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A

addRowGap(JPanel, GuiTools.GBHelper, int) - Static method in class org.obolibrary.gui.GuiTools
Add an additional row with a fixed size for layout purposes.
allowDangling - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
anchorCenter() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Set the anchor to center.

B

buildAllOboOwlFiles(String, OBORunnerConfiguration, Logger, OWLOntologyManager) - Static method in class org.obolibrary.cli.OBODiffRunner
makes OWL from all selected ontologies.
buildAllOboOwlFiles(String, OBORunnerConfiguration, Logger, OWLOntologyManager) - Static method in class org.obolibrary.cli.OBORunner
makes OWL from all selected ontologies.
buildDir - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

C

convert(OBODoc, boolean) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
convertURL(String, String) - Static method in class org.obolibrary.obo2owl.Obo2Owl
Static convenience method which: (1) creates an Obo2Owl bridge object (2) parses an obo file from a URL (3) converts that to an OWL ontology (4) saves the OWL ontology as RDF/XML
createStorer() - Method in class org.obolibrary.owl.LabelFunctionalSyntaxStorerFactory
 
createTextField(String) - Static method in class org.obolibrary.gui.GuiTools
Create a new JTextField and set text value to a give default.

D

DEFAULT_IRI_PREFIX - Static variable in class org.obolibrary.obo2owl.Obo2Owl
Deprecated.
defaultOnt - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
disableRunButton() - Method in class org.obolibrary.gui.GuiMainFrame
 
doesReadValue() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 

E

enableRunButton() - Method in class org.obolibrary.gui.GuiMainFrame
 
executeConversion(OBORunnerConfiguration) - Method in class org.obolibrary.gui.GuiMainFrame
Execute the actual conversion.
expandH() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Expandable Height.
expandMacrosMode - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
expandW() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Expandable Width.
ExportLabelsAsOWL - Class in org.obolibrary.examples
Saves an OWL ontology consisting only of labels argument 1: a file path to an input obo file argument 2: a file path to an output owl file Example: java org.obolibrary.examples.ExportLabelsAsOWL human-phenotype-ontology.obo labels.owl
ExportLabelsAsOWL() - Constructor for class org.obolibrary.examples.ExportLabelsAsOWL
 

F

fill() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Set the fill to both.
followImports - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
format - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

G

GBHelper() - Constructor for class org.obolibrary.gui.GuiTools.GBHelper
 
getDescription() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
getFileSelector(Frame, boolean, String, String, String, String[]) - Static method in class org.obolibrary.gui.SelectDialog
Create a new dialog, which selects a file from the file system.
getFolderSelector(Frame, String, String) - Static method in class org.obolibrary.gui.SelectDialog
Create a new dialog, which selects a folder from the file system.
getName() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
getParameters() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
getSelected() - Method in class org.obolibrary.gui.SelectDialog
Retrieve the selected file/folder.
getSelectedCanonicalPath() - Method in class org.obolibrary.gui.SelectDialog
Retrieve the canonical path of the selected folder.
getSetValueFailure() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
getStrings(JTextArea) - Static method in class org.obolibrary.gui.GuiTools
Retrieve the lines as a list of strings from a given JTextArea.
getValue() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
getVariables() - Method in class org.obolibrary.cli.OBORunnerConfiguration
 
GuiAdvancedDirectionSpecificPanel - Class in org.obolibrary.gui
GUI elements for the advanced settings of the converter
GuiAdvancedDirectionSpecificPanel(boolean, boolean, boolean, String, boolean, boolean) - Constructor for class org.obolibrary.gui.GuiAdvancedDirectionSpecificPanel
Create GUI panel for advanced settings specific for either conversion direction with the given default values.
GuiAdvancedPanel - Class in org.obolibrary.gui
GUI elements for the advanced settings of the converter
GuiAdvancedPanel(Frame, Collection<String>, Collection<String>, String) - Constructor for class org.obolibrary.gui.GuiAdvancedPanel
Create GUI panel for advanced settings with the given default values.
GuiLogPanel - Class in org.obolibrary.gui
Panel for rendering the log in the GUI.
GuiLogPanel(BlockingQueue<String>) - Constructor for class org.obolibrary.gui.GuiLogPanel
Construct a new LogPanel using the given log message queue.
GuiMainFrame - Class in org.obolibrary.gui
GUI main frame, calls all constructors for the sub components.
GuiMainFrame() - Constructor for class org.obolibrary.gui.GuiMainFrame
Default constructor, required only for testing the GUI as bean.
GuiMainFrame(BlockingQueue<String>, OBORunnerConfiguration) - Constructor for class org.obolibrary.gui.GuiMainFrame
Main constructor.
GuiMainPanel - Class in org.obolibrary.gui
GUI component for the minimum number of configurations required for the conversion.
GuiMainPanel(GuiMainFrame, Iterable<String>, String, boolean) - Constructor for class org.obolibrary.gui.GuiMainPanel
Constructor allows to build a panel with default values
GuiTools - Class in org.obolibrary.gui
Tools for the layout and handling of the GUI components.
GuiTools() - Constructor for class org.obolibrary.gui.GuiTools
 
GuiTools.GBHelper - Class in org.obolibrary.gui
Simplify the GridBagConstrains handling.
GuiTools.SizedJPanel - Class in org.obolibrary.gui
All tabbed panels should have the same preferred size.

H

height(int) - Method in class org.obolibrary.gui.GuiTools.GBHelper
Sets the height of the area in terms of rows.

I

indentLeft(int) - Method in class org.obolibrary.gui.GuiTools.GBHelper
Increase indent in the left.
indentRight(int) - Method in class org.obolibrary.gui.GuiTools.GBHelper
Increase indent in the left.
isDisableDocumentChecking - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
isEmpty() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
isExpandMacros - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
isOboToOwl - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

L

LabelFunctionalSyntaxStorerFactory - Class in org.obolibrary.owl
 
LabelFunctionalSyntaxStorerFactory() - Constructor for class org.obolibrary.owl.LabelFunctionalSyntaxStorerFactory
 
LOAD - Static variable in class org.obolibrary.gui.SelectDialog
 

M

main(String[]) - Static method in class org.obolibrary.cli.OBODiffRunner
 
main(String[]) - Static method in class org.obolibrary.cli.OBORunner
 
main(String[]) - Static method in class org.obolibrary.cli.OBORunnerGui
 
main(String[]) - Static method in class org.obolibrary.examples.ExportLabelsAsOWL
 

N

nextCol() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Moves the helper's cursor to the right one column.
nextRow() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Moves the helper's cursor to first col in next row.

O

Obo2Owl - Class in org.obolibrary.obo2owl
 
Obo2Owl() - Constructor for class org.obolibrary.obo2owl.Obo2Owl
 
Obo2Owl(OWLOntologyManager) - Constructor for class org.obolibrary.obo2owl.Obo2Owl
 
OBODiffRunner - Class in org.obolibrary.cli
command line access to obo2owl
OBODiffRunner() - Constructor for class org.obolibrary.cli.OBODiffRunner
 
OBORunner - Class in org.obolibrary.cli
command line access to obo2owl
OBORunner() - Constructor for class org.obolibrary.cli.OBORunner
 
OBORunnerConfigCLIReader - Class in org.obolibrary.cli
 
OBORunnerConfigCLIReader() - Constructor for class org.obolibrary.cli.OBORunnerConfigCLIReader
 
OBORunnerConfiguration - Class in org.obolibrary.cli
 
OBORunnerConfiguration() - Constructor for class org.obolibrary.cli.OBORunnerConfiguration
 
OBORunnerConfiguration.ExpandMacrosModeOptions - Enum in org.obolibrary.cli
 
OBORunnerConfiguration.Variable<T> - Class in org.obolibrary.cli
 
OBORunnerGui - Class in org.obolibrary.cli
GUI access for converter.
OBORunnerGui() - Constructor for class org.obolibrary.cli.OBORunnerGui
 
omitOntsToDownload - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
ontsToDownload - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
org.obolibrary.cli - package org.obolibrary.cli
 
org.obolibrary.examples - package org.obolibrary.examples
 
org.obolibrary.gui - package org.obolibrary.gui
 
org.obolibrary.obo2owl - package org.obolibrary.obo2owl
 
org.obolibrary.owl - package org.obolibrary.owl
 
outFile - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
outputdir - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
Owl2Obo - Class in org.obolibrary.obo2owl
 
Owl2Obo() - Constructor for class org.obolibrary.obo2owl.Owl2Obo
 
Owl2Obo(OWLOntologyManager) - Constructor for class org.obolibrary.obo2owl.Owl2Obo
 

P

paths - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

R

readConfig(String[]) - Static method in class org.obolibrary.cli.OBORunnerConfigCLIReader
 
runConversion(OBORunnerConfiguration, Logger, OWLOntologyManager) - Static method in class org.obolibrary.cli.OBODiffRunner
 
runConversion(OBORunnerConfiguration, Logger, OWLOntologyManager, OWLOntologyManager) - Static method in class org.obolibrary.cli.OBORunner
 

S

SAVE - Static variable in class org.obolibrary.gui.SelectDialog
 
SelectDialog - Class in org.obolibrary.gui
Wrapper for the native FileDialog.
SelectDialog() - Constructor for class org.obolibrary.gui.SelectDialog
 
setRealValue(T) - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
setValue(String) - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
show() - Method in class org.obolibrary.gui.SelectDialog
Show the dialog to the user for selection.
showHelp - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
showMemory() - Static method in class org.obolibrary.cli.OBODiffRunner
 
showMemory() - Static method in class org.obolibrary.cli.OBORunner
 
SizedJPanel() - Constructor for class org.obolibrary.gui.GuiTools.SizedJPanel
 
strictConversion - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

T

toString() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 

U

untranslatableAxiomsFile - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

V

value - Variable in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
valueOf(String) - Static method in enum org.obolibrary.cli.OBORunnerConfiguration.ExpandMacrosModeOptions
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.obolibrary.cli.OBORunnerConfiguration.ExpandMacrosModeOptions
Returns an array containing the constants of this enum type, in the order they are declared.
Variable(String, T) - Constructor for class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
version - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

W

width(int) - Method in class org.obolibrary.gui.GuiTools.GBHelper
Sets the width of the area in terms of rows.
writeLabelOWL - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
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