Package org.biopax.paxtools.examples

Class Tutorial

java.lang.Object

org.biopax.paxtools.examples.Tutorial

public class Tutorial
extends Object

This class used for a Paxtools Tutorial during Harmony 2010. It contains most of the examples in the user's guide.

Constructor Summary

Constructors

Constructor	Description
Tutorial()

Method Summary

Modifier and Type	Method	Description
Set	access1(Complex complex)
Set	access2(Complex complex)
void	graphQuery(Model model, PhysicalEntity entity3, PhysicalEntity entity2, PhysicalEntity entity1)
void	highlightWorkaround()
static void	IO(InputStream inputStreamFromFile, OutputStream outputStream)
static void	merge(EditorMap editorMap, Model srcModel2, Model srcModel1)
static void	myFirstModel()
void	simpleTraverse()
static void	tempted(BioPAXIOHandler handler, InputStream inputStream, OutputStream outputStream)

Methods inherited from class java.lang.Object

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

Constructor Details

Tutorial

public Tutorial()

Method Details

myFirstModel

public static void myFirstModel()

IO

public static void IO(InputStream inputStreamFromFile,
 OutputStream outputStream)

tempted

public static void tempted(BioPAXIOHandler handler,
 InputStream inputStream,
 OutputStream outputStream)

merge

public static void merge(EditorMap editorMap,
 Model srcModel2,
 Model srcModel1)

access1

public Set access1(Complex complex)

access2

public Set access2(Complex complex)

graphQuery

public void graphQuery(Model model,
 PhysicalEntity entity3,
 PhysicalEntity entity2,
 PhysicalEntity entity1)

simpleTraverse

public void simpleTraverse()
                    throws FileNotFoundException

Throws:

FileNotFoundException

highlightWorkaround

public void highlightWorkaround()