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# Serialized Form

Package uk.ac.ic.doc.automed

Class uk.ac.ic.doc.automed.AutoMedException implements Serializable

Class uk.ac.ic.doc.automed.DataSourceRepositoryException implements Serializable

Class uk.ac.ic.doc.automed.DSRException implements Serializable

Class uk.ac.ic.doc.automed.InconsistentException implements Serializable

Class uk.ac.ic.doc.automed.IntegrityException implements Serializable

Serialized Fields

### className

    java.lang.String className

### operation

    int operation

### objectID

    int objectID

### objectID2

    int objectID2

Class uk.ac.ic.doc.automed.MDRException implements Serializable

Class uk.ac.ic.doc.automed.ModelDefinitionsRepositoryException implements Serializable

Class uk.ac.ic.doc.automed.NotFoundException implements Serializable

Class uk.ac.ic.doc.automed.NotImplementedException implements Serializable

Class uk.ac.ic.doc.automed.RepositoryAccessException implements Serializable

Serialized Fields

### cause

    java.lang.Exception cause

Class uk.ac.ic.doc.automed.SchemaModelingRepositoryException implements Serializable

Class uk.ac.ic.doc.automed.SchemaTransformationRepositoryException implements Serializable

Class uk.ac.ic.doc.automed.SSMDRException implements Serializable

Class uk.ac.ic.doc.automed.STRException implements Serializable

Class uk.ac.ic.doc.automed.TemplateExecutionRepositoryException implements Serializable

Class uk.ac.ic.doc.automed.TemplateTransformationRepositoryException implements Serializable

Class uk.ac.ic.doc.automed.TemplateTransformationSyntaxRepositoryException implements Serializable

Package uk.ac.ic.doc.automed.reps

Class uk.ac.ic.doc.automed.reps.AutoRepException implements Serializable

Serialized Fields

### cause

    java.lang.Exception cause

Class uk.ac.ic.doc.automed.reps.BadSchemaException implements Serializable

Serialized Fields

### badSchema

    Schema badSchema

Class uk.ac.ic.doc.automed.reps.ConstructSchemeSyntaxException implements Serializable

Class uk.ac.ic.doc.automed.reps.IllegalOperationException implements Serializable

Class uk.ac.ic.doc.automed.reps.SchemasNotIdenticalException implements Serializable

Serialized Fields

### fromSchema

    Schema fromSchema

### toSchema

    Schema toSchema

### fromObjects

    SchemaObject[] fromObjects

### toObjects

    SchemaObject[] toObjects

Class uk.ac.ic.doc.automed.reps.SyntaxException implements Serializable

Class uk.ac.ic.doc.automed.reps.TypeMismatchException implements Serializable

Class uk.ac.ic.doc.automed.reps.UnexpectedTokenException implements Serializable

Package uk.ac.ic.doc.automed.editor

Class uk.ac.ic.doc.automed.editor.CommandLineException implements Serializable

Class uk.ac.ic.doc.automed.editor.ConfigException implements Serializable

Class uk.ac.ic.doc.automed.editor.EditorException implements Serializable

Class uk.ac.ic.doc.automed.editor.EditorPanel implements Serializable

Serialized Fields

### vertexComponent

    java.util.Map vertexComponent

### adjacents

    java.util.Map adjacents

### vertices

    java.util.Map vertices

### edges

    java.util.Map edges

### selectOffset

    int selectOffset

### dragging

    boolean dragging

### justActivated

    boolean justActivated

### fm

    java.awt.FontMetrics fm

### ef

    Gui.EditorFrame ef

Class uk.ac.ic.doc.automed.editor.Gui implements Serializable

Serialized Fields

### ep

    Gui.EditorFrame ep

### editorFrames

    java.util.Map editorFrames

### rootActions

    java.util.List rootActions

### networkActions

    java.util.List networkActions

### schemaActions

    java.util.List schemaActions

### objectActions

    java.util.List objectActions

### selected

    java.util.List selected

### pathSel

    boolean[] pathSel

Class uk.ac.ic.doc.automed.editor.Gui.EditorFrame implements Serializable

Serialized Fields

### rootPane

    javax.swing.JRootPane rootPane

### contentPane

    java.awt.Container contentPane

### glassPane

    java.awt.Component glassPane

### editorPanel

    EditorPanel editorPanel

### target

    java.lang.Object target

### parentTarget

    java.lang.Object parentTarget

### selected

    java.util.List selected

### pathSel

    boolean[] pathSel

### rootActions

    java.util.List rootActions

### networkActions

    java.util.List networkActions

### schemaActions

    java.util.List schemaActions

### objectActions

    java.util.List objectActions

### rootMenu

    javax.swing.JPopupMenu rootMenu

### networkMenu

    javax.swing.JPopupMenu networkMenu

### schemaMenu

    javax.swing.JPopupMenu schemaMenu

### objectMenu

    javax.swing.JPopupMenu objectMenu

Class uk.ac.ic.doc.automed.editor.GUITool implements Serializable

Serialized Fields

### window

    java.awt.Container window

### wLayout

    java.awt.GridBagLayout wLayout

### line

    int line

Class uk.ac.ic.doc.automed.editor.MatchingTool implements Serializable

Serialized Fields

### elementsTables1

    java.util.ArrayList elementsTables1

### elementsColumns1

    java.util.ArrayList elementsColumns1

### elementsColumnEdges1

    java.util.ArrayList elementsColumnEdges1

### elementsTables2

    java.util.ArrayList elementsTables2

### elementsColumns2

    java.util.ArrayList elementsColumns2

### elementsColumnEdges2

    java.util.ArrayList elementsColumnEdges2

### discoveredRels

    SchemaElementPairRelationship[] discoveredRels

### validatedRels

    java.util.ArrayList validatedRels

### schemas

    Schema[] schemas

### integratedSchema

    Schema integratedSchema

### precisionRels

    java.util.ArrayList precisionRels

### numofinstancesRels

    java.util.ArrayList numofinstancesRels

### existenceRels

    java.util.ArrayList existenceRels

### model

    MatchingTool.MyTableModel model

### jtable

    javax.swing.JTable jtable

### validateItem

    javax.swing.JMenuItem validateItem

### exitItem

    javax.swing.JMenuItem exitItem

### outputTextArea

    javax.swing.JTextArea outputTextArea

### comboBoxRenderer

    MatchingTool.ComboBoxRenderer comboBoxRenderer

### renderer

    MatchingTool.MyDefaultTableCellRenderer renderer

### results

    javax.swing.JTabbedPane results

### waitCursor

    java.awt.Cursor waitCursor

### normalCursor

    java.awt.Cursor normalCursor

### STOP

    boolean STOP

### RELATIONSHIPS_DISCOVERED

    boolean RELATIONSHIPS_DISCOVERED

### SCHEMAS_INTEGRATED

    boolean SCHEMAS_INTEGRATED

Class uk.ac.ic.doc.automed.editor.PathwayOptimiserTool implements Serializable

Serialized Fields

### transTable

    javax.swing.JTable transTable

### option1

    javax.swing.JButton option1

### option2

    javax.swing.JButton option2

### cancelButton

    javax.swing.JButton cancelButton

### tempP

    TempPathway tempP

### pathwayIsOptimisable

    boolean pathwayIsOptimisable

### pathwayIsWellformed

    boolean pathwayIsWellformed

### notWellformedMsg

    java.lang.String notWellformedMsg

Class uk.ac.ic.doc.automed.editor.PatternWritingTool implements Serializable

Serialized Fields

### yatta

    Model yatta

### rootnode

    Construct rootnode

### yattanode

    Construct yattanode

### sequence

    Construct sequence

### ROOT_CONSTRUCT

    java.lang.String ROOT_CONSTRUCT

### YATTANODE_CONSTRUCT

    java.lang.String YATTANODE_CONSTRUCT

### SEQUENCE_CONSTRUCT

    java.lang.String SEQUENCE_CONSTRUCT

### windowname

    java.lang.String windowname

### gbLayout

    java.awt.GridBagLayout gbLayout

### ssdText

    javax.swing.JTextArea ssdText

### ssdfText

    javax.swing.JTextField ssdfText

### parentCombo

    javax.swing.JComboBox parentCombo

### sobjName

    javax.swing.JTextField sobjName

### typeText

    javax.swing.JTextField typeText

### orderCombo

    javax.swing.JComboBox orderCombo

### fullScheme

    javax.swing.JTextArea fullScheme

### sequenceInfo

    javax.swing.JTextArea sequenceInfo

### sobjText

    javax.swing.JTextArea sobjText

### pnameText

    javax.swing.JTextField pnameText

### patternText

    javax.swing.JTextField patternText

### groupText

    javax.swing.JTextField groupText

### addButton1

    javax.swing.JButton addButton1

### removeButton1

    javax.swing.JButton removeButton1

### addButton

    javax.swing.JButton addButton

### removeButton

    javax.swing.JButton removeButton

### editButton

    javax.swing.JButton editButton

### helpButton

    javax.swing.JButton helpButton

### matchButton

    javax.swing.JButton matchButton

### browseButton

    javax.swing.JButton browseButton

### saveButton

    javax.swing.JButton saveButton

### cancelButton

    javax.swing.JButton cancelButton

### nextWindow

    javax.swing.JButton nextWindow

### complex

    javax.swing.JRadioButton complex

### atomic

    javax.swing.JRadioButton atomic

### one

    javax.swing.JRadioButton one

### onezero

    javax.swing.JRadioButton onezero

### gtone

    javax.swing.JRadioButton gtone

### gtzero

    javax.swing.JRadioButton gtzero

### ctype

    java.lang.String[] ctype

### complexList

    javax.swing.JComboBox complexList

### atype

    java.lang.String[] atype

### atomicList

    javax.swing.JComboBox atomicList

### any

    javax.swing.JRadioButton any

### before

    javax.swing.JRadioButton before

### after

    javax.swing.JRadioButton after

### key

    javax.swing.JRadioButton key

### nonkey

    javax.swing.JRadioButton nonkey

### treePanel

    PatternWritingTool.DynamicTree treePanel

### name_node

    java.util.HashMap name_node

### treePanelPW

    PatternWritingTool.DynamicTree treePanelPW

### fullN_keyN

    java.util.HashMap fullN_keyN

### ssdModel

    PatternWritingTool.MyTableModel ssdModel

### ssdTable

    javax.swing.JTable ssdTable

### ssdrowCount

    int ssdrowCount

### selectedRow

    int selectedRow

### ssd

    java.lang.String ssd

### url

    java.lang.String url

### schema

    java.lang.String schema

### selectedType

    java.lang.String selectedType

### selectedParent

    java.lang.String selectedParent

### parentType

    java.lang.String parentType

### selectedOrder

    java.lang.String selectedOrder

### selectedCard

    java.lang.String selectedCard

### selectedKey

    java.lang.String selectedKey

### selectedSequence

    java.lang.String selectedSequence

### s

    Schema s

### sobj

    SchemaObject sobj

### ssdf

    SSDFormat ssdf

### ssdfName

    java.lang.String ssdfName

### SOS

    java.util.Vector SOS

### SPS

    java.util.Vector SPS

### node_background_colour

    java.awt.Color node_background_colour

### root_background_colour

    java.awt.Color root_background_colour

### seq_background_colour

    java.awt.Color seq_background_colour

### text_colour

    java.awt.Color text_colour

### text_background_colour

    java.awt.Color text_background_colour

### orderedParent

    java.util.Vector orderedParent

### pname

    java.lang.String pname

### pattern

    java.lang.String pattern

### myHighlightPainter

    javax.swing.text.Highlighter.HighlightPainter myHighlightPainter

### basePainter

    javax.swing.text.Highlighter.HighlightPainter basePainter

Class uk.ac.ic.doc.automed.editor.PatternWritingTool.DynamicTree implements Serializable

Serialized Fields

### rootNode

    javax.swing.tree.DefaultMutableTreeNode rootNode

### treeModel

    javax.swing.tree.DefaultTreeModel treeModel

### tree

    javax.swing.JTree tree

### toolkit

    java.awt.Toolkit toolkit

Class uk.ac.ic.doc.automed.editor.ReportException implements Serializable

Serialized Fields

### e

    java.lang.Exception e

### msgText

    java.lang.String msgText

### msg

    javax.swing.JTextArea msg

### summary

    javax.swing.JTextArea summary

### details

    javax.swing.JTextArea details

### ste

    java.lang.StackTraceElement[] ste

Class uk.ac.ic.doc.automed.editor.SemanticException implements Serializable

Class uk.ac.ic.doc.automed.editor.SyntaxException implements Serializable

Class uk.ac.ic.doc.automed.editor.UnexpectedTokenException implements Serializable

Class uk.ac.ic.doc.automed.editor.UserAction implements Serializable

Package uk.ac.bbk.dcs.automed.xml

Class uk.ac.bbk.dcs.automed.xml.XMLException implements Serializable

Class uk.ac.bbk.dcs.automed.xml.XMLNotFoundException implements Serializable

Package uk.ac.ic.doc.automed.wrappers

Class uk.ac.ic.doc.automed.wrappers.DataSourceException implements Serializable

Package uk.ac.ic.doc.automed.tml

Class uk.ac.ic.doc.automed.tml.NotOptimisableException implements Serializable

Package uk.ac.bbk.dcs.automed.qproc.functions

Class uk.ac.bbk.dcs.automed.qproc.functions.ModifiedArray implements Serializable

Package uk.ac.ic.doc.automed.gui

Class uk.ac.ic.doc.automed.gui.Arc implements Serializable

Serialized Fields

### style

    java.lang.String style

### bgColour

    java.lang.String bgColour

### fgColour

    java.lang.String fgColour

### text

    java.lang.String text

### fontName

    java.lang.String fontName

### fontSize

    int fontSize

### fontStyle

    int fontStyle

### fontColour

    java.lang.String fontColour

### textLocation

    java.lang.String textLocation

### location

    java.awt.Point location

### arcWidth

    int arcWidth

### arcHeight

    int arcHeight

### startAngle

    int startAngle

### endAngle

    int endAngle

### graphics

    java.awt.Graphics graphics

### textPosition

    java.awt.Point textPosition

### font

    java.awt.Font font

### arc2d

    java.awt.geom.Arc2D.Double arc2d

### assigned

    java.awt.Point assigned

### west

    java.awt.Point west

### south

    java.awt.Point south

### north

    java.awt.Point north

### east

    java.awt.Point east

Class uk.ac.ic.doc.automed.gui.ArgPane implements Serializable

Serialized Fields

### argPane

    ArgPane argPane

### inputPane

    javax.swing.JPanel inputPane

### buttonsPane

    javax.swing.JPanel buttonsPane

### textField

    javax.swing.JTextField textField

### extend

    javax.swing.JButton extend

### leftArrow

    javax.swing.JButton leftArrow

### rightArrow

    javax.swing.JButton rightArrow

### contruct

    javax.swing.JButton contruct

### set

    javax.swing.JButton set

### argDescriptions

    java.lang.String[] argDescriptions

### argPos

    int argPos

### argValues

    java.util.Vector argValues

### extendable

    boolean extendable

Class uk.ac.ic.doc.automed.gui.ArgumentsDialog implements Serializable

Serialized Fields

### argPane

    ArgPane argPane

Class uk.ac.ic.doc.automed.gui.Box implements Serializable

Serialized Fields

### style

    java.lang.String style

### bgColour

    java.lang.String bgColour

### fgColour

    java.lang.String fgColour

### text

    java.lang.String text

### fontName

    java.lang.String fontName

### fontSize

    int fontSize

### fontStyle

    int fontStyle

### fontColour

    java.lang.String fontColour

### textLocation

    java.lang.String textLocation

### rounded

    boolean rounded

### arcWidth

    int arcWidth

### arcHeight

    int arcHeight

### layout

    java.lang.String layout

### layoutAxis

    java.lang.String layoutAxis

### graphics

    java.awt.Graphics graphics

### textPosition

    java.awt.Point textPosition

### font

    java.awt.Font font

Class uk.ac.ic.doc.automed.gui.GUIException implements Serializable

Serialized Fields

### cause

    java.lang.Exception cause

Class uk.ac.ic.doc.automed.gui.IntegrateDialog implements Serializable

Serialized Fields

### ok

    javax.swing.JButton ok

### cancel

    javax.swing.JButton cancel

### schema1

    javax.swing.JTextField schema1

### schema2

    javax.swing.JTextField schema2

### waitCursor

    java.awt.Cursor waitCursor

### defaultCursor

    java.awt.Cursor defaultCursor

Class uk.ac.ic.doc.automed.gui.LoadDialog implements Serializable

Serialized Fields

### list

    javax.swing.JList list

### value

    java.lang.String value

### cancelButton

    javax.swing.JButton cancelButton

### owner

    java.awt.Component owner

Class uk.ac.ic.doc.automed.gui.Rhombus implements Serializable

Serialized Fields

### style

    java.lang.String style

### bgColour

    java.lang.String bgColour

### fgColour

    java.lang.String fgColour

### text

    java.lang.String text

### fontName

    java.lang.String fontName

### fontSize

    int fontSize

### fontStyle

    int fontStyle

### fontColour

    java.lang.String fontColour

### textLocation

    java.lang.String textLocation

### extend

    int extend

### graphics

    java.awt.Graphics graphics

### textPosition

    java.awt.Point textPosition

### font

    java.awt.Font font

### polygon

    java.awt.Polygon polygon

### assigned

    java.awt.Point assigned

Class uk.ac.ic.doc.automed.gui.SchemaCanvas implements Serializable

Serialized Fields

### scrollpane

    javax.swing.JScrollPane scrollpane

### objectFocused

    GraphicObject objectFocused

### pointDifference

    java.awt.Point pointDifference

### manager

    GraphicManager manager

### tooltip

    ToolTip tooltip

Class uk.ac.ic.doc.automed.gui.SchemaTool implements Serializable

Serialized Fields

### leftCanvas

    SchemaCanvas leftCanvas

### rightCanvas

    SchemaCanvas rightCanvas

### load

    javax.swing.JMenuItem load

### exit

    javax.swing.JMenuItem exit

### integrate

    javax.swing.JMenuItem integrate

### loadDialog

    LoadDialog loadDialog

### compound

    javax.swing.border.Border compound

### left

    javax.swing.JPanel left

### right

    javax.swing.JPanel right

### list

    javax.swing.JList list

### optionPane

    javax.swing.JOptionPane optionPane

### infoDialog

    javax.swing.JDialog infoDialog

### integrateDialog

    javax.swing.JDialog integrateDialog

### execute

    javax.swing.JButton execute

### argDialog

    ArgumentsDialog argDialog

### transformation

    CompositeTransformation transformation

### waitCursor

    java.awt.Cursor waitCursor

### defaultCursor

    java.awt.Cursor defaultCursor

### argumentSequences

    java.util.Vector argumentSequences

Class uk.ac.ic.doc.automed.gui.ToolTip implements Serializable

Serialized Fields

### text

    java.lang.String text

Package uk.ac.ic.doc.automed.templates.gui

Class uk.ac.ic.doc.automed.templates.gui.DrawingObject implements Serializable

Serialized Fields

### cid

    int cid

### obid

    int obid

### highlighted

    boolean highlighted

### enabled

    boolean enabled

### xPos

    int xPos

### yPos

    int yPos

### name

    java.lang.String name

### nameDimensions

    java.awt.Dimension nameDimensions

### justDragged

    boolean justDragged

### parent

    SchemaPanel parent

### mySchemaObject

    SchemaObject mySchemaObject

### schemeObjects

    SchemaObject[] schemeObjects

Class uk.ac.ic.doc.automed.templates.gui.InputForm implements Serializable

Serialized Fields

### isEditable

    boolean isEditable

### isList

    boolean isList

### listSize

    int listSize

### inputItems

    java.util.Vector inputItems

### myArgument

    TTemplateInputArgument myArgument

### currentlyFocusedItem

    InputItem currentlyFocusedItem

### observer

    java.awt.Component observer

### dialogueManager

    TemplateInputDialogue dialogueManager

### topToolbars

    javax.swing.JPanel topToolbars

### popUpButton

    javax.swing.JButton popUpButton

### listButton

    javax.swing.JButton listButton

### singleButton

    javax.swing.JButton singleButton

### breakButton

    javax.swing.JButton breakButton

### isSetButton

    javax.swing.JButton isSetButton

Class uk.ac.ic.doc.automed.templates.gui.LoadDialog implements Serializable

Serialized Fields

### list

    javax.swing.JList list

### value

    java.lang.String value

### cancelButton

    javax.swing.JButton cancelButton

### owner

    java.awt.Component owner

Class uk.ac.ic.doc.automed.templates.gui.SchemaFrame implements Serializable

Serialized Fields

### load

    javax.swing.JMenuItem load

### execute

    javax.swing.JMenuItem execute

### exit

    javax.swing.JMenuItem exit

### backButton

    javax.swing.JButton backButton

### frontButton

    javax.swing.JButton frontButton

### executeButton

    javax.swing.JButton executeButton

### schemaPanelScroller

    javax.swing.JScrollPane schemaPanelScroller

### transformationsScroller

    javax.swing.JScrollPane transformationsScroller

### mainPanel

    javax.swing.JPanel mainPanel

### loadedSchemas

    java.util.Vector loadedSchemas

### panelsOfSchemas

    java.util.Hashtable panelsOfSchemas

### currentlyDisplayedSchema

    int currentlyDisplayedSchema

Class uk.ac.ic.doc.automed.templates.gui.SchemaPanel implements Serializable

Serialized Fields

### objects

    java.util.Vector objects

### currentSID

    int currentSID

### observer

    java.awt.Component observer

### schemaName

    java.lang.String schemaName

### dialogueManager

    DialogueManager dialogueManager

### objectMap

    java.util.Hashtable objectMap

### loadedSchema

    Schema loadedSchema

Class uk.ac.ic.doc.automed.templates.gui.TemplateDialogueLauncher implements Serializable

Serialized Fields

### owner

    java.awt.Frame owner

### list

    javax.swing.JList list

### listScroller

    javax.swing.JScrollPane listScroller

### descriptionScroller

    javax.swing.JScrollPane descriptionScroller

### descriptionPane

    javax.swing.JTextPane descriptionPane

### okButton

    javax.swing.JButton okButton

### cancelButton

    javax.swing.JButton cancelButton

### names

    java.lang.String[] names

### descriptions

    java.util.Hashtable descriptions

### transIds

    java.util.Hashtable transIds

### selectedTransId

    java.lang.Integer selectedTransId

Package uk.ac.ic.doc.automed.templates.wrapper

Class uk.ac.ic.doc.automed.templates.wrapper.TemplateDefinitionException implements Serializable

Serialized Fields

### cause

    java.lang.Exception cause

Package uk.ac.bbk.dcs.automed.hdmstore

Class uk.ac.bbk.dcs.automed.hdmstore.HdmStoreException implements Serializable

Package uk.ac.ic.doc.automed.matching

Class uk.ac.ic.doc.automed.matching.IntegratorException implements Serializable

Class uk.ac.ic.doc.automed.matching.InvalidElementException implements Serializable

Class uk.ac.ic.doc.automed.matching.RelationshipConflictException implements Serializable

Class uk.ac.ic.doc.automed.matching.RelationshipExtractorException implements Serializable

Class uk.ac.ic.doc.automed.matching.UninstantiatedElementException implements Serializable

Class uk.ac.ic.doc.automed.matching.UninstantiatedException implements Serializable

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