Package | Description |
---|---|
edu.ucsd.sbrg.escher | |
edu.ucsd.sbrg.escher.converter |
Provides converters for Escher JSON to community standards (SBGN, SBML) and vice-versa.
|
edu.ucsd.sbrg.escher.gui |
Classes for the graphical user interface.
|
edu.ucsd.sbrg.escher.model |
Represents model classes for representation of Escher's components.
|
edu.ucsd.sbrg.escher.util |
Provides utility methods, e.g. validation, Jackson mappers, command line options, etc.
|
Modifier and Type | Method and Description |
---|---|
static EscherMap |
EscherConverter.convert(org.sbgn.bindings.Sbgn document,
de.zbit.util.prefs.SBProperties properties)
Calls SBGN-ML to Escher converter.
|
static EscherMap |
EscherConverter.parseEscherJson(File input)
Parses given JSON file into an
EscherMap instance using Jackson. |
static EscherMap |
EscherConverter.parseEscherJson(InputStream stream)
Parses an
InputStream that represents an Escher JSON file into an
EscherMap instance using Jackson. |
static EscherMap |
EscherConverter.parseSBGNML(File input,
de.zbit.util.prefs.SBProperties properties) |
static EscherMap |
EscherConverter.parseSBGNML(InputStream is,
de.zbit.util.prefs.SBProperties properties)
Parses an SBGNML input and calls a convert method to
EscherMap . |
Modifier and Type | Method and Description |
---|---|
static List<EscherMap> |
EscherConverter.convert(org.sbml.jsbml.SBMLDocument document,
de.zbit.util.prefs.SBProperties properties)
Calls SBML Layout Extension to Escher converter.
|
Modifier and Type | Method and Description |
---|---|
static <T> T |
EscherConverter.convert(EscherMap map,
Class<? extends T> format,
de.zbit.util.prefs.SBProperties properties)
Generic method which converts the given
EscherMap instance to the specified
generic parameter format , by calling the corresponding converter. |
static void |
EscherConverter.writeEscherJson(EscherMap map,
File output)
Serializes an
EscherMap instance to JSON and writes to output file. |
Modifier and Type | Method and Description |
---|---|
static void |
EscherConverter.writeEscherJson(List<EscherMap> mapList,
File output)
Serializes a
List to JSON and writes to output directory. |
Modifier and Type | Field and Description |
---|---|
protected EscherMap |
SBGN2Escher.escherMap
Output Escher map.
|
Modifier and Type | Field and Description |
---|---|
protected List<EscherMap> |
SBML2Escher.escherMaps
List of escher maps converted from the layouts exported from the SBML document.
|
Modifier and Type | Method and Description |
---|---|
EscherMap |
SBGN2Escher.convert(org.sbgn.bindings.Sbgn document)
Converts
Sbgn document to EscherMap by iteratively creating nodes,
reactions, etc. |
Modifier and Type | Method and Description |
---|---|
List<EscherMap> |
SBML2Escher.convert(org.sbml.jsbml.SBMLDocument doc)
Converts an
SBMLDocument to a list of EscherMap s by iteratively creating nodes,
reactions, etc. |
Modifier and Type | Method and Description |
---|---|
abstract T |
Escher2Standard.convert(EscherMap map) |
org.sbml.jsbml.SBMLDocument |
Escher2SBML.convert(EscherMap map) |
org.sbgn.bindings.Sbgn |
Escher2SBGN.convert(EscherMap escherMap) |
void |
Escher2Standard.preprocessDataStructure(EscherMap escherMap)
Pre-processes every reaction in a data structure
|
Modifier and Type | Method and Description |
---|---|
protected List<de.zbit.io.OpenedFile<EscherMap>> |
EscherParserWorker.doInBackground() |
de.zbit.io.OpenedFile<EscherMap> |
EscherMapDisplay.getOpenedFile() |
Modifier and Type | Method and Description |
---|---|
protected void |
EscherParserWorker.process(List<de.zbit.io.OpenedFile<EscherMap>> chunks) |
Constructor and Description |
---|
EscherConverterWorker(EscherMap map,
Class<? extends T> format,
de.zbit.util.prefs.SBProperties properties) |
Constructor and Description |
---|
EscherMapDisplay(de.zbit.io.OpenedFile<EscherMap> openedFile,
de.zbit.util.prefs.SBProperties properties) |
Modifier and Type | Method and Description |
---|---|
EscherMap |
EscherMap.clone() |
Modifier and Type | Method and Description |
---|---|
Node |
EscherReaction.findMidmarker(EscherMap map) |
Constructor and Description |
---|
EscherMap(EscherMap escherMap)
Copy constructor.
|
Modifier and Type | Method and Description |
---|---|
EscherMap |
EscherParser.parse(File jsonFile)
Deprecated.
|
EscherMap |
EscherParser.parse(InputStream inputStream,
String defaultMapId)
Deprecated.
|
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