Package de.unirostock.sems.bives.sbml.algorithm

Class SBMLConnectorPreprocessor

java.lang.Object

de.unirostock.sems.bives.algorithm.Connector

de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor

public class SBMLConnectorPreprocessor
extends de.unirostock.sems.bives.algorithm.Connector

The Class SBMLConnectorPreprocessor to pre-compute a mapping.

Author:

Martin Scharm

Field Summary

Fields inherited from class de.unirostock.sems.bives.algorithm.Connector

allowDifferentIds, careAboutNames, conMgmt, docA, docB, stricterNames

Constructor Summary

Constructors

Constructor	Description
SBMLConnectorPreprocessor(de.unirostock.sems.bives.algorithm.Connector preprocessor)	Instantiates a new sBML connector preprocessor.
SBMLConnectorPreprocessor(de.unirostock.sems.bives.algorithm.Connector preprocessor, boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames)	Instantiates a new sBML connector preprocessor.
SBMLConnectorPreprocessor(SBMLDocument sbmlDocA, SBMLDocument sbmlDocB)	Instantiates a new sBML connector preprocessor.
SBMLConnectorPreprocessor(SBMLDocument sbmlDocA, SBMLDocument sbmlDocB, boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames)	Instantiates a new sBML connector preprocessor.

Method Summary

Modifier and Type	Method	Description
protected void	connect()
protected void	init()

Methods inherited from class de.unirostock.sems.bives.algorithm.Connector

findConnections, getConnections, getDocA, getDocB, nodeAssign

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLConnectorPreprocessor

public SBMLConnectorPreprocessor(SBMLDocument sbmlDocA,
                                 SBMLDocument sbmlDocB,
                                 boolean allowDifferentIds,
                                 boolean careAboutNames,
                                 boolean stricterNames)

Instantiates a new sBML connector preprocessor.

Parameters:

sbmlDocA - the original document

sbmlDocB - the modified document

allowDifferentIds - may mapped entities have different ids? see Diff.ALLOW_DIFFERENT_IDS

careAboutNames - should we care about names? see Diff.CARE_ABOUT_NAMES

stricterNames - should we handle the names very strictly? see Diff.STRICTER_NAMES

SBMLConnectorPreprocessor

public SBMLConnectorPreprocessor(SBMLDocument sbmlDocA,
                                 SBMLDocument sbmlDocB)

Instantiates a new sBML connector preprocessor. Uses default values for the mapping, see Diff.ALLOW_DIFFERENT_IDS, Diff.CARE_ABOUT_NAMES, and Diff.STRICTER_NAMES.

Parameters:

sbmlDocA - the original document

sbmlDocB - the modified document

SBMLConnectorPreprocessor

public SBMLConnectorPreprocessor(de.unirostock.sems.bives.algorithm.Connector preprocessor,
                                 boolean allowDifferentIds,
                                 boolean careAboutNames,
                                 boolean stricterNames)

Instantiates a new sBML connector preprocessor.

Parameters:

preprocessor - the preprocessor

allowDifferentIds - may mapped entities have different ids? see Diff.ALLOW_DIFFERENT_IDS

careAboutNames - should we care about names? see Diff.CARE_ABOUT_NAMES

stricterNames - should we handle the names very strictly? see Diff.STRICTER_NAMES

SBMLConnectorPreprocessor

public SBMLConnectorPreprocessor(de.unirostock.sems.bives.algorithm.Connector preprocessor)

Instantiates a new sBML connector preprocessor. Uses default values for the mapping, see Diff.ALLOW_DIFFERENT_IDS, Diff.CARE_ABOUT_NAMES, and Diff.STRICTER_NAMES.

Parameters:

preprocessor - the preprocessor

Method Detail

init

protected void init()
             throws de.unirostock.sems.bives.exception.BivesConnectionException

Specified by:

init in class de.unirostock.sems.bives.algorithm.Connector

Throws:

de.unirostock.sems.bives.exception.BivesConnectionException

connect

protected void connect()
                throws de.unirostock.sems.bives.exception.BivesConnectionException

Specified by:

connect in class de.unirostock.sems.bives.algorithm.Connector

Throws:

de.unirostock.sems.bives.exception.BivesConnectionException