Package org.cy3sbml.layout

Class LayoutTools

java.lang.Object

org.cy3sbml.layout.LayoutTools

public class LayoutTools
extends Object

Utilities for working with layouts.

Saves the node positions of a network view to a file and applies them to a network view. The nodes are matched by their cyId, which is unique for every node of an SBML network and the same in every import of the model, also for the nodes of elements without SBML id (rules, kinetic laws, units, math, ...). The positions of old layout files, which have only the SBML id, are matched by the SBML id. The glyph nodes of a layout network, where the glyphs of one element (aliases) have the same cyId, are matched by the glyph.

Constructor Summary

Constructors

Constructor	Description
LayoutTools(ServiceAdapter adapter)

Method Summary

Modifier and Type	Method	Description
int	loadLayoutForViewFromFile(org.cytoscape.view.model.CyNetworkView view, File file)	Moves every node of the view with a position in the file to that position.
void	loadLayoutOfCurrentViewFromFile(File file)	Load layout of current view from file.
void	saveLayoutOfCurrentViewInFile(File file)	Save layout of current view in file.
int	saveLayoutOfViewInFile(org.cytoscape.view.model.CyNetworkView view, File file)	Save layout of given view in file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

LayoutTools

public LayoutTools(ServiceAdapter adapter)

Method Details

saveLayoutOfCurrentViewInFile

public void saveLayoutOfCurrentViewInFile(File file)
                                   throws IOException

Save layout of current view in file.

Throws:

IOException - if the file could not be written

saveLayoutOfViewInFile

public int saveLayoutOfViewInFile(org.cytoscape.view.model.CyNetworkView view,
 File file)
                           throws IOException

Save layout of given view in file. Nodes without cyId and SBML id (not created by cy3sbml) are not saved.

Returns:

the number of saved node positions

Throws:

IOException - if the file could not be written

loadLayoutOfCurrentViewFromFile

public void loadLayoutOfCurrentViewFromFile(File file)

Load layout of current view from file.

loadLayoutForViewFromFile

public int loadLayoutForViewFromFile(org.cytoscape.view.model.CyNetworkView view,
 File file)

Moves every node of the view with a position in the file to that position.

Returns:

number of positioned nodes