Serialized Form (OWLTools-Parent 0.2.2-SNAPSHOT API)

Package org.geneontology.lego.model
- Class org.geneontology.lego.model.LegoTools.UnExpectedStructureException extends Exception implements Serializable
  
  serialVersionUID:
  
  -3343544020570925182L
Package owltools
- Class owltools.TBoxUnFoldingTool.NonDeterministicUnfoldException extends Exception implements Serializable
  
  serialVersionUID:
  
  337910909767722849L
Package owltools.cli
- Class owltools.cli.CommandRunner.OptionException extends Exception implements Serializable
  
  serialVersionUID:
  
  8770773099868997872L
Package owltools.gaf.godb
- Class owltools.gaf.godb.ReferentialIntegrityException extends Exception implements Serializable
Package owltools.gaf.rules
- Class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException extends Exception implements Serializable
  
  serialVersionUID:
  
  4692086624612112588L
Package owltools.graph
- Class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet extends HashSet<OWLGraphEdge> implements Serializable
  
  serialVersionUID:
  
  -3155229334639121333L
- Class owltools.graph.SharedLabelException extends Exception implements Serializable
Package owltools.io
- Class owltools.io.OWLJSONFormat extends org.semanticweb.owlapi.model.OWLOntologyFormat implements Serializable
  - Serialized Fields
    - idSpaceManager
```
org.coode.owlapi.obo.parser.IDSpaceManager idSpaceManager
```
Package owltools.mooncat
- Class owltools.mooncat.SpeciesMergeUtil.UnmergeableOntologyException extends Exception implements Serializable
Package owltools.mooncat.ontologymetadata
- Class owltools.mooncat.ontologymetadata.ImportChainDotWriter.UnExpectedStructureException extends Exception implements Serializable
Package owltools.ontologyrelease
- Class owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException extends Exception implements Serializable
  
  serialVersionUID:
  
  3027646526727891643L
  - Serialized Fields
    - message
```
String message
```
    - reasons
```
List<E> reasons
```
    - hint
```
String hint
```
Package owltools.ontologyrelease.gui
- Class owltools.ontologyrelease.gui.OortGuiAdvancedPanel extends org.obolibrary.gui.GuiTools.SizedJPanel implements Serializable
  
  serialVersionUID:
  
  6890664004411145411L
  - Serialized Fields
    - panel
```
JPanel panel
```
    - assertedCheckBox
```
JCheckBox assertedCheckBox
```
    - simpleCheckBox
```
JCheckBox simpleCheckBox
```
    - expandXrefsCheckBox
```
JCheckBox expandXrefsCheckBox
```
    - recreateMireot
```
JCheckBox recreateMireot
```
    - repairAnnotationCardinality
```
JCheckBox repairAnnotationCardinality
```
    - expandShortcutRelations
```
JCheckBox expandShortcutRelations
```
    - writeELOntologyCheckBox
```
JCheckBox writeELOntologyCheckBox
```
    - justifyAssertedSubclasses
```
JCheckBox justifyAssertedSubclasses
```
    - writeSubSets
```
JCheckBox writeSubSets
```
    - gafToOwl
```
JCheckBox gafToOwl
```
    - writeOWL
```
JCheckBox writeOWL
```
    - writeOWX
```
JCheckBox writeOWX
```
    - writeOBO
```
JCheckBox writeOBO
```
    - versionReportFiles
```
JCheckBox versionReportFiles
```
    - addSupportFromImports
```
JCheckBox addSupportFromImports
```
    - allowOverwrite
```
JCheckBox allowOverwrite
```
    - catalogXMLField
```
JTextField catalogXMLField
```
    - hermitRadioButton
```
JRadioButton hermitRadioButton
```
    - factppRadioButton
```
JRadioButton factppRadioButton
```
    - jcelRadioButton
```
JRadioButton jcelRadioButton
```
    - elkRadioButton
```
JRadioButton elkRadioButton
```
    - moreRadioButton
```
JRadioButton moreRadioButton
```
    - ontologyCheckBoxes
```
Map<K,V> ontologyCheckBoxes
```
    - frame
```
Frame frame
```
- Class owltools.ontologyrelease.gui.OortGuiMainFrame extends JFrame implements Serializable
  
  serialVersionUID:
  
  6955854898081677364L
  - Serialized Fields
    - allPanel
```
JPanel allPanel
```
    - mainPanel
```
OortGuiMainPanel mainPanel
```
    - advancedPanel
```
OortGuiAdvancedPanel advancedPanel
```
    - dynamicOntologyPanel
```
OortGuiQueryOntologyPanel dynamicOntologyPanel
```
    - logPanel
```
org.obolibrary.gui.GuiLogPanel logPanel
```
    - logQueue
```
BlockingQueue<E> logQueue
```
    - parameters
```
OortGuiConfiguration parameters
```
    - tabbedPane
```
JTabbedPane tabbedPane
```
    - releaseButton
```
JButton releaseButton
```
- Class owltools.ontologyrelease.gui.OortGuiMainPanel extends org.obolibrary.gui.GuiTools.SizedJPanel implements Serializable
  
  serialVersionUID:
  
  1281395185956670966L
  - Serialized Fields
    - frame
```
Frame frame
```
    - inputSourcesJList
```
JList<E> inputSourcesJList
```
    - outputFolderTextField
```
JTextField outputFolderTextField
```
    - rdfXmlRadioButton
```
JRadioButton rdfXmlRadioButton
```
    - sources
```
LinkedHashMap<K,V> sources
```
- Class owltools.ontologyrelease.gui.OortGuiMenuBar extends JMenuBar implements Serializable
  
  serialVersionUID:
  
  -8587366759371533588L
  - Serialized Fields
    - frame
```
OortGuiMainFrame frame
```
    - parameters
```
OortConfiguration parameters
```
    - loadItem
```
JMenuItem loadItem
```
    - storeItem
```
JMenuItem storeItem
```
    - exitItem
```
JMenuItem exitItem
```
    - fileMenu
```
JMenu fileMenu
```
    - fileHistory
```
owltools.ontologyrelease.gui.OortGuiMenuBar.FileHistory fileHistory
```
- Class owltools.ontologyrelease.gui.OortGuiQueryOntologyPanel extends org.obolibrary.gui.GuiTools.SizedJPanel implements Serializable
  
  serialVersionUID:
  
  -1161204664170884076L
  - Serialized Fields
    - frame
```
Frame frame
```
    - panel
```
JPanel panel
```
    - activateCheckBox
```
JCheckBox activateCheckBox
```
    - removeQueryTermCheckBox
```
JCheckBox removeQueryTermCheckBox
```
    - queryOntologyField
```
JTextField queryOntologyField
```
    - queryTargetField
```
JTextField queryTargetField
```
    - queryTargetIriRadioButton
```
JRadioButton queryTargetIriRadioButton
```
    - queryTargetLabelRadioButton
```
JRadioButton queryTargetLabelRadioButton
```
    - subComponents
```
List<E> subComponents
```
Package owltools.sim
- Class owltools.sim.SimEngine.SimilarityAlgorithmException extends Exception implements Serializable
Package owltools.sim2
- Class owltools.sim2.CutoffException extends Exception implements Serializable
  
  serialVersionUID:
  
  -2061400251377976252L
  - Serialized Fields
    - measure
```
String measure
```
    - cutoff
```
Double cutoff
```
    - value
```
Double value
```
    - valueType
```
Class<T> valueType
```
- Class owltools.sim2.NoElementAttributeMapException extends Exception implements Serializable
  
  serialVersionUID:
  
  430378513452288525L
- Class owltools.sim2.UnknownOWLClassException extends Exception implements Serializable
Package owltools.sim2.kb
- Class owltools.sim2.kb.OwlSimVarianceEntityReferenceNotFoundException extends Exception implements Serializable
  
  serialVersionUID:
  
  6423212555022436347L
Package owltools.util
- Class owltools.util.BloomFilter extends Object implements Serializable
  
  serialVersionUID:
  
  227290544971419817L
  - Serialized Fields
    - bitset
```
BitSet bitset
```
    - bitSetSize
```
int bitSetSize
```
    - bitsPerElement
```
double bitsPerElement
```
    - expectedNumberOfFilterElements
```
int expectedNumberOfFilterElements
```
    - numberOfAddedElements
```
int numberOfAddedElements
```
    - k
```
int k
```

Serialized Form

Package org.geneontology.lego.model

Class org.geneontology.lego.model.LegoTools.UnExpectedStructureException extends Exception implements Serializable

Package owltools

Class owltools.TBoxUnFoldingTool.NonDeterministicUnfoldException extends Exception implements Serializable

Package owltools.cli

Class owltools.cli.CommandRunner.OptionException extends Exception implements Serializable

Package owltools.gaf.godb

Class owltools.gaf.godb.ReferentialIntegrityException extends Exception implements Serializable

Package owltools.gaf.rules

Class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException extends Exception implements Serializable

Package owltools.graph

Class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet extends HashSet<OWLGraphEdge> implements Serializable

Class owltools.graph.SharedLabelException extends Exception implements Serializable

Package owltools.io

Class owltools.io.OWLJSONFormat extends org.semanticweb.owlapi.model.OWLOntologyFormat implements Serializable

Serialized Fields

idSpaceManager

Package owltools.mooncat

Class owltools.mooncat.SpeciesMergeUtil.UnmergeableOntologyException extends Exception implements Serializable

Package owltools.mooncat.ontologymetadata

Class owltools.mooncat.ontologymetadata.ImportChainDotWriter.UnExpectedStructureException extends Exception implements Serializable

Package owltools.ontologyrelease

Class owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException extends Exception implements Serializable

Serialized Fields

message

reasons

hint

Package owltools.ontologyrelease.gui

Class owltools.ontologyrelease.gui.OortGuiAdvancedPanel extends org.obolibrary.gui.GuiTools.SizedJPanel implements Serializable

Serialized Fields

panel

assertedCheckBox

simpleCheckBox

expandXrefsCheckBox

recreateMireot

repairAnnotationCardinality

expandShortcutRelations

writeELOntologyCheckBox

justifyAssertedSubclasses

writeSubSets

gafToOwl

writeOWL

writeOWX

writeOBO

versionReportFiles

addSupportFromImports

allowOverwrite

catalogXMLField

hermitRadioButton

factppRadioButton

jcelRadioButton

elkRadioButton

moreRadioButton

ontologyCheckBoxes

frame

Class owltools.ontologyrelease.gui.OortGuiMainFrame extends JFrame implements Serializable

Serialized Fields

allPanel

mainPanel

advancedPanel

dynamicOntologyPanel

logPanel

logQueue

parameters

tabbedPane

releaseButton

Class owltools.ontologyrelease.gui.OortGuiMainPanel extends org.obolibrary.gui.GuiTools.SizedJPanel implements Serializable

Serialized Fields

frame

inputSourcesJList

outputFolderTextField

rdfXmlRadioButton

sources

Class owltools.ontologyrelease.gui.OortGuiMenuBar extends JMenuBar implements Serializable

Serialized Fields

frame

parameters

loadItem

storeItem