Download metingear Free Java Code

.gitignore/*www.ja  va  2  s  .  c  om*/
action/LICENSE
action/NOTICE
action/pom.xml
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/AddAnnotation.java
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/AddAuthorAnnotation.java
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/AddCitation.java
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/AssignFlags.java
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/ClearAnnotations.java
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/CreateSubset.java
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/DeleteEntities.java
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/MergeEntities.java
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/ReassignIdentifiers.java
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/Resync.java
action/src/main/java/uk/ac/ebi/mnb/dialog/edit/SplitMetabolites.java
action/src/main/java/uk/ac/ebi/mnb/dialog/file/ExportMetabolitesMDL.java
action/src/main/java/uk/ac/ebi/mnb/dialog/file/ExportStoichiometricMatrix.java
action/src/main/java/uk/ac/ebi/mnb/dialog/file/NewEntity.java
action/src/main/java/uk/ac/ebi/mnb/dialog/file/NewGeneProduct.java
action/src/main/java/uk/ac/ebi/mnb/dialog/file/NewMetabolite.java
action/src/main/java/uk/ac/ebi/mnb/dialog/file/NewReaction.java
action/src/main/java/uk/ac/ebi/mnb/dialog/file/ReactionField.java
action/src/main/java/uk/ac/ebi/mnb/dialog/file/importation/ImportModelSeed.java
action/src/main/java/uk/ac/ebi/mnb/dialog/file/importation/ImportSBML.java
action/src/main/java/uk/ac/ebi/mnb/dialog/popup/AlignmentViewer.java
action/src/main/java/uk/ac/ebi/mnb/dialog/popup/AutoComplete.java
action/src/main/java/uk/ac/ebi/mnb/dialog/popup/CrossReferenceEditorDialog.java
action/src/main/java/uk/ac/ebi/mnb/dialog/popup/PopupDialog.java
action/src/main/java/uk/ac/ebi/mnb/dialog/preferences/ResourceUpdater.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/AddFlags.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/AutomaticCrossReference.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/ChokePoint.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/CollapseStructures.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/CompareReconstruction.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/CuratedReconciliation.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/DownloadStructuresDialog.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/MergeLoci.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/RemoveWorstStructures.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/SequenceHomology.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/TransferAnnotations.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/assign/AssignReactions.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/compare/AlignReconstruction.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/curate/AssignStructure.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/curate/DatabaseSearch.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/curate/ManualCrossReferenceModule.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/curate/MetaboliteCurator.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/curate/PeptideGenerator.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/curate/WebSearch.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/gap/NonConsumptionMetabolites.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/gap/NonProductionMetabolites.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/gap/RootNonProductionMetabolites.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/gap/TerminalNonConsumptionMetabolites.java
action/src/main/java/uk/ac/ebi/mnb/dialog/tools/stoichiometry/CreateMatrix.java
action/src/main/resources/uk/ac/ebi/caf/action/action.properties
action/src/main/resources/uk/ac/ebi/mnb/dialog/file/importation/modelseed.properties
action/src/main/resources/uk/ac/ebi/mnb/dialog/popup/minus_12x12.png
action/src/main/resources/uk/ac/ebi/mnb/dialog/popup/minus_16x16.png
action/src/main/resources/uk/ac/ebi/mnb/dialog/popup/plus_12x12.png
action/src/main/resources/uk/ac/ebi/mnb/dialog/popup/plus_16x16.png
action/src/test/java/uk/ac/ebi/mnb/dialog/file/ReactionFieldTest.java
api/LICENSE
api/NOTICE
api/pom.xml
api/src/main/java/uk/ac/ebi/metingear/view/ControlAction.java
api/src/main/java/uk/ac/ebi/metingear/view/ControlDialog.java
api/src/main/java/uk/ac/ebi/metingear/view/Controllable.java
api/src/main/java/uk/ac/ebi/metingear/view/PlugableAction.java
api/src/main/java/uk/ac/ebi/metingear/view/PlugableDialog.java
api/src/main/java/uk/ac/ebi/metingear/view/Processable.java
api/src/main/java/uk/ac/ebi/metingear/view/ProcessingDialog.java
api/src/main/java/uk/ac/ebi/metingeer/interfaces/menu/ContextAction.java
api/src/main/java/uk/ac/ebi/metingeer/interfaces/menu/ContextResponder.java
api/src/main/java/uk/ac/ebi/mnb/interfaces/DialogController.java
api/src/main/java/uk/ac/ebi/mnb/interfaces/EntityTable.java
api/src/main/java/uk/ac/ebi/mnb/interfaces/EntityTableModel.java
api/src/main/java/uk/ac/ebi/mnb/interfaces/EntityView.java
api/src/main/java/uk/ac/ebi/mnb/interfaces/MainController.java
api/src/main/java/uk/ac/ebi/mnb/interfaces/SelectionController.java
api/src/main/java/uk/ac/ebi/mnb/interfaces/TargetedUpdate.java
api/src/main/java/uk/ac/ebi/mnb/interfaces/UndoableEntityEdit.java
api/src/main/java/uk/ac/ebi/mnb/interfaces/Updatable.java
api/src/main/java/uk/ac/ebi/mnb/interfaces/ViewController.java
api/src/main/resources/META-INF/licenses/apache-1.1
api/src/main/resources/META-INF/licenses/apache-2.0
api/src/main/resources/META-INF/licenses/asm-license
api/src/main/resources/META-INF/licenses/charts4j-license
api/src/main/resources/META-INF/licenses/cpl-1.0
api/src/main/resources/META-INF/licenses/jgoodies-license
api/src/main/resources/META-INF/licenses/jsbml-license
api/src/main/resources/META-INF/licenses/lgpl-2.1
app/LICENSE
app/NOTICE
app/pom.xml
app/src/main/java/mnb/todo/PredictGPR.java
app/src/main/java/mnb/todo/ReactionBalancerTask.java
app/src/main/java/mnb/view/old/GraphPanel.java
app/src/main/java/mnb/view/old/ReactionArrow.java
app/src/main/java/mnb/view/old/ReactionGraph.java
app/src/main/java/uk/ac/ebi/metingear/Main.java
app/src/main/java/uk/ac/ebi/metingear/PreMain.java
app/src/main/java/uk/ac/ebi/metingear/launch/ActionLauncherFactory.java
app/src/main/java/uk/ac/ebi/metingear/launch/ApplicationLauncher.java
app/src/main/java/uk/ac/ebi/metingear/launch/DialogLauncherFactory.java
app/src/main/java/uk/ac/ebi/metingear/launch/MacApplicationLauncher.java
app/src/main/java/uk/ac/ebi/metingear/launch/PluginLoader.java
app/src/main/java/uk/ac/ebi/metingear/preference/PreferenceFrame.java
app/src/main/java/uk/ac/ebi/metingear/preference/PreferencePanel.java
app/src/main/java/uk/ac/ebi/metingear/view/ViewToggle.java
app/src/main/java/uk/ac/ebi/mnb/editors/CrossReferenceCellEditor.java
app/src/main/java/uk/ac/ebi/mnb/main/MainView.java
app/src/main/java/uk/ac/ebi/mnb/main/Toolbar.java
app/src/main/java/uk/ac/ebi/mnb/menu/BuildMenu.java
app/src/main/java/uk/ac/ebi/mnb/menu/ContextMenu.java
app/src/main/java/uk/ac/ebi/mnb/menu/EditMenu.java
app/src/main/java/uk/ac/ebi/mnb/menu/EditUndoButtons.java
app/src/main/java/uk/ac/ebi/mnb/menu/FileMenu.java
app/src/main/java/uk/ac/ebi/mnb/menu/GapAnalysis.java
app/src/main/java/uk/ac/ebi/mnb/menu/MainMenuBar.java
app/src/main/java/uk/ac/ebi/mnb/menu/RunMenu.java
app/src/main/java/uk/ac/ebi/mnb/menu/ToolsMenu.java
app/src/main/java/uk/ac/ebi/mnb/menu/ViewMenu.java
app/src/main/java/uk/ac/ebi/mnb/menu/build/CatFamAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/build/MassChargeBalanceDialog.java
app/src/main/java/uk/ac/ebi/mnb/menu/build/PredictGPR.java
app/src/main/java/uk/ac/ebi/mnb/menu/build/PredictGPRDialog.java
app/src/main/java/uk/ac/ebi/mnb/menu/build/PriamAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/build/RunTasksAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/build/StoichiometryAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/file/ExportSBMLAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/file/ImportENAXML.java
app/src/main/java/uk/ac/ebi/mnb/menu/file/ImportKGML.java
app/src/main/java/uk/ac/ebi/mnb/menu/file/ImportPeptidesAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/file/ImportXLSAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/file/NewProject.java
app/src/main/java/uk/ac/ebi/mnb/menu/file/NewProjectAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/file/OpenAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/file/SaveAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/file/SaveAsProjectAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/popup/CloseProject.java
app/src/main/java/uk/ac/ebi/mnb/menu/popup/SetActiveProject.java
app/src/main/java/uk/ac/ebi/mnb/menu/reconciliation/AddCrossReferenceDialog.java
app/src/main/java/uk/ac/ebi/mnb/menu/view/ReactionGraphAction.java
app/src/main/java/uk/ac/ebi/mnb/menu/view/ToggleInspectorToolbar.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/AbstractEntityInspector.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/AbstractEntityPanel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/AbstractEntityTable.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/AbstractEntityTableModel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/AbstractEntityView.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/ColumnDescriptor.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/DataType.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/InspectorToolbar.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/ProjectView.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/components/AnnotationTable.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/components/AnnotationTableModel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/components/InternalReferenceModel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/components/InternalReferences.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/components/control/AnnotationControlManager.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/components/control/AnnotationTableControl.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/components/control/ChemicalStructureControl.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/components/control/ObservationBasedAnnotationControl.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/gene/GeneInspector.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/gene/GenePanel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/gene/GeneTable.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/gene/GeneTableModel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/gene/GeneView.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/general/GeneralInspector.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/general/GeneralPanel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/general/GeneralTable.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/general/GeneralTableModel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/general/GeneralView.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/metabolite/MetaboliteInspector.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/metabolite/MetabolitePanel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/metabolite/MetaboliteTable.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/metabolite/MetaboliteTableModel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/metabolite/MetaboliteView.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/protein/ProductInspector.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/protein/ProductPanel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/protein/ProductTable.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/protein/ProductTableModel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/protein/ProductView.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/reaction/ReactionInspector.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/reaction/ReactionPanel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/reaction/ReactionTable.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/reaction/ReactionTableModel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/reaction/ReactionView.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/tasks/TaskInspector.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/tasks/TaskPanel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/tasks/TaskTable.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/tasks/TaskTableModel.java
app/src/main/java/uk/ac/ebi/mnb/view/entity/tasks/TaskView.java
app/src/main/java/uk/ac/ebi/mnb/view/source/SourceController.java
app/src/main/resources/META-INF/licenses/apache-1.1
app/src/main/resources/META-INF/licenses/apache-2.0
app/src/main/resources/META-INF/licenses/asm-license
app/src/main/resources/META-INF/licenses/charts4j-license
app/src/main/resources/META-INF/licenses/cpl-1.0
app/src/main/resources/META-INF/licenses/jgoodies-license
app/src/main/resources/META-INF/licenses/jsbml-license
app/src/main/resources/META-INF/licenses/lgpl-2.1
app/src/main/resources/config/metingear-log.properties
app/src/main/resources/config/projectmanager.properties
app/src/main/resources/mnb/view/images/flags/amber_flag.png
app/src/main/resources/mnb/view/images/flags/green_flag.png
app/src/main/resources/mnb/view/images/flags/red_flag.png
app/src/main/resources/mnb/view/images/flags/white_flag.png
app/src/main/resources/uk/ac/ebi/caf/action/action.properties
app/src/main/resources/uk/ac/ebi/metingear/Info.plist
app/src/main/resources/uk/ac/ebi/metingear/splash.png
app/src/main/resources/uk/ac/ebi/metingear/view/gen-selected.png
app/src/main/resources/uk/ac/ebi/metingear/view/gen.png
app/src/main/resources/uk/ac/ebi/metingear/view/met-selected.png
app/src/main/resources/uk/ac/ebi/metingear/view/met.png
app/src/main/resources/uk/ac/ebi/metingear/view/pro-selected.png
app/src/main/resources/uk/ac/ebi/metingear/view/pro.png
app/src/main/resources/uk/ac/ebi/metingear/view/rxn-selected.png
app/src/main/resources/uk/ac/ebi/metingear/view/rxn.png
app/src/main/resources/uk/ac/ebi/mnb/view/entity/components/control/evidence.png
app/src/test/java/uk/ac/ebi/metabolicreconstructionapplication/AppTest.java
app/src/test/java/uk/ac/ebi/mnb/view/entity/AbstractEntityTableTest.java
app/src/test/java/uk/ac/ebi/mnb/view/entity/components/control/AnnotationControlManagerTest.java
core/LICENSE
core/NOTICE
core/nb-configuration.xml
core/pom.xml
core/src/main/java/uk/ac/ebi/chemet/render/source/AbbreviationAccessor.java
core/src/main/java/uk/ac/ebi/chemet/render/source/AccessionAccessor.java
core/src/main/java/uk/ac/ebi/chemet/render/source/Accessor.java
core/src/main/java/uk/ac/ebi/chemet/render/source/CollectionSourceItem.java
core/src/main/java/uk/ac/ebi/chemet/render/source/EntitySourceItem.java
core/src/main/java/uk/ac/ebi/chemet/render/source/EntitySubset.java
core/src/main/java/uk/ac/ebi/chemet/render/source/MetaboliteSourceItem.java
core/src/main/java/uk/ac/ebi/chemet/render/source/NameAccessor.java
core/src/main/java/uk/ac/ebi/chemet/render/source/ProductSourceItem.java
core/src/main/java/uk/ac/ebi/chemet/render/source/ReactionSourceItem.java
core/src/main/java/uk/ac/ebi/chemet/render/source/ReconstructionSourceItem.java
core/src/main/java/uk/ac/ebi/chemet/render/source/TaskSourceItem.java
core/src/main/java/uk/ac/ebi/metingear/SourceListTransferHandler.java
core/src/main/java/uk/ac/ebi/metingear/TransferableEntity.java
core/src/main/java/uk/ac/ebi/metingear/search/DocumentFactory.java
core/src/main/java/uk/ac/ebi/metingear/search/FieldType.java
core/src/main/java/uk/ac/ebi/metingear/search/SearchManager.java
core/src/main/java/uk/ac/ebi/metingear/search/SearchableIndex.java
core/src/main/java/uk/ac/ebi/mnb/core/AbstractMessage.java
core/src/main/java/uk/ac/ebi/mnb/core/CloseDialogAction.java
core/src/main/java/uk/ac/ebi/mnb/core/ControllerAction.java
core/src/main/java/uk/ac/ebi/mnb/core/ControllerDialog.java
core/src/main/java/uk/ac/ebi/mnb/core/ControllerDialogItem.java
core/src/main/java/uk/ac/ebi/mnb/core/DropdownMenuItem.java
core/src/main/java/uk/ac/ebi/mnb/core/EntityMap.java
core/src/main/java/uk/ac/ebi/mnb/core/ErrorMessage.java
core/src/main/java/uk/ac/ebi/mnb/core/ExpandButton.java
core/src/main/java/uk/ac/ebi/mnb/core/ExpandComponent.java
core/src/main/java/uk/ac/ebi/mnb/core/ExpandableComponentGroup.java
core/src/main/java/uk/ac/ebi/mnb/core/FileChooserAction.java
core/src/main/java/uk/ac/ebi/mnb/core/ProcessDialogAction.java
core/src/main/java/uk/ac/ebi/mnb/core/TaskManager.java
core/src/main/java/uk/ac/ebi/mnb/core/UpdatableDialogItem.java
core/src/main/java/uk/ac/ebi/mnb/core/Utilities.java
core/src/main/java/uk/ac/ebi/mnb/core/WarningMessage.java
core/src/main/java/uk/ac/ebi/mnb/view/AboutDialog.java
core/src/main/java/uk/ac/ebi/mnb/view/BorderlessScrollPane.java
core/src/main/java/uk/ac/ebi/mnb/view/DropdownDialog.java
core/src/main/java/uk/ac/ebi/mnb/view/ReconstructionChooser.java
core/src/main/java/uk/ac/ebi/mnb/view/labels/ActionLabel.java
core/src/main/java/uk/ac/ebi/mnb/view/labels/InternalLinkLabel.java
core/src/main/resources/META-INF/licenses/apache-1.1
core/src/main/resources/META-INF/licenses/apache-2.0
core/src/main/resources/META-INF/licenses/asm-license
core/src/main/resources/META-INF/licenses/charts4j-license
core/src/main/resources/META-INF/licenses/cpl-1.0
core/src/main/resources/META-INF/licenses/jgoodies-license
core/src/main/resources/META-INF/licenses/jsbml-license
core/src/main/resources/META-INF/licenses/lgpl-2.1
core/src/main/resources/uk/ac/ebi/caf/action/action.properties
core/src/main/resources/uk/ac/ebi/metingeer/images/inspector/evidence.png
core/src/test/java/uk/ac/ebi/mnb/core/EntityMapTest.java
edit/LICENSE
edit/NOTICE
edit/pom.xml
edit/src/main/java/uk/ac/ebi/edit/entity/AbbreviationSetter.java
edit/src/main/java/uk/ac/ebi/edit/entity/EntityEdit.java
edit/src/main/java/uk/ac/ebi/edit/entity/FieldManager.java
edit/src/main/java/uk/ac/ebi/edit/entity/NameSetter.java
edit/src/main/java/uk/ac/ebi/metingear/AppliableEdit.java
edit/src/main/java/uk/ac/ebi/metingear/EditBuilder.java
edit/src/main/java/uk/ac/ebi/metingear/association/GeneProductToReactionAssociation.java
edit/src/main/java/uk/ac/ebi/metingear/association/GeneProductToReactionDissociation.java
edit/src/main/java/uk/ac/ebi/metingear/association/GeneToGeneProductAssociation.java
edit/src/main/java/uk/ac/ebi/metingear/association/GeneToGeneProductDissociation.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/AddEntitiesEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/AddProductEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/AddReactantEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/MergeMetaboliteEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/RemoveGeneEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/RemoveGeneProduct.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/RemoveMetaboliteEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/RemoveParticipantEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/RemoveProductEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/RemoveReactantEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/RemoveReactionEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/RenameMetaboliteEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/ReplaceMetaboliteEdit.java
edit/src/main/java/uk/ac/ebi/metingear/edit/entity/SplitMetaboliteEdit.java
edit/src/main/java/uk/ac/ebi/mnb/edit/AbbreviationEdit.java
edit/src/main/java/uk/ac/ebi/mnb/edit/AccessionEdit.java
edit/src/main/java/uk/ac/ebi/mnb/edit/AddAnnotationEdit.java
edit/src/main/java/uk/ac/ebi/mnb/edit/DeleteAnnotation.java
edit/src/main/java/uk/ac/ebi/mnb/edit/DeleteEntitiesEdit.java
edit/src/main/java/uk/ac/ebi/mnb/edit/NameEdit.java
edit/src/main/java/uk/ac/ebi/mnb/edit/RemoveAnnotationEdit.java
edit/src/main/java/uk/ac/ebi/mnb/edit/ReplaceAnnotationEdit.java
edit/src/main/resources/META-INF/licenses/apache-1.1
edit/src/main/resources/META-INF/licenses/apache-2.0
edit/src/main/resources/META-INF/licenses/asm-license
edit/src/main/resources/META-INF/licenses/charts4j-license
edit/src/main/resources/META-INF/licenses/cpl-1.0
edit/src/main/resources/META-INF/licenses/jgoodies-license
edit/src/main/resources/META-INF/licenses/jsbml-license
edit/src/main/resources/META-INF/licenses/lgpl-2.1
edit/src/main/resources/uk/ac/ebi/mnb/edit/close_16x16.png
edit/src/test/java/uk/ac/ebi/metingear/EditBuilderTest.java
edit/src/test/java/uk/ac/ebi/metingear/association/GeneProductToReactionAssociationTest.java
edit/src/test/java/uk/ac/ebi/metingear/association/GeneProductToReactionDissociationTest.java
edit/src/test/java/uk/ac/ebi/metingear/association/GeneToGeneProductAssociationTest.java
edit/src/test/java/uk/ac/ebi/metingear/association/GeneToGeneProductDissociationTest.java
edit/src/test/java/uk/ac/ebi/metingear/edit/entity/AddProductEditTest.java
edit/src/test/java/uk/ac/ebi/metingear/edit/entity/AddReactantEditTest.java
edit/src/test/java/uk/ac/ebi/metingear/edit/entity/MergeMetaboliteEditTest.java
edit/src/test/java/uk/ac/ebi/metingear/edit/entity/RemoveMetaboliteEditTest.java
edit/src/test/java/uk/ac/ebi/metingear/edit/entity/RemoveParticipantEditTest.java
edit/src/test/java/uk/ac/ebi/metingear/edit/entity/RemoveProductEditTest.java
edit/src/test/java/uk/ac/ebi/metingear/edit/entity/RemoveReactantEditTest.java
edit/src/test/java/uk/ac/ebi/metingear/edit/entity/RenameMetaboliteEditTest.java
edit/src/test/java/uk/ac/ebi/metingear/edit/entity/ReplaceMetaboliteEditTest.java
edit/src/test/java/uk/ac/ebi/metingear/edit/entity/SplitMetaboliteEditTest.java
extensions/LICENSE
extensions/README
extensions/annotation/README
extensions/annotation/pom.xml
extensions/annotation/src/main/java/uk/ac/ebi/metingear/edit/AddNote.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/edit/AddNotePlugin.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/file/ImportCrossReferences.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/file/ImportCrossReferencesPlugin.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/tools/annotation/ExpandUniProtReference.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/tools/annotation/ExpandUniProtReferencePlugin.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/tools/annotation/ExtractAnnotations.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/tools/annotation/ExtractAnnotationsPlugin.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/tools/annotation/ExtractReferences.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/tools/annotation/ExtractReferencesPlugin.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/tools/annotation/RenameFromResource.java
extensions/annotation/src/main/java/uk/ac/ebi/metingear/tools/annotation/RenameFromResourcePlugin.java
extensions/annotation/src/main/resources/META-INF/services/uk.ac.ebi.metingear.view.PlugableAction
extensions/annotation/src/main/resources/META-INF/services/uk.ac.ebi.metingear.view.PlugableDialog
extensions/annotation/src/main/resources/uk/ac/ebi/caf/action/action.properties
extensions/annotation/src/main/resources/uk/ac/ebi/metingear/dialog-config.yml
extensions/extension/LICENSE
extensions/extension/NOTICE
extensions/extension/pom.xml
extensions/extension/src/main/java/uk/ac/ebi/metingear/view/AbstractControlAction.java
extensions/extension/src/main/java/uk/ac/ebi/metingear/view/AbstractControlDialog.java
extensions/extension/src/main/java/uk/ac/ebi/metingear/view/AbstractProcessingDialog.java
extensions/link/pom.xml
extensions/link/src/main/java/uk/ac/ebi/metingear/tools/link/AssociateReactions.java
extensions/link/src/main/java/uk/ac/ebi/metingear/tools/link/AssociateReactionsPlugin.java
extensions/link/src/main/java/uk/ac/ebi/metingear/tools/link/MergeTool.java
extensions/link/src/main/java/uk/ac/ebi/metingear/tools/link/MergeToolPlugin.java
extensions/link/src/main/resources/META-INF/services/uk.ac.ebi.metingear.view.PlugableDialog
extensions/link/src/main/resources/uk/ac/ebi/caf/action/action.properties
extensions/link/src/main/resources/uk/ac/ebi/metingear/dialog-config.yml
extensions/pom.xml
extensions/structure/LICENSE
extensions/structure/README
extensions/structure/pom.xml
extensions/structure/src/main/java/uk/ac/ebi/metingear/tools/structure/GenerateStructureDiagram.java
extensions/structure/src/main/java/uk/ac/ebi/metingear/tools/structure/GenerateStructureDiagramPlugin.java
extensions/structure/src/main/resources/META-INF/services/uk.ac.ebi.metingear.view.PlugableDialog
extensions/structure/src/main/resources/uk/ac/ebi/caf/action/action.properties
import/LICENSE
import/NOTICE
import/jsbml.log
import/pom.xml
import/src/main/java/mnb/io/resolve/AutomatedReconciler.java
import/src/main/java/mnb/io/resolve/BasicReconciler.java
import/src/main/java/mnb/io/resolve/EntryReconciler.java
import/src/main/java/mnb/io/tabular/EntityResolver.java
import/src/main/java/mnb/io/tabular/ExcelEntityResolver.java
import/src/main/java/mnb/io/tabular/ExcelModelProperties.java
import/src/main/java/mnb/io/tabular/NamedEntityResolver.java
import/src/main/java/mnb/io/tabular/parser/ReactionParser.java
import/src/main/java/mnb/io/tabular/parser/UnparsableReactionError.java
import/src/main/java/mnb/io/tabular/preparse/PreparsedEntry.java
import/src/main/java/mnb/io/tabular/preparse/PreparsedMetabolite.java
import/src/main/java/mnb/io/tabular/preparse/PreparsedReaction.java
import/src/main/java/mnb/io/tabular/preparse/PreparsedSheet.java
import/src/main/java/mnb/io/tabular/type/EntityColumn.java
import/src/main/java/mnb/io/tabular/type/ReactionColumn.java
import/src/main/java/mnb/io/tabular/type/TableDescription.java
import/src/main/java/mnb/io/tabular/util/ExcelUtilities.java
import/src/main/java/mnb/io/tabular/xls/HSSFPreparsedSheet.java
import/src/main/java/uk/ac/ebi/mnb/importer/xls/wizzard/AdditionalOptions.java
import/src/main/java/uk/ac/ebi/mnb/importer/xls/wizzard/ExcelImportDialog.java
import/src/main/java/uk/ac/ebi/mnb/importer/xls/wizzard/MetaboliteColumnChooser.java
import/src/main/java/uk/ac/ebi/mnb/importer/xls/wizzard/ReactionColumnChooser.java
import/src/main/java/uk/ac/ebi/mnb/importer/xls/wizzard/RowNumberTable.java
import/src/main/java/uk/ac/ebi/mnb/importer/xls/wizzard/SelectionTable.java
import/src/main/java/uk/ac/ebi/mnb/importer/xls/wizzard/SheetChooserDialog.java
import/src/main/java/uk/ac/ebi/mnb/importer/xls/wizzard/WizzardStage.java
import/src/main/java/uk/ac/ebi/mnb/parser/ExcelHelper.java
import/src/main/java/uk/ac/ebi/mnb/parser/ExcelXLSHelper.java
import/src/main/java/uk/ac/ebi/mnb/xls/options/ExcelColumnType.java
import/src/main/java/uk/ac/ebi/mnb/xls/options/ImporterOptions.java
import/src/main/java/uk/ac/ebi/mnb/xls/options/SheetType.java
import/src/main/resources/META-INF/licenses/apache-1.1
import/src/main/resources/META-INF/licenses/apache-2.0
import/src/main/resources/META-INF/licenses/asm-license
import/src/main/resources/META-INF/licenses/cpl-1.0
import/src/main/resources/META-INF/licenses/jgoodies-license
import/src/main/resources/META-INF/licenses/jsbml-license
import/src/main/resources/META-INF/licenses/lgpl-2.1
import/src/main/resources/uk/ac/ebi/caf/action/action.properties
import/src/test/java/mnb/io/tabular/preparse/PreparsedEntryTest.java
import/src/test/java/uk/ac/ebi/mnb/parser/AppTest.java
optimise/LICENSE
optimise/NOTICE
optimise/pom.xml
optimise/src/main/java/uk/ac/ebi/metabolomes/execs/GapMethodsMain.java
optimise/src/main/java/uk/ac/ebi/metabolomes/gap/filling/GapFillingFactory.java
optimise/src/main/java/uk/ac/ebi/metabolomes/gap/filling/GapFillingMethod.java
optimise/src/main/java/uk/ac/ebi/metabolomes/gap/filling/IterativeExpansion.java
optimise/src/main/java/uk/ac/ebi/metabolomes/gap/filling/SingleExpansion.java
optimise/src/main/java/uk/ac/ebi/metabolomes/optimise/GapBridger.java
optimise/src/main/java/uk/ac/ebi/metabolomes/optimise/GapFill.java
optimise/src/main/java/uk/ac/ebi/optimise/CPLEXConstraints.java
optimise/src/main/java/uk/ac/ebi/optimise/ReactionBalancer.java
optimise/src/main/java/uk/ac/ebi/optimise/SimulationUtil.java
optimise/src/main/java/uk/ac/ebi/optimise/gap/GapFill.java
optimise/src/main/java/uk/ac/ebi/optimise/gap/GapFillOld.java
optimise/src/main/java/uk/ac/ebi/optimise/gap/GapFind.java
optimise/src/main/resources/META-INF/licenses/apache-1.1
optimise/src/main/resources/META-INF/licenses/apache-2.0
optimise/src/main/resources/META-INF/licenses/asm-license
optimise/src/main/resources/META-INF/licenses/cpl-1.0
optimise/src/main/resources/META-INF/licenses/jgoodies-license
optimise/src/main/resources/META-INF/licenses/jsbml-license
optimise/src/main/resources/META-INF/licenses/lgpl-2.1
optimise/src/test/java/uk/ac/ebi/metabolomes/optimise/GapFindTest.java
pom.xml