rand - Variable in class org.gersteinlab.tyna.webapp.data.FileDataStore
A random number generator
RDBDataStore - Class in org.gersteinlab.tyna.webapp.data
This class is the agent for accessing databases.
RDBDataStore(HttpSession) - Constructor for class org.gersteinlab.tyna.webapp.data.RDBDataStore
This method is used to get a connection to the database with configurations specified in the configuration file.
read(boolean) - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
 
read() - Method in class org.gersteinlab.tyna.cytoscape.InteractionsReader2
Calls read(false)
READ - Static variable in class org.gersteinlab.tyna.webapp.security.SecurityController
Read access mode.
readerClass - Variable in class org.gersteinlab.tyna.webapp.data.NetworkFormat
The reader class for reading networks of this format
readGraph(InputStream, boolean, boolean) - Method in class org.gersteinlab.tyna.core.io.CSVIO
 
readGraph(Reader, boolean, boolean) - Method in class org.gersteinlab.tyna.core.io.CSVIO
 
readGraph(InputStream, boolean, boolean) - Method in interface org.gersteinlab.tyna.core.io.GraphReader
Read the graph from an input stream.
readGraph(Reader, boolean, boolean) - Method in interface org.gersteinlab.tyna.core.io.GraphReader
Read the graph from a reader.
readGraph(InputStream, boolean, boolean) - Method in class org.gersteinlab.tyna.core.io.SIFIO
 
readGraph(Reader, boolean, boolean) - Method in class org.gersteinlab.tyna.core.io.SIFIO
 
readGraph(InputStream, boolean, boolean) - Method in class org.gersteinlab.tyna.core.io.TDIO
 
readGraph(Reader, boolean, boolean) - Method in class org.gersteinlab.tyna.core.io.TDIO
 
REG_EXP - Static variable in class org.gersteinlab.tyna.core.operators.NodeIdFilter
 
register(User, String) - Method in class org.gersteinlab.tyna.webapp.security.SecurityController
Register for a new account.
removeAttr(Object) - Method in class org.gersteinlab.tyna.core.graph.Edge
Remove the value of an attribute from the node.
removeAttr(Object) - Method in class org.gersteinlab.tyna.core.graph.Node
Remove the value of an attribute from the node.
removeAttribute(String) - Method in class org.gersteinlab.tyna.webapp.security.SecurityController
Remove the value of an attribute from session.
revEdges - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph
The reverse edges of the graph if it is directed.
rollback() - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Rollback the current transaction.
root - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.DuplicateTree
 
root - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.HeadTailTree
 
run() - Method in class org.gersteinlab.tyna.webapp.util.HouseKeeper
 

S

saveGraph(Graph) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
Copy the content of the input graph to this object.
sc - Variable in class org.gersteinlab.tyna.webapp.data.FileDataStore
Security controller
sc - Variable in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Security controller
SD - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
SecurityController - Class in org.gersteinlab.tyna.webapp.security
This class is responsible for the security of the web application.
SecurityController(HttpSession) - Constructor for class org.gersteinlab.tyna.webapp.security.SecurityController
Create a new object.
SecurityException - Exception in org.gersteinlab.tyna.webapp.security
This class represents an exception due to a security problem.
SecurityException() - Constructor for exception org.gersteinlab.tyna.webapp.security.SecurityException
Default constructor: create a new object without an error message.
SecurityException(String) - Constructor for exception org.gersteinlab.tyna.webapp.security.SecurityException
Create a new object with an error message.
SecurityException(Throwable) - Constructor for exception org.gersteinlab.tyna.webapp.security.SecurityException
Create a new object with the cause of this exception.
SecurityException(String, Throwable) - Constructor for exception org.gersteinlab.tyna.webapp.security.SecurityException
Create a new object with an error message and the cause of this exception.
sendButton - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 
SEPARATED - Static variable in class org.gersteinlab.tyna.core.operators.MotifMiner
 
serialize(CyNetwork) - Static method in class org.gersteinlab.tyna.cytoscape.InteractionsSerializer2
 
session - Variable in class org.gersteinlab.tyna.webapp.data.FileDataStore
The current HTTP session
session - Variable in class org.gersteinlab.tyna.webapp.security.SecurityController
The current HTTP session.
setAttr(Object, Object) - Method in class org.gersteinlab.tyna.core.graph.AbstractGraph
 
setAttr(Object, Object) - Method in class org.gersteinlab.tyna.core.graph.Edge
Set the value of an attribute of the edge.
setAttr(Object, Object) - Method in interface org.gersteinlab.tyna.core.graph.Graph
Set the value of an attribute of the graph.
setAttr(Object, Object) - Method in class org.gersteinlab.tyna.core.graph.Node
Set the value of an attribute of the node.
setAttribute(String, Object) - Method in class org.gersteinlab.tyna.webapp.security.SecurityController
Set the value of an attribute to session.
setAutoCommit(boolean) - Method in class org.gersteinlab.tyna.webapp.data.RDBDataStore
Set auto commit of the connection.
setCreated(Timestamp) - Method in class org.gersteinlab.tyna.webapp.data.Category
Set the time of category creation.
setCreated(Timestamp) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set the time of network creation.
setCreatorId(Integer) - Method in class org.gersteinlab.tyna.webapp.data.Category
Set the ID of th category creator.
setCreatorId(Integer) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set the ID of th network creator.
setCreatorName(String) - Method in class org.gersteinlab.tyna.webapp.data.Category
Set the name of th category creator.
setCreatorName(String) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set the name of th network creator.
setDescription(String) - Method in class org.gersteinlab.tyna.webapp.data.Category
Set the category description.
setDescription(String) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set the network description.
setDescription(String) - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Set the network format description.
setEmail(String) - Method in class org.gersteinlab.tyna.webapp.data.User
Set the email.
setFormatId(Integer) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set the ID of the network format.
setFormatName(String) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set the name of the network format.
setId(Integer) - Method in class org.gersteinlab.tyna.webapp.data.Category
Set the category ID.
setId(Integer) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set the network ID.
setId(Integer) - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Set the network format ID.
setId(Integer) - Method in class org.gersteinlab.tyna.webapp.data.NetworkType
Set the network type ID.
setId(Integer) - Method in class org.gersteinlab.tyna.webapp.data.User
Set the user ID.
setInstitution(String) - Method in class org.gersteinlab.tyna.webapp.data.User
Set the institution.
setIsDirected(Boolean) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set if the network is directed.
setIsMultigraph(Boolean) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set if the network is a multigraph.
setIsPublic(Boolean) - Method in class org.gersteinlab.tyna.webapp.data.Category
Set if the category is public.
setIsPublic(Boolean) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set if the network is public.
setName(String) - Method in class org.gersteinlab.tyna.webapp.data.Category
Set the category name.
setName(String) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set the network name.
setName(String) - Method in class org.gersteinlab.tyna.webapp.data.NetworkAttr
Set the network attribute name.
setName(String) - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Set the network format name.
setName(String) - Method in class org.gersteinlab.tyna.webapp.data.NetworkType
Set the network type name.
setName(String) - Method in class org.gersteinlab.tyna.webapp.data.User
Set the login name.
setNetworkId(Integer) - Method in class org.gersteinlab.tyna.webapp.data.NetworkAttr
Set the network ID.
setReaderClass(String) - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Set the reader class that reads data of this format.
setSuffix(String) - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Set the network format file suffix.
setType(Integer) - Method in class org.gersteinlab.tyna.webapp.data.Network
Set the network type.
setValue(String) - Method in class org.gersteinlab.tyna.webapp.data.NetworkAttr
Set the network attribute value.
setWeight(double) - Method in class org.gersteinlab.tyna.core.graph.Edge
Set the edge weight.
setWriterClass(String) - Method in class org.gersteinlab.tyna.webapp.data.NetworkFormat
Set the writer class that reads data of this format.
SIFIO - Class in org.gersteinlab.tyna.core.io
This class represents the IO unit for the SIF format for directed graphs.
SIFIO() - Constructor for class org.gersteinlab.tyna.core.io.SIFIO
 
SimpleGraph - Interface in org.gersteinlab.tyna.core.graph
This interface declares that each implemented class is a graph that does not contain duplicate edges, and does not contain self loops.
SimpleStats - Class in org.gersteinlab.tyna.core.util
This class provides utility methods for calculating some basic statistics from a series of numbers.
SimpleStats() - Constructor for class org.gersteinlab.tyna.core.util.SimpleStats
Create a new empty object.
StatisticsFilter - Class in org.gersteinlab.tyna.core.operators
This class defines the statistical filter, which is a unary graph operator.
StatisticsFilter(String, String, double, String, boolean) - Constructor for class org.gersteinlab.tyna.core.operators.StatisticsFilter
Create a new statistics filter.
storeCategoryPerm(long, Category) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a category permanently.
storeCategoryTemp(InputStream) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a category temporarily.
storeCategoryTemp(Reader) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a category temporarily.
storeFile(InputStream, File) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a file.
storeFile(Reader, File) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a file.
storeNetworkFromObj(long, Network) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a network from a serialized graph object.
storeNetworkPerm(long, Network) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a network permanently.
storeNetworkTemp(InputStream) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a network temporarily.
storeNetworkTemp(Reader) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a network temporarily.
storeTempFile(InputStream, String) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a file temporarily.
storeTempFile(Reader, String) - Method in class org.gersteinlab.tyna.webapp.data.FileDataStore
Store a file temporarily.
suffix - Variable in class org.gersteinlab.tyna.webapp.data.NetworkFormat
File suffix.
sum - Variable in class org.gersteinlab.tyna.core.util.SimpleStats
Sum of the values.
sumSq - Variable in class org.gersteinlab.tyna.core.util.SimpleStats
Sum of squares of the values.

T

TDIO - Class in org.gersteinlab.tyna.core.io
This class represents the IO unit for a simple tab-delimited format that assumes a directed or undirected, simple or multi graph with no edge attributes.
TDIO() - Constructor for class org.gersteinlab.tyna.core.io.TDIO
 
tempDir - Variable in class org.gersteinlab.tyna.webapp.data.FileDataStore
The temp directory
termination - Variable in class org.gersteinlab.tyna.core.graph.AbstractGraph.DuplicateTree
 
TextUtil - Class in org.gersteinlab.tyna.webapp.util
This class provides utility methods for converting text between different formats.
TextUtil() - Constructor for class org.gersteinlab.tyna.webapp.util.TextUtil
 
toHTMLValue(String) - Static method in class org.gersteinlab.tyna.webapp.util.TextUtil
Convert a string into a format suitable for HTML values.
toString() - Method in class org.gersteinlab.tyna.core.graph.Node
 
toString() - Method in class org.gersteinlab.tyna.core.util.NodePair
 
toXMLTagName(String) - Static method in class org.gersteinlab.tyna.webapp.util.TextUtil
Convert a string into a format suitable for XML tag names.
toXMLValue(String) - Static method in class org.gersteinlab.tyna.webapp.util.TextUtil
Convert a string into a format suitable for XML tag values.
TYNA - Interface in org.gersteinlab.tyna.webservice
This interface defines the tYNA web service.
TYNADownloadWin - Class in org.gersteinlab.tyna.cytoscape
This class defines the download window of the tYNA plugin for Cytoscape.
TYNADownloadWin(JFrame) - Constructor for class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
Constructor: creates a new object and draws the window.
TYNAPlugin - Class in org.gersteinlab.tyna.cytoscape
This class defines the tYNA plugin for Cytoscape.
TYNAPlugin() - Constructor for class org.gersteinlab.tyna.cytoscape.TYNAPlugin
Default constructor: creates a new object, creates the windows, and initializes the menu itmes.
TYNASoapBindingImpl - Class in org.gersteinlab.tyna.webservice
This class defines the actual implementation of the tYNA web service.
TYNASoapBindingImpl() - Constructor for class org.gersteinlab.tyna.webservice.TYNASoapBindingImpl
 
TYNAUploadWin - Class in org.gersteinlab.tyna.cytoscape
This class defines the upload window of the tYNA plugin for Cytoscape.
TYNAUploadWin(JFrame) - Constructor for class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
Constructor: creates a new object and draws the window.
type - Variable in class org.gersteinlab.tyna.webapp.data.Network
Network type

U

UnaryOperator - Interface in org.gersteinlab.tyna.core.operators
This class defines the interface for unary graph operators, which take one graph as input, and returns a single graph as output.
UndirectedGraph - Interface in org.gersteinlab.tyna.core.graph
This interface declares that each implemented class is an undirected graph.
UndirectedMultiGraph - Class in org.gersteinlab.tyna.core.graph
This class represents an undirected multigraph.
UndirectedMultiGraph() - Constructor for class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
Default constructor: creates an empty graph.
UndirectedMultiGraph(Graph) - Constructor for class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph
 
UndirectedMultiGraph.UndirectedMultiGraphEdgeIterator - Class in org.gersteinlab.tyna.core.graph
 
UndirectedMultiGraph.UndirectedMultiGraphEdgeIterator() - Constructor for class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph.UndirectedMultiGraphEdgeIterator
Constructor: initialize the iteration state.
UndirectedSimpleGraph - Class in org.gersteinlab.tyna.core.graph
This class represents an undirected simple graph.
UndirectedSimpleGraph() - Constructor for class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
Default constructor: creates an empty graph.
UndirectedSimpleGraph(Graph) - Constructor for class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph
 
UndirectedSimpleGraph.UndirectedSimpleGraphEdgeIterator - Class in org.gersteinlab.tyna.core.graph
 
UndirectedSimpleGraph.UndirectedSimpleGraphEdgeIterator() - Constructor for class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph.UndirectedSimpleGraphEdgeIterator
Constructor: initialize the iteration state.
Union - Class in org.gersteinlab.tyna.core.operators
This class defines the union binary operator.
Union() - Constructor for class org.gersteinlab.tyna.core.operators.Union
 
uploadItem - Variable in class org.gersteinlab.tyna.cytoscape.TYNAPlugin
 
uploadNetwork(String, String, String, Network) - Method in interface org.gersteinlab.tyna.webservice.TYNA
Upload a network into the tYNA database.
uploadNetwork(String, String, String, Network) - Method in class org.gersteinlab.tyna.webservice.TYNASoapBindingImpl
 
uploadWin - Variable in class org.gersteinlab.tyna.cytoscape.TYNAPlugin
 
User - Class in org.gersteinlab.tyna.webapp.data
This class contains the information of a user.
User() - Constructor for class org.gersteinlab.tyna.webapp.data.User
Default constructor: creates an empty object.
User(Integer, String, String, String) - Constructor for class org.gersteinlab.tyna.webapp.data.User
Creates a new object that stores the supplied information.
USER - Static variable in class org.gersteinlab.tyna.webapp.security.SecurityController
Constant for getting the user information.
usernameField - Variable in class org.gersteinlab.tyna.cytoscape.TYNADownloadWin
 
usernameField - Variable in class org.gersteinlab.tyna.cytoscape.TYNAUploadWin
 

V

VALUE - Static variable in class org.gersteinlab.tyna.core.operators.StatisticsFilter
 
value - Variable in class org.gersteinlab.tyna.core.util.MutableDouble
The current value of the double
value - Variable in class org.gersteinlab.tyna.core.util.MutableInteger
The current value of the integer
value - Variable in class org.gersteinlab.tyna.webapp.data.NetworkAttr
Network attribute value.

W

weight - Variable in class org.gersteinlab.tyna.core.graph.Edge
The weight of the edge.
WRITE - Static variable in class org.gersteinlab.tyna.webapp.security.SecurityController
Write access mode.
writeGraph(Graph, OutputStream) - Method in class org.gersteinlab.tyna.core.io.CSVIO
 
writeGraph(Graph, Writer) - Method in class org.gersteinlab.tyna.core.io.CSVIO
 
writeGraph(Graph, OutputStream) - Method in interface org.gersteinlab.tyna.core.io.GraphWriter
Write the graph to an output stream.
writeGraph(Graph, Writer) - Method in interface org.gersteinlab.tyna.core.io.GraphWriter
Write the graph to a writer.
writeGraph(Graph, OutputStream) - Method in class org.gersteinlab.tyna.core.io.SIFIO
 
writeGraph(Graph, Writer) - Method in class org.gersteinlab.tyna.core.io.SIFIO
 
writeGraph(Graph, OutputStream) - Method in class org.gersteinlab.tyna.core.io.TDIO
 
writeGraph(Graph, Writer) - Method in class org.gersteinlab.tyna.core.io.TDIO
 
writerClass - Variable in class org.gersteinlab.tyna.webapp.data.NetworkFormat
The writer class for writing networks of this format

A B C D E F G H I K L M N O P R S T U V W