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Paxtools Console Application and Examples
package org.biopax.paxtools.examples;
import org.biopax.paxtools.controller.*;
import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.BioPAXFactory;
import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level3.*;
import org.biopax.paxtools.query.QueryExecuter;
import org.biopax.paxtools.query.algorithm.Direction;
import org.biopax.paxtools.util.Filter;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
/**
* This class used for a Paxtools Tutorial during Harmony 2010. It contains most of the examples in the user's guide.
*/
public class Tutorial
{
public static void myFirstModel()
{
BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory();
Model model = factory.createModel();
Protein protein1 = model.addNew(Protein.class,
"http://biopax.org/tutorial/test1");
protein1.addName("Tutorial Example Small molecule Transporter 1");
protein1.setDisplayName("TEST1");
BiochemicalReaction rxn1 = model.addNew(BiochemicalReaction.class,
"http://biopax.org/tutorial/rxn1");
rxn1.addLeft(protein1);
}
public static void IO(InputStream inputStreamFromFile,
OutputStream outputStream)
{
BioPAXIOHandler handler = new SimpleIOHandler(); // auto-detects Level
Model model = handler.convertFromOWL(inputStreamFromFile);
handler.convertToOWL(model, outputStream);
String id1 = null, id2 = null, id3 = null;
handler.convertToOWL(model, outputStream, id1, id2, id3);
}
public static void tempted(BioPAXIOHandler handler, InputStream inputStream,
OutputStream outputStream)
{
//read initial model
Model model1 = handler.convertFromOWL(inputStream);
//create an empty model
Model model2 = model1.getLevel().getDefaultFactory().createModel();
//extract reaction
model2.add(model1.getByID("The_reaction_id"));
//write it out
handler.convertToOWL(model2, outputStream);
}
/**
* A controller that excises/extracts an element and all the elements it is
* dependent on from a model and adds them into a new model.
*/
class Excisor implements Visitor
{
private Traverser traverser;
private EditorMap editorMap;
private Model targetModel;
public Excisor(EditorMap editorMap)
{
this.editorMap = editorMap;
this.traverser = new Traverser(editorMap, this);
}
public Excisor(EditorMap editorMap, boolean filtering)
{
this.editorMap = editorMap;
if (filtering)
//We will filter nextStep property, as Reactome pathways leads
//outside the current pathway. Step processes are listed in the
//pathwayComponent property as well so this does not affect the fetcher.
{
final Filter nextStepFilter = new Filter()
{
public boolean filter(PropertyEditor editor)
{
return !editor.getProperty().equals("nextStep");
}
};
this.traverser = new Traverser(editorMap, this, nextStepFilter);
} else this.traverser = new Traverser(editorMap, this);
}
//The visitor will add all elements that are reached into the new model,
// and recursively traverse it
public void visit(BioPAXElement domain, Object range, Model model,
PropertyEditor editor)
{
// We are only interested in the BioPAXElements since
// primitive fields are always copied by value
if (range != null && range instanceof BioPAXElement)
{
BioPAXElement bpe = (BioPAXElement) range;
if (!targetModel.contains(bpe))
{
targetModel.add(bpe);
traverser.traverse(bpe, model);
}
}
}
public Model excise(Model sourceModel, String... ids)
{
// Create a new model that will contain the element(s) of interest
this.targetModel = editorMap.getLevel().getDefaultFactory().createModel();
for (String id : ids)
{
// Get the BioPAX element
BioPAXElement bpe = sourceModel.getByID(id);
// Add it to the model
targetModel.add(bpe);
// Add the elements that bpe is dependent on
traverser.traverse(bpe, sourceModel);
}
return targetModel;
}
}
public static void merge(EditorMap editorMap, Model srcModel2,
Model srcModel1)
{
Model targetModel = editorMap.getLevel().getDefaultFactory().createModel();
Merger merger = new Merger(editorMap);
merger.merge(targetModel, srcModel1, srcModel2);
}
public Set access1(Complex complex)
{
Set xrefs = new HashSet();
recursivelyObtainMembers(complex, xrefs);
return xrefs;
}
private void recursivelyObtainMembers(Complex complex,
Set xrefs)
{
for (PhysicalEntity pe : complex.getComponent())
{
if (pe instanceof Complex)
{
recursivelyObtainMembers((Complex) pe, xrefs);
} else
{
Set memberxrefs =
((SimplePhysicalEntity) pe).getEntityReference().getXref();
for (Xref xref : memberxrefs)
{
if (xref instanceof UnificationXref)
{
xrefs.add((UnificationXref) xref);
}
}
}
}
}
@SuppressWarnings({"unchecked"}) public Set access2(Complex complex)
{
Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
// Set up the Path Accessor
PathAccessor pathAccessor = new PathAccessor(
"ProteinReference/xref:UnificationXref", BioPAXLevel.L3);
// Iterate through all proteins in the model
for (Protein currentProtein : model.getObjects(Protein.class))
{
Set unificationXrefs = pathAccessor.getValueFromBean(currentProtein);
for (Xref currentRef : unificationXrefs)
{
System.out.println(
"Unification XRef: " + currentRef.getDb() + ": " + currentRef.getId());
}
}
PathAccessor accessor = new PathAccessor(
"Complex/component*/EntityReference/xref:UnificationXref", BioPAXLevel.L3);
return new PathAccessor(
"Complex/component*/EntityReference/xref:UnificationXref",
BioPAXLevel.L3).getValueFromBean(complex);
}
public void graphQuery(Model model, PhysicalEntity entity3,
PhysicalEntity entity2, PhysicalEntity entity1)
{
Set sourceSet = new HashSet();
// Add the related source PhysicalEntity (or children) objects to the
// source set
Collections.addAll(sourceSet, entity1, entity2, entity3);
int limit = 2;
// Direction can be upstream, downstream, or bothstream.
Direction direction = Direction.BOTHSTREAM;
Set result = QueryExecuter.runNeighborhood(sourceSet, model,
limit, direction, null);
Completer c = new Completer(SimpleEditorMap.get(BioPAXLevel.L3));
result = c.complete(result, model);
}
public void simpleTraverse() throws FileNotFoundException
{
// Load a sample DNA Repair BioPAX File via Simple IO Handler
FileInputStream fin = new FileInputStream("test_data/dna_repair.owl");
BioPAXIOHandler handler = new SimpleIOHandler();
Model model = handler.convertFromOWL(fin);
// Iterate through all BioPAX Elements and Display RDF ID and Class Name
Set elementSet = model.getObjects();
for (BioPAXElement currentElement : elementSet)
{
String rdfId = currentElement.getUri();
String className = currentElement.getClass().getName();
System.out.println("Element: " + rdfId + ": " + className);
}
// Get Proteins Only
Set proteinSet = model.getObjects(Protein.class);
for (Protein currentProtein : proteinSet)
{
System.out.println("Protein: " + currentProtein.getName() + ": " +
currentProtein.getDisplayName());
}
// Iterate through all proteins in the model
proteinSet = model.getObjects(Protein.class);
for (Protein currentProtein : proteinSet)
{
EntityReference entityReference = currentProtein.getEntityReference();
if (entityReference != null)
{
Set xrefSet = entityReference.getXref();
for (Xref currentRef : xrefSet)
{
if (currentRef instanceof UnificationXref)
{
System.out.println(
"Unification XRef: " + currentRef.getDb() + ": " + currentRef.getId
());
}
}
}
}
}
public void highlightWorkaround()
{
myFirstModel();
IO(null, null);
Excisor ex = new Excisor(null);
access1(null);
graphQuery(null, null, null, null);
}
}