This page lists all of the methods currently contained in the GraphPerspective class that will need to be replaced or whose functionality must be otherwise supported in 3.0. The methods are grouped according to how they are supported by the current proposed API: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/mes/api/

• Found in getNodeCount, getEdgeCount
  • public int getNodeCount();
  • public int getEdgeCount();
• Found in getNodeList, getEdgeList

  • public Iterator<Node> nodesIterator();

  • public List<Node> nodesList();

  • public int[] getNodeIndicesArray();

  • public Iterator<Edge> edgesIterator();

  • public List<Edge> edgesList();

  • public int[] getEdgeIndicesArray();
  • public int[] getEdgeIndicesArray(
• Found in contains
  • public boolean containsNode( Node node );
  • public boolean containsNode( Node node, boolean recurse );
  • public boolean containsEdge( Edge edge );
  • public boolean containsEdge( Edge edge, boolean recurse );
  • public boolean edgeExists( Node from, Node to );
  • public boolean edgeExists( int from_node_index, int to_node_index );
• Found in getNeighborList, getAdjacentEdgeList, getConnectingEdgeList

  • public List<Node> neighborsList( Node node );

  • public int[] neighborsArray( int node_index );

  • public List<Edge> edgesList( Node from, Node to );

  • public List<Edge> edgesList(int from_node_index,

  • public int[] getEdgeIndicesArray(int from_node_index,

  • public List<Edge> getAdjacentEdgesList( Node node, boolean include_undirected_edges, boolean incoming_edges, boolean outgoing_edges );

  • public int[] getAdjacentEdgeIndicesArray( int node_index,

  • public List<Edge> getConnectingEdges( List<Node> nodes );

  • public int[] getConnectingEdgeIndicesArray( int[] node_indices );
• Found in getIndex, getNode, getEdge
  • public int getIndex( Node node );
  • public int getRootGraphNodeIndex( int root_graph_node_index );
  • public Node getNode( int index );
  • public int getIndex( Edge edge );
  • public int getRootGraphEdgeIndex( int root_graph_edge_index );
  • public Edge getEdge( int index );

• Found in part of CyEdge

  • public boolean isEdgeDirected( int edge_index );

• Supported in CyNetwork, but we're talking about a slightly different model. This is a result of root graph thinking. The Node is first created in the root graph, then it's added to a perspective

  • public int addNode(int cytoscape_node);
  • public Node addNode(Node cytoscape_node);
  • public int addEdge(int cytoscape_edge);
  • public Edge addEdge(Edge cytoscape_edge);
• Found in remove*
  • public boolean removeEdge(int edge_index, boolean set_remove);
  • public boolean removeNode(int node_index, boolean set_remove);
• Found in getIdentifier()
  • public String getIdentifier();
• should go away - identifier should not be mutable
  • public String setIdentifier(String new_id);
• subsumed by getNeighborList - possibly put in a util class
  • public boolean isNeighbor( Node a_node, Node another_node );
  • public boolean isNeighbor( int a_node_index, int another_node_index );
• subsumed by getAdjacentEdgeList - possibly put in a util class
  • public int getEdgeCount(Node from,
  • public int getEdgeCount( int from_node_index,
• subsumed by getAdjacentEdgeList - possibly put in a util class
  • public int getInDegree( Node node );
  • public int getInDegree( int node_index );
  • public int getInDegree( Node node, boolean count_undirected_edges );
  • public int getInDegree( int node_index, boolean count_undirected_edges );
  • public int getOutDegree( Node node );
  • public int getOutDegree( int node_index );
  • public int getOutDegree( Node node, boolean count_undirected_edges );
  • public int getOutDegree( int node_index, boolean count_undirected_edges );
  • public int getDegree( Node node );
  • public int getDegree( int node_index );
• subsumed by getEdge().getSourceNode().getIndex()
  • public int getEdgeSourceIndex( int edge_index );
  • public int getEdgeTargetIndex( int edge_index );
• should be in a factory

  • public GraphPerspective createGraphPerspective( Node[] nodes, Edge[] edges);

  • public GraphPerspective createGraphPerspective( Collection<Node> nodes, Collection<Edge> edges);

  • public GraphPerspective createGraphPerspective(int[] node_indices,

  • public GraphPerspective createGraphPerspective( int[] node_indices );

• I think title should be a network attribute
  • public String getTitle();
  • public void setTitle(String new_id);
• ??? Write a separate support class
  • public void selectAllNodes();
  • public void selectAllEdges();
  • public void unselectAllNodes();
  • public void unselectAllEdges();

  • public void setSelectedNodeState(Collection<Node> nodes, boolean selected_state);

  • public void setSelectedNodeState(Node node, boolean selected_state);

  • public void setSelectedEdgeState(Collection<Edge> edges, boolean selected_state);

  • public void setSelectedEdgeState(Edge edge, boolean selected_state);
  • public boolean isSelected(Node node);
  • public boolean isSelected(Edge edge);

  • public Set<Node> getSelectedNodes();

  • public Set<Edge> getSelectedEdges();

  • public void addSelectEventListener(SelectEventListener listener);

  • public void removeSelectEventListener(SelectEventListener listener);

  • public SelectFilter getSelectFilter();

• Hide/Restore nodes/edges are somewhat confusingly named. To "hide a node" really means to remove a node from the GraphPerspective. The node would still exist in the root graph, but would not be part of the GraphPerspective any longer. If we no longer have a RootGraph, then all of this is accomplished using existing removeNode/removeEdge methods. This means that these methods should probably go away.

  • public Node hideNode( Node node );
  • public int hideNode( int node_index );

  • public List<Node> hideNodes( List<Node> nodes );

  • public int[] hideNodes( int[] node_indices );
  • public Node restoreNode( Node node );
  • public int restoreNode( int node_index );

  • public List<Node> restoreNodes( List<Node> nodes );

  • public List<Node> restoreNodes(List<Node> nodes, boolean restore_incident_edges);

  • public int [] restoreNodes(int [] node_indices, boolean restore_incident_edges);
  • public int[] restoreNodes( int[] node_indices );
  • public Edge hideEdge( Edge edge );
  • public int hideEdge( int edge_index );

  • public List<Edge> hideEdges( List<Edge> edges );

  • public int[] hideEdges( int[] edge_indices );
  • public Edge restoreEdge( Edge edge );
  • public int restoreEdge( int edge_index );

  • public List<Edge> restoreEdges( List<Edge> edges );

  • public int[] restoreEdges( int[] edge_indices );
• ???

  • public void addGraphPerspectiveChangeListener( GraphPerspectiveChangeListener listener );

  • public void removeGraphPerspectiveChangeListener( GraphPerspectiveChangeListener listener );

• ???
  • public Object clone();

  • public RootGraph getRootGraph();

• ???

  • public GraphPerspective join( GraphPerspective peer );

  • public void appendNetwork(GraphPerspective network);

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