org.biopax.paxtools.io.sbgn

Class L3ToSBGNPDConverter

java.lang.Object

org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

public class L3ToSBGNPDConverter
extends Object

This class converts BioPAX L3 model into SBGN PD. It does not layout the objects, leaves location information unassigned. This version ignores several BioPAX L3 features during conversion:

• Parent-child relationship between physical entities
• Parent-child relationship between entity references
• Binding features and covalent binding features of physical entities

Also note that:

• Compartment is just a controlled vocabulary in BioPAX, so nesting and neighborhood relations between compartments are not handled here.
• Control structures in BioPAX and in SBGN PD are a little different. We use AND and NOT glyphs to approximate controls in BioPAX. However, ANDing everything is not really proper because BioPAX do not imply a logical operator between controllers.

Author:

Ozgun Babur

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	doLayout Flag to run a layout before writing down the sbgn.
protected FeatureDecorator	featStrGen This class is used for generating short printable strings (text in info boxes) from recognized entity features.
protected boolean	flattenComplexContent Option to flatten nested complexes.
static String	IS_UBIQUE Ubique label.
protected Map<String,Set<String>>	sbgn2BPMap Mapping from SBGN IDs to the IDs of the related objects in BioPAX.
protected UbiqueDetector	ubiqueDet This class is used for detecting ubiques.
protected boolean	useTwoGlyphsForReversibleConversion SBGN process glyph can be used to show reversible reactions.

Constructor Summary

Constructors

Constructor and Description
L3ToSBGNPDConverter() Empty constructor.
L3ToSBGNPDConverter(UbiqueDetector ubiqueDet, FeatureDecorator featStrGen, boolean doLayout) Constructor with parameters.

Method Summary

Modifier and Type	Method and Description
org.sbgn.bindings.Sbgn	createSBGN(Model model) Creates an Sbgn object from the given model.
Map<String,Set<String>>	getSbgn2BPMap() Gets the mapping from SBGN IDs to BioPAX IDs.
boolean	isFlattenComplexContent()
boolean	isUseTwoGlyphsForReversibleConversion() Getter class for the parameter useTwoGlyphsForReversibleConversion.
void	setFlattenComplexContent(boolean flattenComplexContent)
void	setUseTwoGlyphsForReversibleConversion(boolean useTwoGlyphsForReversibleConversion) Sets the option to use two glyphs for the reversible conversion.
void	writeSBGN(Model model, OutputStream stream) Converts the given model to SBGN, and writes in the specified output stream.
void	writeSBGN(Model model, String file) Converts the given model to SBGN, and writes in the specified file.

Methods inherited from class java.lang.Object

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

Field Detail

IS_UBIQUE

public static final String IS_UBIQUE

Ubique label.

See Also:

Constant Field Values

ubiqueDet

protected UbiqueDetector ubiqueDet

This class is used for detecting ubiques.

featStrGen

protected FeatureDecorator featStrGen

This class is used for generating short printable strings (text in info boxes) from recognized entity features.

doLayout

protected boolean doLayout

Flag to run a layout before writing down the sbgn.

sbgn2BPMap

protected Map<String,Set<String>> sbgn2BPMap

Mapping from SBGN IDs to the IDs of the related objects in BioPAX.

flattenComplexContent

protected boolean flattenComplexContent

Option to flatten nested complexes.

useTwoGlyphsForReversibleConversion

protected boolean useTwoGlyphsForReversibleConversion

SBGN process glyph can be used to show reversible reactions. In that case two ports of the process will only have product glyphs. However, this creates an incompatibility with BioPAX: reversible biochemical reactions can have catalysis with a direction. But if we use a single glyph for the process and direct that catalysis to it, then the direction of the catalysis will be lost. If we use two process nodes for the reversible reaction (one for left-to-right and another for right-to-left), then we can direct the directed catalysis to only the relevant process glyph. Also note that the layout do not support ports. If layout is run, the ports are removed. In that case it will be impossible to distinguish left and right components of the reversible process glyph because they will all be product edges.

Constructor Detail

L3ToSBGNPDConverter

public L3ToSBGNPDConverter()

Empty constructor.

L3ToSBGNPDConverter

public L3ToSBGNPDConverter(UbiqueDetector ubiqueDet,
                           FeatureDecorator featStrGen,
                           boolean doLayout)

Constructor with parameters.

Parameters:

ubiqueDet - Ubique detector class

featStrGen - feature string generator class

doLayout - whether we want to perform layout after SBGN creation.

Method Detail

isUseTwoGlyphsForReversibleConversion

public boolean isUseTwoGlyphsForReversibleConversion()

Getter class for the parameter useTwoGlyphsForReversibleConversion.

Returns:

whether use two glyphs for the reversible conversion

setUseTwoGlyphsForReversibleConversion

public void setUseTwoGlyphsForReversibleConversion(boolean useTwoGlyphsForReversibleConversion)

Sets the option to use two glyphs for the reversible conversion.

Parameters:

useTwoGlyphsForReversibleConversion - give true if use two glyphs

isFlattenComplexContent

public boolean isFlattenComplexContent()

setFlattenComplexContent

public void setFlattenComplexContent(boolean flattenComplexContent)

writeSBGN

public void writeSBGN(Model model,
                      String file)

Converts the given model to SBGN, and writes in the specified file.

Parameters:

model - model to convert

file - file to write

writeSBGN

public void writeSBGN(Model model,
                      OutputStream stream)

Converts the given model to SBGN, and writes in the specified output stream.

Parameters:

model - model to convert

stream - output stream to write

createSBGN

public org.sbgn.bindings.Sbgn createSBGN(Model model)

Creates an Sbgn object from the given model.

Parameters:

model - model to convert to SBGN

Returns:

SBGN representation of the model

getSbgn2BPMap

public Map<String,Set<String>> getSbgn2BPMap()

Gets the mapping from SBGN IDs to BioPAX IDs. This mapping is currently one-to-many, but has potential to become many-to-many in the future.

Returns:

sbgn-to-biopax mapping