Uses of Interface
phenote.datamodel.CharacterI

Packages that use CharacterI

phenote.charactertemplate
phenote.dataadapter	Generalized methods for creating customized Data Adapters
phenote.dataadapter.delimited
phenote.dataadapter.fly
phenote.dataadapter.phenosyntax
phenote.dataadapter.worm
phenote.datamodel
phenote.edit
phenote.gui
phenote.gui.field
phenote.gui.selection
phenote.matrix.model

Uses of CharacterI in phenote.charactertemplate

Methods in phenote.charactertemplate that return CharacterI

CharacterI

CharacterTemplateTableFormat.setColumnValue(CharacterI character, java.lang.Object editedValue, int column)

Methods in phenote.charactertemplate that return types with arguments of type CharacterI

java.util.List<CharacterI>	CharacterTemplateTable.getAllCharacters()
java.util.Collection<CharacterI>	TreeChooser.getChosenTemplates(java.util.Collection<CharacterI> candidates)
java.util.Collection<CharacterI>	TemplateChooser.getChosenTemplates(java.util.Collection<CharacterI> candidates)
abstract java.util.Collection<CharacterI>	AbstractTemplateChooser.getChosenTemplates(java.util.Collection<CharacterI> candidates)
java.util.List<CharacterI>	CharacterTemplateTable.getMarkedCharacters()
ca.odell.glazedlists.swing.EventSelectionModel<CharacterI>	CharacterTemplateTable.getSelectionModel()

Methods in phenote.charactertemplate with parameters of type CharacterI

java.lang.Object	CharacterTemplateTableFormat.getColumnValue(CharacterI character, int column)
boolean	CharacterTemplateTable.isCharacterMarked(CharacterI character)
boolean	CharacterTemplateTableFormat.isEditable(CharacterI character, int column)
void	CharacterTemplateTable.setCharacterIsMarked(CharacterI character, boolean selected)
CharacterI	CharacterTemplateTableFormat.setColumnValue(CharacterI character, java.lang.Object editedValue, int column)

Method parameters in phenote.charactertemplate with type arguments of type CharacterI

java.util.Collection<CharacterI>	TreeChooser.getChosenTemplates(java.util.Collection<CharacterI> candidates)
java.util.Collection<CharacterI>	TemplateChooser.getChosenTemplates(java.util.Collection<CharacterI> candidates)
abstract java.util.Collection<CharacterI>	AbstractTemplateChooser.getChosenTemplates(java.util.Collection<CharacterI> candidates)
void	CharacterTemplateTable.setCharactersAreMarked(java.util.List<CharacterI> characters, boolean marked)
void	CharacterTemplateTable.setMarkedCharacters(java.util.Collection<CharacterI> charactersToMark)

Uses of CharacterI in phenote.dataadapter

Methods in phenote.dataadapter that return types with arguments of type CharacterI

java.util.List<CharacterI>	CharacterListManager.getCharList()
java.util.List<CharacterI>	CharacterListManager.getNonBlankList() return all characters that arent blanks.

Methods in phenote.dataadapter with parameters of type CharacterI

protected ConstraintStatus	RequiredFieldConstraint.checkCharCommit(CharacterI chr)
protected abstract ConstraintStatus	AbstractCommitConstraint.checkCharCommit(CharacterI chr) Check char and return ConstraintStatus
protected java.lang.String	AllFieldsGroupAdapter.makeNameFromChar(CharacterI c)
protected abstract java.lang.String	AbstractGroupAdapter.makeNameFromChar(CharacterI c) This is where subclasses come in and do their thing
protected org.obo.datamodel.OBOClass	AbstractGroupAdapter.makeOboClassFromChar(CharacterI c)
protected void	AbstractGroupAdapter.setIdField(CharacterI c, java.lang.String id) overridden by worm

Uses of CharacterI in phenote.dataadapter.delimited

Methods in phenote.dataadapter.delimited that return CharacterI

(package private) CharacterI

DelimitedChar.getCharacter()

Methods in phenote.dataadapter.delimited with parameters of type CharacterI

(package private) void

DelimFieldParser.parseField(java.lang.String[] items, CharacterI chr)

Constructors in phenote.dataadapter.delimited with parameters of type CharacterI

DelimitedChar(CharacterI ch)

Uses of CharacterI in phenote.dataadapter.fly

Methods in phenote.dataadapter.fly that return CharacterI

(package private) CharacterI

FlyCharacter.getCharacter()

Methods in phenote.dataadapter.fly with parameters of type CharacterI

protected java.lang.String

FlyGenotypeGroupAdapter.makeNameFromChar(CharacterI c)

Constructors in phenote.dataadapter.fly with parameters of type CharacterI

FlyCharacter(CharacterI c)

Uses of CharacterI in phenote.dataadapter.phenosyntax

Methods in phenote.dataadapter.phenosyntax that return CharacterI

(package private) CharacterI

PhenoSyntaxChar.getCharacter()

Constructors in phenote.dataadapter.phenosyntax with parameters of type CharacterI

PhenoSyntaxChar(CharacterI ch)

Uses of CharacterI in phenote.dataadapter.worm

Methods in phenote.dataadapter.worm that return CharacterI

CharacterI

WormAdapterReference.getCharacterReference(java.lang.String refID)

Methods in phenote.dataadapter.worm with parameters of type CharacterI

protected ConstraintStatus	WormInteractionConstraint.checkCharCommit(CharacterI chr) do constraint check for commit time on a character return ConstraintStatus indication if constraint passed and error msg
protected ConstraintStatus	WormConstraint.checkCharCommit(CharacterI chr) do constraint check for commit time on a character return ConstraintStatus indication if constraint passed and error msg
void	WormAdapterReference.commitReference(CharacterI cMain, java.sql.Connection c, java.sql.Statement s)
protected java.lang.String	WormReferenceGroupAdapter.makeNameFromChar(CharacterI c)
protected void	WormReferenceGroupAdapter.setIdField(CharacterI c, java.lang.String id) this should be read only and probably hidden

Uses of CharacterI in phenote.datamodel

Classes in phenote.datamodel that implement CharacterI

class	AbstractCharacter
class	AnnotationCharacter CharacterI for OBOAnnotations
class	Character The Character datamodel is a generic hash of CharField-CharFieldValues CharFieldValues are free text or from ontologies This is the straightontabular implementation of CharacterI In the table view a character represents a row

Methods in phenote.datamodel that return CharacterI

CharacterI	CharacterI.cloneCharacter()
CharacterI	Character.cloneCharacter()
CharacterI	AnnotationCharacter.cloneCharacter()
CharacterI	ValueCharacterList.get(int i)
CharacterI	CharacterListI.get(int i)
CharacterI	CharacterList.get(int i)
CharacterI	PhenotypeCharacterWrapper.getCharacter()
CharacterI	CharFieldValue.getCharacter()
CharacterI	Comparison.getObject()
CharacterI	Comparison.getSubject()
static CharacterI	CharacterIFactory.makeChar() static sugar
CharacterI	CharacterIFactory.makeCharacter()

Methods in phenote.datamodel that return types with arguments of type CharacterI

ca.odell.glazedlists.EventList<CharacterI>	ValueCharacterList.getList()
ca.odell.glazedlists.EventList<CharacterI>	CharacterListI.getList()
ca.odell.glazedlists.EventList<CharacterI>	CharacterList.getList()
ca.odell.glazedlists.EventList<CharacterI>	ValueCharacterList.getNonBlankList() return all characters that arent blanks.
ca.odell.glazedlists.EventList<CharacterI>	CharacterListI.getNonBlankList() return all characters that arent blanks.
ca.odell.glazedlists.EventList<CharacterI>	CharacterList.getNonBlankList() return all characters that arent blanks.

Methods in phenote.datamodel with parameters of type CharacterI

void	ValueCharacterList.add(CharacterI c)
void	CharacterListI.add(CharacterI c)
void	CharacterList.add(CharacterI c)
void	ValueCharacterList.add(int order, CharacterI c)
void	CharacterListI.add(int order, CharacterI c)
void	CharacterList.add(int i, CharacterI c)
void	AnnotationCharacter.addComparison(org.obo.datamodel.OBOProperty relation, CharacterI relatedChar) Make comparison relationship between 2 annotations
CharFieldValue	CharFieldValue.cloneCharFieldValue(CharacterI newCharacter, CharField newField)
CharFieldValue	CharFieldValue.cloneValueForChar(CharacterI newChar)
static CharFieldValue	CharFieldValue.emptyValue(CharacterI c, CharField cf)
boolean	CharacterI.equals(CharacterI c)
boolean	AbstractCharacter.equals(CharacterI ch)
boolean	CharacterI.fieldEquals(CharacterI c, CharField cf)
boolean	AbstractCharacter.fieldEquals(CharacterI c, CharField cf) by default check if single char field val from field is equal, eventually should get hip to potential lists of values
protected CharFieldValue	AnnotationCharacter.getCharFieldValue(org.obo.datamodel.DanglingObject oboInst, CharacterI character, CharField field)
CharFieldValue	BasicAnnotationMappingDriver.getCharFieldValue(org.obo.datamodel.Instance oboInst, CharacterI character, CharField field)
protected CharFieldValue	AnnotationCharacter.getCharFieldValue(org.obo.datamodel.Instance oboInst, CharacterI character, CharField field)
CharFieldValue	BasicAnnotationMappingDriver.getCharFieldValue(org.obo.datamodel.OBOClass oboclass, CharacterI character, CharField field)
CharFieldValue	AnnotationMappingDriver.getCharFieldValue(org.obo.datamodel.OBOClass oboclass, CharacterI character, CharField field)
protected CharFieldValue	AnnotationCharacter.getCharFieldValue(org.obo.datamodel.OBOClass oboClass, CharacterI character, CharField field)
CharFieldValue	BasicAnnotationMappingDriver.getCharFieldValue(java.lang.String s, CharacterI character, CharField field)
CharFieldValue	AnnotationMappingDriver.getCharFieldValue(java.lang.String s, CharacterI character, CharField field)
protected CharFieldValue	AnnotationCharacter.getCharFieldValue(java.lang.String s, CharacterI character, CharField field)
int	ValueCharacterList.indexOf(CharacterI c)
int	CharacterListI.indexOf(CharacterI c)
int	CharacterList.indexOf(CharacterI c)
(package private) static CharFieldValue	CharFieldValue.makeDate(java.lang.String dateString, CharacterI c, CharField cf) dateString is a date, if not valid date throws ParseEx
static CharFieldValue	CharFieldValue.makeListParentValue(CharacterI c, CharField cf)
CharFieldValue	CharField.makeValue(CharacterI c, java.lang.String valueString) if free text returns string charfieldValue, for ontology field valueString is id and searches ontologies for id, throws CharFieldException if invalid date for date field (used to for term not found but now creates dangler instead) this deals with postcomp too) if term is dangler then dangler gets id (valueString) but no name use makeValue(Char,String,String) to get dangler name set as well also deals with lists in format: "xxx","yyy",...
CharFieldValue	CharField.makeValue(CharacterI c, java.lang.String valueString, java.lang.String danglerName) makes value - value string for term is id - if term is dangler (not in ontology) and danglerName is non null, then danglers name is set to danglerName, danglerName is ONLY used for danglers
void	ValueCharacterList.remove(CharacterI c)
void	CharacterListI.remove(CharacterI c)
void	CharacterList.remove(CharacterI c)
(package private) void	CharFieldValue.setCharacter(CharacterI c) set selfs character as well as kids/list(recurse)
void	Comparison.setObject(CharacterI o)
void	Comparison.setSubject(CharacterI s)

Constructors in phenote.datamodel with parameters of type CharacterI

CharFieldValue(java.util.Date d, CharacterI c, CharField cf)

CharFieldValue(org.obo.datamodel.OBOClass o, CharacterI c, CharField cf)
SINGLE VALUE term/class - not list

CharFieldValue(java.lang.String value, CharacterI c, CharField cf)

Comparison(CharacterI sub, org.obo.datamodel.OBOProperty r, CharacterI obj)

PhenotypeCharacterWrapper(CharacterI character)

Constructor parameters in phenote.datamodel with type arguments of type CharacterI

TransferableCharacterList(java.util.List<CharacterI> theCharacters)

Uses of CharacterI in phenote.edit

Methods in phenote.edit that return types with arguments of type CharacterI

java.util.List<CharacterI>	UpdateTransaction.getCharacters()
java.util.List<CharacterI>	TransactionI.getCharacters()
java.util.List<CharacterI>	DeleteTransaction.getCharacters()
java.util.List<CharacterI>	CompoundTransaction.getCharacters()
java.util.List<CharacterI>	AddTransaction.getCharacters()
java.util.List<CharacterI>	UpdateTransaction.getDeletedAnnotations()
java.util.List<CharacterI>	TransactionI.getDeletedAnnotations()
java.util.List<CharacterI>	EditManager.getDeletedAnnotations()
java.util.List<CharacterI>	DeleteTransaction.getDeletedAnnotations() this is for whole row deletes? not del from list field?
java.util.List<CharacterI>	CompoundTransaction.getDeletedAnnotations()
java.util.List<CharacterI>	AddTransaction.getDeletedAnnotations()

Methods in phenote.edit with parameters of type CharacterI

void	EditManager.addCharacter(CharacterI c)
protected void	UpdateTransaction.setOldValue(CharacterI c, CharField cf)

Method parameters in phenote.edit with type arguments of type CharacterI

void	EditManager.copyChars(java.util.List<CharacterI> charsToCopy)
void	EditManager.deleteChars(java.util.List<CharacterI> delChars)
void	EditManager.deleteFromValList(java.lang.Object src, CharFieldValue valToDelete, java.util.List<CharacterI> chars) Ok this is funny, so from each char in chars if they have a CFV with same value/class/string as valToDelete then delete it
static CompoundTransaction	CompoundTransaction.makeCopyTrans(java.util.List<CharacterI> charsToCopy, CharacterListManager clManager)
static CompoundTransaction	CompoundTransaction.makeDelTrans(java.util.List<CharacterI> delChars, CharacterListManager clManager)
static CompoundTransaction	CompoundTransaction.makeUpdate(java.util.List<CharacterI> l, CharField c, CharFieldValue v)
static CompoundTransaction	CompoundTransaction.makeUpdate(java.util.List<CharacterI> l, CharField c, org.obo.datamodel.OBOClass o)
static CompoundTransaction	CompoundTransaction.makeUpdate(java.util.List<CharacterI> crs, CharField cf, java.lang.String v)
void	EditManager.updateModel(java.util.List<CharacterI> l, CharField cf, java.lang.String s, java.lang.Object src)

Constructors in phenote.edit with parameters of type CharacterI

AddTransaction(CharacterI chr, CharacterListManager clManager)

DeleteTransaction(CharacterI c, CharacterListManager clManager)

UpdateTransaction(CharacterI c, CharField cf, CharFieldValue v)
used by character list field gui in character template, v is new value also used by comparisons deals with lists via CFV.makeNewValue im not sure how this works as makeNewValue seems funny

UpdateTransaction(CharacterI c, CharField cf, org.obo.datamodel.OBOClass newTerm)

UpdateTransaction(CharacterI c, CharField cf, java.lang.String newString)

Uses of CharacterI in phenote.gui

Methods in phenote.gui that return CharacterI

(package private) CharacterI	ComparisonCharacterGui.getCharacter()
CharacterI	CharacterTableFormat.setColumnValue(CharacterI character, java.lang.Object editedValue, int column)

Methods in phenote.gui that return types with arguments of type CharacterI

ca.odell.glazedlists.swing.EventSelectionModel<CharacterI>	CharacterTableSource.getSelectionModel()
ca.odell.glazedlists.swing.EventSelectionModel<CharacterI>	CharacterTableController.getSelectionModel()
ca.odell.glazedlists.swing.EventSelectionModel<CharacterI>	CharacterTable.getSelectionModel()

Methods in phenote.gui with parameters of type CharacterI

static java.lang.String	ComparisonCharacterGui.charString(CharacterI c)
java.lang.Object	CharacterTableFormat.getColumnValue(CharacterI character, int column)
boolean	CharacterTableFormat.isEditable(CharacterI character, int column)
(package private) void	ComparisonCharacterGui.setCharacter(CharacterI c)
CharacterI	CharacterTableFormat.setColumnValue(CharacterI character, java.lang.Object editedValue, int column)

Uses of CharacterI in phenote.gui.field

Fields in phenote.gui.field with type parameters of type CharacterI

protected ca.odell.glazedlists.swing.EventSelectionModel<CharacterI>

CharFieldGui.selectionModel

Methods in phenote.gui.field that return types with arguments of type CharacterI

protected java.util.List<CharacterI>

CharFieldGui.getSelectedChars() get selected chars from selection model

Methods in phenote.gui.field with parameters of type CharacterI

boolean	CharFieldMatcher.matches(CharacterI character)
protected void	FreeTextField.setValueFromChar(CharacterI chr)

Method parameters in phenote.gui.field with type arguments of type CharacterI

protected boolean	CharFieldGui.areCharactersEqualForCharField(java.util.List<CharacterI> characters, CharField charField) return true if all values for char field in all characters are the same value(equal) - used for multi select
void	FreeTextField.listChanged(ca.odell.glazedlists.event.ListEvent<CharacterI> listChanges)
void	CharFieldGui.listChanged(ca.odell.glazedlists.event.ListEvent<CharacterI> listChanges) part of ListEventListener interface.
void	FieldPanel.setListSelectionModel(ca.odell.glazedlists.swing.EventSelectionModel<CharacterI> model)
void	CharFieldGui.setListSelectionModel(ca.odell.glazedlists.swing.EventSelectionModel<CharacterI> model)
protected void	FreeTextField.setValueFromChars(java.util.List<CharacterI> characters)
protected void	CharFieldGui.setValueFromChars(java.util.List<CharacterI> characters) Set the gui from the model (selection)

Constructor parameters in phenote.gui.field with type arguments of type CharacterI

BigTextPopup(java.awt.Frame owner, CharField cf, java.util.List<CharacterI> chars)

FieldPanel(boolean doAllFields, boolean addSearchPanel, java.lang.String grp, ca.odell.glazedlists.swing.EventSelectionModel<CharacterI> model)

FieldPanel(boolean doAllFields, boolean addSearchPanel, java.lang.String group, SelectionManager selectionManager, EditManager groupEditMan, ca.odell.glazedlists.swing.EventSelectionModel<CharacterI> model)

PostCompGui(CharField charField, EditManager eManager, SelectionManager selManager, ca.odell.glazedlists.swing.EventSelectionModel<CharacterI> selModel, java.awt.Frame ownerFrame, int minCompChars)

Uses of CharacterI in phenote.gui.selection

Methods in phenote.gui.selection that return types with arguments of type CharacterI

java.util.List<CharacterI>	CharSelectionEvent.getChars()
java.util.List<CharacterI>	CharSelectionEvent.getPreviouslySelectedChars()

Constructor parameters in phenote.gui.selection with type arguments of type CharacterI

CharSelectionEvent(java.lang.Object source, java.util.List<CharacterI> chars, java.util.List<CharacterI> prev)

CharSelectionEvent(java.lang.Object source, java.util.List<CharacterI> chars, java.util.List<CharacterI> prev)

Uses of CharacterI in phenote.matrix.model

Methods in phenote.matrix.model with parameters of type CharacterI

int	CharacterComparator.compare(CharacterI c1, CharacterI c2) A method to perform a String-style comparison on two Characters
java.lang.Object	PhenotypeMatrixRow.getValue(CharacterI character)
java.lang.Object	PhenotypeMatrixColumn.getValue(CharacterI character)
java.lang.Object	MatrixRow.getValue(CharacterI aCharacter)
java.lang.Object	MatrixColumn.getValue(CharacterI aCharacter)
boolean	PhenotypeMatrixRow.isValue(CharacterI character) Determines whether or not a given character contains the same values as the matrix row
boolean	PhenotypeMatrixColumn.isValue(CharacterI character) Determines whether or not a given character contains the same values as the column
boolean	MatrixRow.isValue(CharacterI aCharacter)
boolean	MatrixColumn.isValue(CharacterI aCharacter)

Constructors in phenote.matrix.model with parameters of type CharacterI

PhenotypeMatrixCell(CharacterI ch)
Extracts the desired information from a given character and sets the contents of the matrix cell