Class SBMLConnector
- java.lang.Object
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- de.unirostock.sems.bives.algorithm.Connector
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- de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
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public class SBMLConnector extends de.unirostock.sems.bives.algorithm.Connector
The Class SBMLConnector to connect SBML documents.- Author:
- Martin Scharm
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Constructor Summary
Constructors Constructor Description SBMLConnector(de.unirostock.sems.bives.algorithm.Connector preprocessor)
Instantiates a new SBML connector.SBMLConnector(de.unirostock.sems.bives.algorithm.Connector preprocessor, boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames)
Instantiates a new SBML connector.SBMLConnector(SBMLDocument sbmlDocA, SBMLDocument sbmlDocB)
Instantiates a new SBML connector.SBMLConnector(SBMLDocument sbmlDocA, SBMLDocument sbmlDocB, boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames)
Instantiates a new SBML connector.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
connect()
protected void
init()
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Constructor Detail
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SBMLConnector
public SBMLConnector(SBMLDocument sbmlDocA, SBMLDocument sbmlDocB, boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames)
Instantiates a new SBML connector.- Parameters:
sbmlDocA
- the original documentsbmlDocB
- the modified documentallowDifferentIds
- may mapped entities have different ids? seeDiff.ALLOW_DIFFERENT_IDS
careAboutNames
- should we care about names? seeDiff.CARE_ABOUT_NAMES
stricterNames
- should we handle the names very strictly? seeDiff.STRICTER_NAMES
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SBMLConnector
public SBMLConnector(SBMLDocument sbmlDocA, SBMLDocument sbmlDocB)
Instantiates a new SBML connector. Uses default values for the mapping, seeDiff.ALLOW_DIFFERENT_IDS
,Diff.CARE_ABOUT_NAMES
, andDiff.STRICTER_NAMES
.- Parameters:
sbmlDocA
- the original documentsbmlDocB
- the modified document
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SBMLConnector
public SBMLConnector(de.unirostock.sems.bives.algorithm.Connector preprocessor, boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames)
Instantiates a new SBML connector.- Parameters:
preprocessor
- the preprocessorallowDifferentIds
- may mapped entities have different ids? seeDiff.ALLOW_DIFFERENT_IDS
careAboutNames
- should we care about names? seeDiff.CARE_ABOUT_NAMES
stricterNames
- should we handle the names very strictly? seeDiff.STRICTER_NAMES
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SBMLConnector
public SBMLConnector(de.unirostock.sems.bives.algorithm.Connector preprocessor)
Instantiates a new SBML connector. Uses default values for the mapping, seeDiff.ALLOW_DIFFERENT_IDS
,Diff.CARE_ABOUT_NAMES
, andDiff.STRICTER_NAMES
.- Parameters:
preprocessor
- the preprocessor
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Method Detail
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init
protected void init() throws de.unirostock.sems.bives.exception.BivesConnectionException
- Specified by:
init
in classde.unirostock.sems.bives.algorithm.Connector
- Throws:
de.unirostock.sems.bives.exception.BivesConnectionException
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connect
protected void connect()
- Specified by:
connect
in classde.unirostock.sems.bives.algorithm.Connector
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