org.colomoto.biolqm.io.sbml

Class SBMLqualExport

java.lang.Object

java.lang.Thread

org.colomoto.common.task.AbstractTask<Boolean>

org.colomoto.biolqm.io.BaseExporter

org.colomoto.biolqm.io.sbml.SBMLqualExport

All Implemented Interfaces:

Runnable, Callable<Boolean>, ModelExporter, Task<Boolean>

public class SBMLqualExport
extends BaseExporter

SBML export using JSBML and the "qual" extension.

Author:

Aurelien Naldi

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields inherited from class org.colomoto.biolqm.io.BaseExporter

model, streams

Fields inherited from class org.colomoto.common.task.AbstractTask

canceled

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor and Description
SBMLqualExport(LogicalModel model)
SBMLqualExport(LogicalModel model, boolean addLayout)

Method Summary

Modifier and Type	Method and Description
void	ensureFilled()
void	export()
SBMLQualBundle	getSBMLBundle()
org.sbml.jsbml.SBMLDocument	getSBMLDocument()
org.sbml.jsbml.ext.qual.QualitativeSpecies	getSpecies(NodeInfo ni)
void	setInitialCondition(byte[] state) Apply an initial condition to the exported model.

Methods inherited from class org.colomoto.biolqm.io.BaseExporter

performTask, setDestination

Methods inherited from class org.colomoto.common.task.AbstractTask

background, call, cancel, getResult, getStatus, run

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.colomoto.biolqm.io.ModelExporter

setDestination, setDestination

Methods inherited from interface org.colomoto.common.task.Task

background, cancel, getResult, getStatus, setParameter, setParameters, setParameters

Methods inherited from interface java.util.concurrent.Callable

call

Constructor Detail

SBMLqualExport

public SBMLqualExport(LogicalModel model)

SBMLqualExport

public SBMLqualExport(LogicalModel model,
                      boolean addLayout)

Method Detail

export

public void export()
            throws IOException

Specified by:

export in class BaseExporter

Throws:

IOException

getSBMLDocument

public org.sbml.jsbml.SBMLDocument getSBMLDocument()

getSBMLBundle

public SBMLQualBundle getSBMLBundle()

ensureFilled

public void ensureFilled()

setInitialCondition

public void setInitialCondition(byte[] state)

Apply an initial condition to the exported model.

Parameters:

state - the initial levels for each core component (negative values for unspecified)

getSpecies

public org.sbml.jsbml.ext.qual.QualitativeSpecies getSpecies(NodeInfo ni)