phenote.config
Class Config

java.lang.Object
  phenote.config.Config

public class Config
extends java.lang.Object

Field Summary

static java.lang.String	defaultLogConfigFile
static java.lang.String	FLYBASE_DEFAULT_CONFIG_FILE

Method Summary

void	addFieldConfig(FieldConfig fc)
(package private) phenote.config.xml.FieldDocument.Field	addNewFieldBean() Adds & returns xml Field bean
boolean	autoUpdateIsEnabled()
static void	changeConfig(java.lang.String newCfgFile)
boolean	compareStatementEnabled()
boolean	dataInputServletIsEnabled()
(package private) FieldConfig	getAllFieldCfg(java.lang.String fieldName) should first check field with datatag if has one, and if not then label as label may not be unique - fix this - only uses label at the moment
java.util.List<FieldConfig>	getAllFieldCfgs()
(package private) int	getAllFieldIndex(FieldConfig fc) get index of field config in enabled field config list - returns -1 if not in there -- ex?
java.util.List<OntologyConfig>	getAllOntologies()
AnnotationMappingDriver	getAnnotMappingDriver() mapping for character to obo annot, used for OBO_ANNOTATION character mode meaningless in pure character mode, returns BasicAnnotationMappingDriver by default
phenote.config.xml.AutocompleteSettingsDocument.AutocompleteSettings	getAutocompleteSettings()
phenote.config.xml.CharacterModeDocument.CharacterMode.Mode.Enum	getCharacterMode() returns enum from character mode xml bean itself - why not right?
java.util.List<CharField>	getCharFieldsForSyntaxAbbrev(java.lang.String abb) kinda silly to return list?? so there are 2 fields for "Tag" which perhaps is silly but thats whats happening so need to deal with it
java.lang.String	getConfigAuthor()
java.lang.String	getConfigDesc()
java.lang.String	getConfigName()
java.util.List<DataAdapterI>	getDataAdapters() Returns enabled data adapters - empty list if none enabled
DataAdapterI	getDefaultFileAdapter() LoadSaveMangr uses if no extension works.
phenote.config.xml.GroupDocument.Group	getDefaultGroup()
CharField	getEnbldCharField(int index)
java.util.List<FieldConfig>	getEnbldFieldCfgs() OntologyDataAdapter calls this to figure which ontologies to load This is a list of enabled fields - does not include disabled fields! retname getEnabledFieldConfigs?
int	getEnbldFieldsNum()
int	getEnbldFieldsNum(java.lang.String group)
java.util.Collection<org.obo.dataadapter.OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration>	getExternalDatabaseConfigs()
java.util.Collection<java.lang.String>	getExternalDatabasePaths()
int	getFieldColwidth(int index)
java.util.List<phenote.config.xml.GroupDocument.Group>	getFieldGroups()
java.lang.String	getFieldLabel(int index, java.lang.String group) Gives name of field at index, 0 based (for table heading)
java.util.List<java.lang.String>	getFieldsInGroup(java.lang.String groupName)
(package private) java.util.List<DataAdapterConfig>	getFileAdapConfigs()
GroupAdapterI	getGroupAdapter(java.lang.String groupStr) returns null if group adapter for group not found - ex?
(package private) java.lang.String	getLogConfigFile()
java.net.URL	getLogConfigUrl()
int	getMinCompChars(int fieldIndex)
java.lang.String	getMyPhenoteConfigString() Get config file string that is in my-phenote file - throw io exception if file doesnt exist.
java.util.List<NCBIDataAdapterI>	getNCBIDataAdapters()
OntologyMakerI	getOntMaker(java.lang.String group)
java.util.List<OntologyMakerI>	getOntMakers()
phenote.config.xml.OntologyFileDocument.OntologyFile	getOntologyFileByHandle(java.lang.String handle)
phenote.config.xml.OntologyFileDocument.OntologyFile[]	getOntologyList()
(package private) phenote.config.xml.PhenoteConfigurationDocument	getPhenoDocBean()
QueryableDataAdapterI	getQueryableDataAdapter() Just get first one thats enabled - for now assume theres one
(package private) java.util.List<DataAdapterConfig>	getQueryAdapCfgs() all configs for query adaps - enabled or not
(package private) java.lang.String	getReposUrlDir()
java.lang.String	getSyntaxAbbrevForCharField(CharField cf)
phenote.config.xml.TerminologyDefinitionsDocument.TerminologyDefinitions	getTerminologyDefs() This will retrieve all of the ontology/terminology definitions in a configuration file.
java.lang.String	getTitleForGroup(java.lang.String groupName) Returns null if group w groupName doesnt exist
phenote.config.xml.TerminologyDefinitionsDocument.TerminologyDefinitions.Update.Enum	getUpdateTerminologies() This method will make the "update ontologies" flag pase.
int	getUpdateTimer()
boolean	hasDataAdapters()
boolean	hasEnbldCharField(int index)
(package private) boolean	hasFieldCfgAll(FieldConfig fc) returns true if has field config with same name - contents may differ
boolean	hasGroupAdapter(java.lang.String group)
boolean	hasNCBIAdapter()
boolean	hasOntMakerForGroup(java.lang.String group) returns whether have term maker for given group - there could also be a term maker manager?
boolean	hasOntMakers()
boolean	hasQueryableDataAdapter()
(package private) void	insertFieldConfig(int index, FieldConfig fc) adds to both field config list and xml beans field list
static Config	inst()
boolean	isConfigModified()
boolean	isInitialized()
boolean	isVisible(CharField cf)
void	loadConstraints() load up all constraints from config into ConstraintManager, from constaint list as well as required config fields
void	loadDefaultConfigFile() Changed this to actually do updating of config file by default given that this is now the route in from webstart, without this users will never get config updates - eventually get more sophisticated - give user options of updateFromDefault, revertToMain/Default or personal/ignoreMain/dontupdate
void	loadDefaultFlybaseConfigFile() if all else fails revert to flybase which should be there
static Config	makeConfigFromFile(java.lang.String file)
static Config	newInstance(java.lang.String name, java.lang.String displayName)
static void	reset()
void	saveModifiedConfig()
void	setAutocompleteSettings()
void	setAutoUpdate(boolean enable)
void	setConfigAuthor(java.lang.String author)
void	setConfigDesc(java.lang.String desc)
void	setConfigFile(java.lang.String configFile) This is setting config file with nothing to do with personal config this is for the servlet where config file location is set in web.xml
void	setConfigModified(boolean setting)
void	setConfigName(java.lang.String name)
void	setDataInputServletIsEnabled(boolean enable)
void	setFieldColwidth(int index, int width)
void	setOntologyList(phenote.config.xml.OntologyFileDocument.OntologyFile[] ontologyList)
void	setOverwriteConfigFile(java.lang.String configFile) -c from command line does this - should be always but isnt???
void	setTermHistory(boolean setter)
void	setTerminologyDefs(phenote.config.xml.TerminologyDefinitionsDocument.TerminologyDefinitions termDefs)
void	setUpdateTerminologies(phenote.config.xml.TerminologyDefinitionsDocument.TerminologyDefinitions.Update.Enum updateStatus)
void	setUpdateTimer(int seconds)
void	setUvicGraphIsEnabled(boolean enable)
boolean	shouldUseFieldPanelTabs()
boolean	showLoadingScreen() Loading screen is the elephant splash screen that displays when phenote is initializing ontologies & such at startup.
boolean	termHistoryIsEnabled()
java.lang.String	toString()
void	updateConfigFileWithNewVersion(java.lang.String configFile) This is for when phenote is first installed and one of the default config files is used - the -i option if you will.
boolean	uvicGraphIsEnabled() config flag for enabling uvic shrimp dag graph
static void	writeMyPhenoteDefaultFile(java.lang.String newDefaultFileString) Write name of config file loaded out to .phenote/conf/my-phenote.cfg for use by future startups with no config specified Throws ConfigException if fails to find file

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

FLYBASE_DEFAULT_CONFIG_FILE

public static final java.lang.String FLYBASE_DEFAULT_CONFIG_FILE

See Also:

Constant Field Values

defaultLogConfigFile

public static final java.lang.String defaultLogConfigFile

See Also:

Constant Field Values

Method Detail

inst

public static Config inst()

reset

public static void reset()

newInstance

public static Config newInstance(java.lang.String name,
                                 java.lang.String displayName)

makeConfigFromFile

public static Config makeConfigFromFile(java.lang.String file)
                                 throws ConfigException

Throws:

ConfigException

isInitialized

public boolean isInitialized()

isConfigModified

public boolean isConfigModified()

setConfigModified

public void setConfigModified(boolean setting)

saveModifiedConfig

public void saveModifiedConfig()

setConfigFile

public void setConfigFile(java.lang.String configFile)
                   throws ConfigException

This is setting config file with nothing to do with personal config this is for the servlet where config file location is set in web.xml

Throws:

ConfigException

changeConfig

public static void changeConfig(java.lang.String newCfgFile)
                         throws ConfigException

Throws:

ConfigException

updateConfigFileWithNewVersion

public void updateConfigFileWithNewVersion(java.lang.String configFile)
                                    throws ConfigException

This is for when phenote is first installed and one of the default config files is used - the -i option if you will. The initial config file will get copied to .phenote/my-phenote.cfg if it doesnt already exist. if it exists then this file is ignored

Throws:

ConfigException

setOverwriteConfigFile

public void setOverwriteConfigFile(java.lang.String configFile)
                            throws ConfigException

-c from command line does this - should be always but isnt???

Throws:

ConfigException

loadDefaultConfigFile

public void loadDefaultConfigFile()
                           throws ConfigException

Changed this to actually do updating of config file by default given that this is now the route in from webstart, without this users will never get config updates - eventually get more sophisticated - give user options of updateFromDefault, revertToMain/Default or personal/ignoreMain/dontupdate

Throws:

ConfigException

loadDefaultFlybaseConfigFile

public void loadDefaultFlybaseConfigFile()
                                  throws ConfigException

if all else fails revert to flybase which should be there

Throws:

ConfigException

getMyPhenoteConfigString

public java.lang.String getMyPhenoteConfigString()
                                          throws java.io.IOException

Get config file string that is in my-phenote file - throw io exception if file doesnt exist. todo: should also throw ex if doesnt have a valid file in it?

Throws:

java.io.IOException

writeMyPhenoteDefaultFile

public static void writeMyPhenoteDefaultFile(java.lang.String newDefaultFileString)
                                      throws ConfigException

Write name of config file loaded out to .phenote/conf/my-phenote.cfg for use by future startups with no config specified Throws ConfigException if fails to find file

Throws:

ConfigException

getExternalDatabasePaths

public java.util.Collection<java.lang.String> getExternalDatabasePaths()

getExternalDatabaseConfigs

public java.util.Collection<org.obo.dataadapter.OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration> getExternalDatabaseConfigs()

hasDataAdapters

public boolean hasDataAdapters()

getFileAdapConfigs

java.util.List<DataAdapterConfig> getFileAdapConfigs()

getDataAdapters

public java.util.List<DataAdapterI> getDataAdapters()

Returns enabled data adapters - empty list if none enabled

getDefaultFileAdapter

public DataAdapterI getDefaultFileAdapter()

LoadSaveMangr uses if no extension works. Returns null if no data adapters loaded Otherwise returns 1st enabled adapter. Todo: add isdefault config

uvicGraphIsEnabled

public boolean uvicGraphIsEnabled()

config flag for enabling uvic shrimp dag graph

setUvicGraphIsEnabled

public void setUvicGraphIsEnabled(boolean enable)

dataInputServletIsEnabled

public boolean dataInputServletIsEnabled()

setDataInputServletIsEnabled

public void setDataInputServletIsEnabled(boolean enable)

termHistoryIsEnabled

public boolean termHistoryIsEnabled()

setTermHistory

public void setTermHistory(boolean setter)

autoUpdateIsEnabled

public boolean autoUpdateIsEnabled()

setAutoUpdate

public void setAutoUpdate(boolean enable)

getUpdateTimer

public int getUpdateTimer()

setUpdateTimer

public void setUpdateTimer(int seconds)

shouldUseFieldPanelTabs

public boolean shouldUseFieldPanelTabs()

getCharacterMode

public phenote.config.xml.CharacterModeDocument.CharacterMode.Mode.Enum getCharacterMode()

returns enum from character mode xml bean itself - why not right?

getAnnotMappingDriver

public AnnotationMappingDriver getAnnotMappingDriver()

mapping for character to obo annot, used for OBO_ANNOTATION character mode meaningless in pure character mode, returns BasicAnnotationMappingDriver by default

getAutocompleteSettings

public phenote.config.xml.AutocompleteSettingsDocument.AutocompleteSettings getAutocompleteSettings()

setAutocompleteSettings

public void setAutocompleteSettings()

getLogConfigUrl

public java.net.URL getLogConfigUrl()
                             throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

getLogConfigFile

java.lang.String getLogConfigFile()

addNewFieldBean

phenote.config.xml.FieldDocument.Field addNewFieldBean()

Adds & returns xml Field bean

getEnbldFieldsNum

public int getEnbldFieldsNum()

getEnbldFieldsNum

public int getEnbldFieldsNum(java.lang.String group)

getFieldLabel

public java.lang.String getFieldLabel(int index,
                                      java.lang.String group)

Gives name of field at index, 0 based (for table heading)

getFieldColwidth

public int getFieldColwidth(int index)

setFieldColwidth

public void setFieldColwidth(int index,
                             int width)

getMinCompChars

public int getMinCompChars(int fieldIndex)

hasEnbldCharField

public boolean hasEnbldCharField(int index)

getEnbldCharField

public CharField getEnbldCharField(int index)

getEnbldFieldCfgs

public java.util.List<FieldConfig> getEnbldFieldCfgs()

OntologyDataAdapter calls this to figure which ontologies to load This is a list of enabled fields - does not include disabled fields! retname getEnabledFieldConfigs?

getAllFieldCfgs

public java.util.List<FieldConfig> getAllFieldCfgs()

getAllOntologies

public java.util.List<OntologyConfig> getAllOntologies()

hasFieldCfgAll

boolean hasFieldCfgAll(FieldConfig fc)

returns true if has field config with same name - contents may differ

getAllFieldCfg

FieldConfig getAllFieldCfg(java.lang.String fieldName)

should first check field with datatag if has one, and if not then label as label may not be unique - fix this - only uses label at the moment

isVisible

public boolean isVisible(CharField cf)

getCharFieldsForSyntaxAbbrev

public java.util.List<CharField> getCharFieldsForSyntaxAbbrev(java.lang.String abb)
                                                       throws ConfigException

kinda silly to return list?? so there are 2 fields for "Tag" which perhaps is silly but thats whats happening so need to deal with it

Throws:

ConfigException

getSyntaxAbbrevForCharField

public java.lang.String getSyntaxAbbrevForCharField(CharField cf)

getReposUrlDir

java.lang.String getReposUrlDir()

getPhenoDocBean

phenote.config.xml.PhenoteConfigurationDocument getPhenoDocBean()

hasQueryableDataAdapter

public boolean hasQueryableDataAdapter()

hasNCBIAdapter

public boolean hasNCBIAdapter()

getQueryableDataAdapter

public QueryableDataAdapterI getQueryableDataAdapter()

Just get first one thats enabled - for now assume theres one

getNCBIDataAdapters

public java.util.List<NCBIDataAdapterI> getNCBIDataAdapters()

getQueryAdapCfgs

java.util.List<DataAdapterConfig> getQueryAdapCfgs()

all configs for query adaps - enabled or not

addFieldConfig

public void addFieldConfig(FieldConfig fc)

getAllFieldIndex

int getAllFieldIndex(FieldConfig fc)

get index of field config in enabled field config list - returns -1 if not in there -- ex?

insertFieldConfig

void insertFieldConfig(int index,
                       FieldConfig fc)

adds to both field config list and xml beans field list

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getConfigName

public java.lang.String getConfigName()

setConfigName

public void setConfigName(java.lang.String name)

getConfigDesc

public java.lang.String getConfigDesc()

setConfigDesc

public void setConfigDesc(java.lang.String desc)

getConfigAuthor

public java.lang.String getConfigAuthor()

setConfigAuthor

public void setConfigAuthor(java.lang.String author)

showLoadingScreen

public boolean showLoadingScreen()

Loading screen is the elephant splash screen that displays when phenote is initializing ontologies & such at startup. The current LoadingScreen can go into threadlock and seize up phenote so need ability to disable it defaults to true (false?)

getFieldGroups

public java.util.List<phenote.config.xml.GroupDocument.Group> getFieldGroups()

getFieldsInGroup

public java.util.List<java.lang.String> getFieldsInGroup(java.lang.String groupName)

getTitleForGroup

public java.lang.String getTitleForGroup(java.lang.String groupName)

Returns null if group w groupName doesnt exist

getDefaultGroup

public phenote.config.xml.GroupDocument.Group getDefaultGroup()

hasGroupAdapter

public boolean hasGroupAdapter(java.lang.String group)

getGroupAdapter

public GroupAdapterI getGroupAdapter(java.lang.String groupStr)

returns null if group adapter for group not found - ex?

hasOntMakerForGroup

public boolean hasOntMakerForGroup(java.lang.String group)

returns whether have term maker for given group - there could also be a term maker manager?

getOntMaker

public OntologyMakerI getOntMaker(java.lang.String group)

hasOntMakers

public boolean hasOntMakers()

getOntMakers

public java.util.List<OntologyMakerI> getOntMakers()

compareStatementEnabled

public boolean compareStatementEnabled()

getTerminologyDefs

public phenote.config.xml.TerminologyDefinitionsDocument.TerminologyDefinitions getTerminologyDefs()

This will retrieve all of the ontology/terminology definitions in a configuration file. Included here will be all ontology files, their handle, repository location, and whether or not to update.

Returns:

An object that defines all ontologies/terminologies utilized in the configuration, together with a convenience flag to indicate whether to update some, none, or all ontologies.

setTerminologyDefs

public void setTerminologyDefs(phenote.config.xml.TerminologyDefinitionsDocument.TerminologyDefinitions termDefs)

getOntologyList

public phenote.config.xml.OntologyFileDocument.OntologyFile[] getOntologyList()

Returns:

This returns the an array of ontologies themselves, including the file names, and other metadata (such as version, etc.)

setOntologyList

public void setOntologyList(phenote.config.xml.OntologyFileDocument.OntologyFile[] ontologyList)

getUpdateTerminologies

public phenote.config.xml.TerminologyDefinitionsDocument.TerminologyDefinitions.Update.Enum getUpdateTerminologies()

This method will make the "update ontologies" flag pase.

Returns:

Convenience method to determine the global status of updating ontology files. This will either be None, Some, or All ontologies. This defaults to None if not set in the configuration.

getOntologyFileByHandle

public phenote.config.xml.OntologyFileDocument.OntologyFile getOntologyFileByHandle(java.lang.String handle)

setUpdateTerminologies

public void setUpdateTerminologies(phenote.config.xml.TerminologyDefinitionsDocument.TerminologyDefinitions.Update.Enum updateStatus)

loadConstraints

public void loadConstraints()

load up all constraints from config into ConstraintManager, from constaint list as well as required config fields