Deprecated API

Contents

• Deprecated Packages
• Deprecated Classes
• Deprecated Methods
• Deprecated Constructors
• Deprecated Enum Constants

Deprecated Packages

Package and Description
org.biopax.paxtools.io.sif please use Paxtools pattern module for exporting to the SIF and extended SIF formats.

Deprecated Classes

Class and Description
org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer
org.biopax.paxtools.util.BasicFilterFactory Hibernate ORM/Search will be removed in v5
org.biopax.paxtools.util.DataSourceFieldBridge Hibernate ORM/Search will be removed in v5
org.biopax.paxtools.util.DataSourceFilterFactory Hibernate ORM/Search will be removed in v5
org.biopax.paxtools.util.OrganismFieldBridge Hibernate ORM/Search will be removed in v5
org.biopax.paxtools.util.OrganismFilterFactory Hibernate ORM/Search will be removed in v5
org.biopax.paxtools.pattern.constraint.OtherSide
org.biopax.paxtools.util.ParentPathwayFieldBridge Hibernate ORM/Search will be removed in v5
org.biopax.paxtools.pattern.constraint.ParticipatingPE
org.biopax.paxtools.util.SetStringBridge Hibernate ORM/Search will be removed in v5
org.biopax.paxtools.io.sif.SimpleInteractionConverter use the pattern (new Paxtools' module) api instead
org.biopax.paxtools.util.XrefFieldBridge Hibernate ORM/Search will be removed in v5

Deprecated Methods

Method and Description
org.biopax.paxtools.io.BioPAXIOHandlerAdapter.convertFromMultipleOwlFiles(String...) experimental and incomplete; e.g., files are to be ordered, i.e., a former file should not point to the latter. Use it at your own risk. Or, use #convertFromOWL to get independent models; then, try merging them...
org.biopax.paxtools.impl.level3.L3ElementImpl.getDatasources() use getAnnotations() instead
org.biopax.paxtools.impl.level3.L3ElementImpl.getKeywords() use getAnnotations() instead
org.biopax.paxtools.impl.level3.L3ElementImpl.getOrganisms() use getAnnotations() instead
org.biopax.paxtools.impl.level3.L3ElementImpl.getParentPathways() use getAnnotations() instead
org.biopax.paxtools.io.BioPAXIOHandlerAdapter.isTreatNilAsNull() This problem is fixed and this option is no longer needed for recent BioCyc exports. Enable only if you are parsing a legacy export.
org.biopax.paxtools.io.BioPAXIOHandlerAdapter.L1ToL2Fixes(PropertyEditor, BioPAXElement, Model, String) BioPAX Level 1 exports are extremely rare and obsolete.
org.biopax.paxtools.query.QueryExecuter.runGOI(Set<BioPAXElement>, Model, int, Filter...) Use runPathsBetween instead
org.biopax.paxtools.io.BioPAXIOHandlerAdapter.setConvertingFromLevel1ToLevel2(boolean) BioPAX Level 1 exports are extremely rare and obsolete.
org.biopax.paxtools.io.BioPAXIOHandler.setConvertingFromLevel1ToLevel2(boolean) BioPAX Level 1 exports are obsolete (anyway, L1 input is always converted to L2 automatically).
org.biopax.paxtools.io.BioPAXIOHandlerAdapter.treatNilAsNull(boolean) This problem is fixed and this option is no longer needed for recent BioCyc exports. Enable only if you are parsing a legacy export.

Deprecated Constructors

Constructor and Description
org.biopax.paxtools.controller.ShallowCopy(EditorMap) use Level based constructor instead.

Deprecated Enum Constants

Enum Constant and Description
org.biopax.paxtools.model.level3.ControlType.ACTIVATION_UNKMECH LEVEL 1 workaround
org.biopax.paxtools.model.level3.ControlType.INHIBITION_UNKMECH LEVEL 1 workaround