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java.lang.Objectdata.petrinets.PetriNetCreator
public class PetriNetCreator
Generates a Petri net which integrates data from an arbitrary number of
networks
, complex sets
and
purification data sets
. To get a detailed
description about the topology of these Petri nets please consult the
manual of this library.
Note: This implementation does not explicitly build the full
Petri net in-memory but just outputs it to a given output stream or file.
The Petri nets classes Place
, Transition
and Arc
are currently only used as helping data objects for reading a Petri net
from a file. See also: parsePlace(String)
and
parseTransition(String)
Constructor Summary | |
---|---|
PetriNetCreator(File file)
Creates a new Petri net creator which writes its output to a given file. |
|
PetriNetCreator(OutputStream out)
Creates a new Petri net creator which writes its output to a given output stream. |
|
PetriNetCreator(String file)
Creates a new Petri net creator which writes its output to a given file. |
Method Summary | |
---|---|
void |
addComplexSet(ComplexSet set,
String name)
Adds a ComplexSet which will be integrated into the Petri net. |
void |
addInteractionNetwork(ProteinNetwork net,
String name,
boolean insertScores)
Adds a ProteinNetwork which will be integrated into the Petri net. |
void |
addPurificationData(PurificationData data,
String name)
Adds a purification data set which will be
integrated into the Petri net. |
void |
close()
Closes the output stream this creator is writing to. |
void |
createPetriNet()
Creates the Petri net and writes it to the output specified in the constructor. |
static void |
main(String[] args)
|
static Place |
parsePlace(String line)
Parses a place from a given Petri net input line |
static Transition |
parseTransition(String line)
Parses a transition from a given Petri net input line |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PetriNetCreator(String file) throws FileNotFoundException
file
- output file for the Petri net
FileNotFoundException
- if the output file could not be openedpublic PetriNetCreator(File file) throws FileNotFoundException
file
- output file for the Petri net
FileNotFoundException
- if the output file could not be openedpublic PetriNetCreator(OutputStream out)
out
- output stream the Petri net will be written toMethod Detail |
---|
public void addInteractionNetwork(ProteinNetwork net, String name, boolean insertScores)
ProteinNetwork
which will be integrated into the Petri net.
net
- network to be integratedname
- the name this network will be referenced by in the Petri netinsertScores
- insert weights of edges into the Petri net?public void addComplexSet(ComplexSet set, String name)
ComplexSet
which will be integrated into the Petri net.
set
- complex set to be integratedname
- the name this complex set will be referenced by in the Petri netpublic void addPurificationData(PurificationData data, String name)
purification data set
which will be
integrated into the Petri net.
data
- purification data set to be integratedname
- the name this dataset set will be referenced by in the Petri netpublic void createPetriNet() throws IOException
IOException
- if an input/output error occuredpublic static Place parsePlace(String line) throws ProCopeException
line
- line from the input data
ProCopeException
- if the line could not be parsedpublic static Transition parseTransition(String line)
line
- line from the input data
ProCopeException
- if the line could not be parsedpublic static void main(String[] args) throws FileNotFoundException, IOException
FileNotFoundException
IOException
public void close()
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