Serialized Form

Package org.gersteinlab.tyna.core.graph

Class org.gersteinlab.tyna.core.graph.AbstractGraph extends java.lang.Object implements Serializable

Serialized Fields

nodes

java.util.Map nodes

The nodes of the graph.

edges

java.util.Map edges

The edges of the graph. A (node1 -> neighbors) map, where neighbors is a (node2 -> attributes) map, and attributes could be a map or a list of map, depending on whether the graph is a simple graph or a multigraph.

revEdges

java.util.Map revEdges

The reverse edges of the graph if it is directed. For undirected graph, it points to edges.

attrs

java.util.Map attrs

The attributes of the graph.

edgeCount

int edgeCount

The number of edges in the graph.

lastModified

long lastModified

The last modified time of the graph.

Class org.gersteinlab.tyna.core.graph.AbstractMultiGraph extends AbstractGraph implements Serializable

Class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph extends AbstractGraph implements Serializable

Class org.gersteinlab.tyna.core.graph.DirectedMultiGraph extends AbstractMultiGraph implements Serializable

Class org.gersteinlab.tyna.core.graph.DirectedSimpleGraph extends AbstractSimpleGraph implements Serializable

Class org.gersteinlab.tyna.core.graph.Edge extends java.lang.Object implements Serializable

Serialized Fields

node1

Node node1

The first node of the edge.

node2

Node node2

The second node of the edge.

weight

double weight

The weight of the edge.

attrs

java.util.Map attrs

Other attributes of the edge (can be null).

Class org.gersteinlab.tyna.core.graph.GraphTypeException extends java.lang.Exception implements Serializable

Class org.gersteinlab.tyna.core.graph.Node extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.Object id

The ID of the node.

attrs

java.util.Map attrs

The (possibly null) other attributes of the node.

Class org.gersteinlab.tyna.core.graph.UndirectedMultiGraph extends AbstractMultiGraph implements Serializable

Class org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph extends AbstractSimpleGraph implements Serializable

Package org.gersteinlab.tyna.core.io

Class org.gersteinlab.tyna.core.io.InputFormatException extends java.lang.Exception implements Serializable

Class org.gersteinlab.tyna.core.io.OutputFormatException extends java.lang.Exception implements Serializable

Package org.gersteinlab.tyna.webapp.config

Class org.gersteinlab.tyna.webapp.config.Config extends java.util.Properties implements Serializable

Class org.gersteinlab.tyna.webapp.config.ConfigException extends java.lang.Exception implements Serializable

Package org.gersteinlab.tyna.webapp.data

Class org.gersteinlab.tyna.webapp.data.Category extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.Integer id

Category ID.

name

java.lang.String name

Category name.

description

java.lang.String description

Category description.

creatorId

java.lang.Integer creatorId

ID of the category creator.

creatorName

java.lang.String creatorName

Name of the category creator.

created

java.sql.Timestamp created

Time of category creation.

isPublic

java.lang.Boolean isPublic

Is the category public.

Class org.gersteinlab.tyna.webapp.data.Network extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.Integer id

Network ID.

name

java.lang.String name

Network name.

description

java.lang.String description

Network description.

formatId

java.lang.Integer formatId

Id of network format.

formatName

java.lang.String formatName

Name of network format.

isDirected

java.lang.Boolean isDirected

Is the network directed.

isMultigraph

java.lang.Boolean isMultigraph

Is the network a multigraph.

creatorId

java.lang.Integer creatorId

ID of the network creator.

creatorName

java.lang.String creatorName

Name of the network creator.

created

java.sql.Timestamp created

Time of network creation.

isPublic

java.lang.Boolean isPublic

Is the network public.

type

java.lang.Integer type

Network type

Class org.gersteinlab.tyna.webapp.data.NetworkAttr extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

Network attribute name.

value

java.lang.String value

Network attribute value.

networkId

java.lang.Integer networkId

Network ID.

Class org.gersteinlab.tyna.webapp.data.NetworkFormat extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.Integer id

Network format ID.

name

java.lang.String name

Network format name.

description

java.lang.String description

Network format description.

suffix

java.lang.String suffix

File suffix.

readerClass

java.lang.String readerClass

The reader class for reading networks of this format

writerClass

java.lang.String writerClass

The writer class for writing networks of this format

Class org.gersteinlab.tyna.webapp.data.NetworkType extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.Integer id

Network type ID.

name

java.lang.String name

Network type name.

Class org.gersteinlab.tyna.webapp.data.User extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.Integer id

User ID.

name

java.lang.String name

Login name.

email

java.lang.String email

Email.

institution

java.lang.String institution

Institution.

Package org.gersteinlab.tyna.webapp.security

Class org.gersteinlab.tyna.webapp.security.SecurityException extends java.lang.Exception implements Serializable

Package org.gersteinlab.tyna.webapp.util

Class org.gersteinlab.tyna.webapp.util.FileDownload extends javax.servlet.http.HttpServlet implements Serializable

Class org.gersteinlab.tyna.webapp.util.HouseKeeper extends javax.servlet.http.HttpServlet implements Serializable

Serialized Fields

context

javax.servlet.ServletContext context

keeperThread

java.lang.Thread keeperThread

Package org.gersteinlab.tyna.cytoscape

Class org.gersteinlab.tyna.cytoscape.TYNADownloadWin extends javax.swing.JFrame implements Serializable

Serialized Fields

loginCheckBox

javax.swing.JCheckBox loginCheckBox

usernameField

javax.swing.JTextField usernameField

passwordField

javax.swing.JPasswordField passwordField

listTypeBox

javax.swing.JComboBox listTypeBox

listButton

javax.swing.JButton listButton

networksTable

javax.swing.JTable networksTable

loadButton

javax.swing.JButton loadButton

networks

Network[] networks

columnNames

java.lang.Object[] columnNames

Class org.gersteinlab.tyna.cytoscape.TYNAUploadWin extends javax.swing.JFrame implements Serializable

Serialized Fields

loginCheckBox

javax.swing.JCheckBox loginCheckBox

usernameField

javax.swing.JTextField usernameField

passwordField

javax.swing.JPasswordField passwordField

privateCheckBox

javax.swing.JCheckBox privateCheckBox

networkNameField

javax.swing.JTextField networkNameField

networkDescArea

javax.swing.JTextArea networkDescArea

networkTypeBox

javax.swing.JComboBox networkTypeBox

directedCheckBox

javax.swing.JCheckBox directedCheckBox

multigraphCheckBox

javax.swing.JCheckBox multigraphCheckBox

openWinCheckBox

javax.swing.JCheckBox openWinCheckBox

sendButton

javax.swing.JButton sendButton