org.colomoto.biolqm.io.sbml

Class SBMLqualImport

java.lang.Object

java.lang.Thread

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

org.colomoto.biolqm.io.BaseLoader

org.colomoto.biolqm.io.sbml.SBMLqualImport

All Implemented Interfaces:

Runnable, Callable<LogicalModel>, ModelLoader, ModelTask, Task<LogicalModel>

public class SBMLqualImport
extends BaseLoader

Crude SBML import 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.BaseLoader

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
SBMLqualImport()

Method Summary

Modifier and Type	Method and Description
int	getIndexForName(String name) Retrieve the model component corresponding to a SBML ID.
SBMLQualBundle	getQualBundle()
LogicalModel	performTask() Placeholder for the actual implementation.

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

setSource

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.ModelLoader

setSource, setSource

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

SBMLqualImport

public SBMLqualImport()

Method Detail

getQualBundle

public SBMLQualBundle getQualBundle()

performTask

public LogicalModel performTask()
                         throws IOException

Description copied from class: AbstractTask

Placeholder for the actual implementation.

Specified by:

performTask in class AbstractTask<LogicalModel>

Returns:

the result of the computation

Throws:

IOException

getIndexForName

public int getIndexForName(String name)

Retrieve the model component corresponding to a SBML ID.

Parameters:

name - a SBML ID for a species

Returns:

the index of the corresponding component in the LogicalModel