medusa.dataio

Class DataLoader

java.lang.Object

medusa.dataio.DataLoader

All Implemented Interfaces:

java.lang.Runnable

public class DataLoader
extends java.lang.Object
implements java.lang.Runnable

Class for saving, loading and exporting Graph objects to text file formats. Also writes graphs to postscript and pajek formats.

Field Summary

Fields

Modifier and Type	Field and Description
static int	LOAD_MEDUSA
static int	LOAD_TABBED

Constructor Summary

Constructors

Constructor and Description
DataLoader()
DataLoader(int x, int y) Constructs a new DataLoader and passes the graph size information.
DataLoader(int x, int y, java.lang.String fileName)

Method Summary

Modifier and Type	Method and Description
void	convertToRealDistances(Graph g)
Graph	getGraph()
int	getProgress()
java.lang.String	getStatus()
boolean	isBusy() Lets other methods know if the DataLoader is busy.
boolean	isDone()
Graph	load(java.lang.String fileName) Loads a medusa format file.
Graph	loadSimplest(java.lang.String fileName) Loads the simplest possible file of three columns: node1 node2 identity This can be used for instance by biologists who run BLAST searches with the -m 8 option.
void	normalizePositions(Graph g)
Graph	readParameters(java.lang.String edges, java.lang.String nodes) For applets.
void	run()
void	save(BasicGraph graph, java.lang.String fileName) Writes the graph to file
void	save(Graph graph, java.lang.String fileName, double scale) This method is not very nice...
void	saveAsArena3D(Graph g, java.lang.String saveFileName)
void	saveAsBiolayout(Graph g, java.lang.String saveFileName)
void	saveAsCytoscape(Graph g, java.lang.String saveFileName)
void	saveAsEPS(Graph g, java.lang.String saveFileName, MedusaSettings ss, int nodeSize, int fontSize)
void	saveAsGraphViz(Graph g, java.lang.String saveFileName)
void	saveAsPajek(Graph g, java.lang.String saveFileName)
void	saveAsPS(Graph g, java.lang.String saveFileName, MedusaSettings ss) Draw the graph to postscript format
void	saveAsPS(Graph g, java.lang.String saveFileName, MedusaSettings ss, int nodeSize, int fontSize)
void	saveHTMLParameters(Graph g, java.lang.String fileName)
void	setFileName(java.lang.String fileName) The file to load.
void	setLoadType(int loadType)
void	start()
void	stop()

Methods inherited from class java.lang.Object

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

Field Detail

LOAD_MEDUSA

public static final int LOAD_MEDUSA

See Also:

Constant Field Values

LOAD_TABBED

public static final int LOAD_TABBED

See Also:

Constant Field Values

Constructor Detail

DataLoader

public DataLoader(int x,
                  int y)

Constructs a new DataLoader and passes the graph size information. Usually, graphs are 600x600 in size.

Parameters:

width -

height -

DataLoader

public DataLoader(int x,
                  int y,
                  java.lang.String fileName)

Parameters:

width -

height -

fileName -

DataLoader

public DataLoader()

Method Detail

setLoadType

public void setLoadType(int loadType)

start

public void start()

stop

public void stop()

getGraph

public Graph getGraph()

Returns:

the graph object

run

public void run()

Specified by:

run in interface java.lang.Runnable

isDone

public boolean isDone()

getStatus

public java.lang.String getStatus()

getProgress

public int getProgress()

isBusy

public boolean isBusy()

Lets other methods know if the DataLoader is busy.

Returns:

true if busy

setFileName

public void setFileName(java.lang.String fileName)

The file to load. Set this before running the load thread.

Parameters:

fileName -

save

public void save(BasicGraph graph,
                 java.lang.String fileName)
          throws java.io.IOException

Writes the graph to file

Parameters:

graph -

fileName -

Throws:

java.io.IOException

save

public void save(Graph graph,
                 java.lang.String fileName,
                 double scale)
          throws java.io.IOException

This method is not very nice... will need to be rewritten. The scale function is generally messy.

Throws:

java.io.IOException

load

public Graph load(java.lang.String fileName)
           throws java.io.IOException,
                  DataFormatException

Loads a medusa format file.

Parameters:

fileName - File to load

Returns:

returns a Graph object which is passed to Medusa

Throws:

java.io.IOException

DataFormatException

loadSimplest

public Graph loadSimplest(java.lang.String fileName)
                   throws java.io.IOException,
                          DataFormatException

Loads the simplest possible file of three columns: node1 node2 identity This can be used for instance by biologists who run BLAST searches with the -m 8 option. If identity is greater than 1.0, it is rescaled.

Parameters:

fileName -

Returns:

Throws:

java.io.IOException

DataFormatException

readParameters

public Graph readParameters(java.lang.String edges,
                            java.lang.String nodes)

For applets. Get parameter lines, e.g nodes and edges, from the applet context and create a new graph.

Parameters:

edges -

nodes -

Returns:

convertToRealDistances

public void convertToRealDistances(Graph g)

normalizePositions

public void normalizePositions(Graph g)

saveAsPS

public void saveAsPS(Graph g,
                     java.lang.String saveFileName,
                     MedusaSettings ss)
              throws java.io.IOException

Draw the graph to postscript format

Throws:

java.io.IOException

saveAsPS

public void saveAsPS(Graph g,
                     java.lang.String saveFileName,
                     MedusaSettings ss,
                     int nodeSize,
                     int fontSize)
              throws java.io.IOException

Throws:

java.io.IOException

saveAsEPS

public void saveAsEPS(Graph g,
                      java.lang.String saveFileName,
                      MedusaSettings ss,
                      int nodeSize,
                      int fontSize)
               throws java.io.IOException

Throws:

java.io.IOException

saveAsPajek

public void saveAsPajek(Graph g,
                        java.lang.String saveFileName)
                 throws java.io.IOException

Throws:

java.io.IOException

saveAsArena3D

public void saveAsArena3D(Graph g,
                          java.lang.String saveFileName)
                   throws java.io.IOException

Throws:

java.io.IOException

saveAsBiolayout

public void saveAsBiolayout(Graph g,
                            java.lang.String saveFileName)
                     throws java.io.IOException

Throws:

java.io.IOException

saveAsCytoscape

public void saveAsCytoscape(Graph g,
                            java.lang.String saveFileName)
                     throws java.io.IOException

Throws:

java.io.IOException

saveAsGraphViz

public void saveAsGraphViz(Graph g,
                           java.lang.String saveFileName)
                    throws java.io.IOException

Throws:

java.io.IOException

saveHTMLParameters

public void saveHTMLParameters(Graph g,
                               java.lang.String fileName)
                        throws java.io.IOException

Throws:

java.io.IOException