public class L3ToSBGNPDConverter extends Object
Modifier and Type | Field and Description |
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protected boolean |
doLayout
Flag to run a layout before writing down the sbgn.
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protected FeatureDecorator |
featStrGen
This class is used for generating short printable strings (text in info boxes) from
recognized entity features.
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protected boolean |
flattenComplexContent
Option to flatten nested complexes.
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static String |
IS_UBIQUE
Ubique label.
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protected Map<String,Set<String>> |
sbgn2BPMap
Mapping from SBGN IDs to the IDs of the related objects in BioPAX.
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protected UbiqueDetector |
ubiqueDet
This class is used for detecting ubiques.
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protected boolean |
useTwoGlyphsForReversibleConversion
SBGN process glyph can be used to show reversible reactions.
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Constructor and Description |
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L3ToSBGNPDConverter()
Empty constructor.
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L3ToSBGNPDConverter(UbiqueDetector ubiqueDet,
FeatureDecorator featStrGen,
boolean doLayout)
Constructor with parameters.
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Modifier and Type | Method and Description |
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org.sbgn.bindings.Sbgn |
createSBGN(Model model)
Creates an Sbgn object from the given model.
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Map<String,Set<String>> |
getSbgn2BPMap()
Gets the mapping from SBGN IDs to BioPAX IDs.
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boolean |
isFlattenComplexContent() |
boolean |
isUseTwoGlyphsForReversibleConversion()
Getter class for the parameter useTwoGlyphsForReversibleConversion.
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void |
setFlattenComplexContent(boolean flattenComplexContent) |
void |
setUseTwoGlyphsForReversibleConversion(boolean useTwoGlyphsForReversibleConversion)
Sets the option to use two glyphs for the reversible conversion.
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void |
writeSBGN(Model model,
OutputStream stream)
Converts the given model to SBGN, and writes in the specified output stream.
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void |
writeSBGN(Model model,
String file)
Converts the given model to SBGN, and writes in the specified file.
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public static final String IS_UBIQUE
protected UbiqueDetector ubiqueDet
protected FeatureDecorator featStrGen
protected boolean doLayout
protected Map<String,Set<String>> sbgn2BPMap
protected boolean flattenComplexContent
protected boolean useTwoGlyphsForReversibleConversion
public L3ToSBGNPDConverter()
public L3ToSBGNPDConverter(UbiqueDetector ubiqueDet, FeatureDecorator featStrGen, boolean doLayout)
ubiqueDet
- Ubique detector classfeatStrGen
- feature string generator classdoLayout
- whether we want to perform layout after SBGN creation.public boolean isUseTwoGlyphsForReversibleConversion()
public void setUseTwoGlyphsForReversibleConversion(boolean useTwoGlyphsForReversibleConversion)
useTwoGlyphsForReversibleConversion
- give true if use two glyphspublic boolean isFlattenComplexContent()
public void setFlattenComplexContent(boolean flattenComplexContent)
public void writeSBGN(Model model, String file)
model
- model to convertfile
- file to writepublic void writeSBGN(Model model, OutputStream stream)
model
- model to convertstream
- output stream to writepublic org.sbgn.bindings.Sbgn createSBGN(Model model)
model
- model to convert to SBGNpublic Map<String,Set<String>> getSbgn2BPMap()
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