apollo.config
Class Style

java.lang.Object
  apollo.config.Style

public class Style
extends java.lang.Object

A Style is basically config options for a particular data adapter

Field Summary

protected static org.apache.log4j.Logger	logger
protected java.util.Hashtable	parameters General way to store config variables.

Constructor Summary

Style(java.lang.String styleFileString)

Method Summary

void	addAnnotationComment(java.lang.String comment) Add a canned annotation comment.
void	addParameter(java.lang.String name, java.lang.String value) Whenever we add a new parameter to the style file, we've been adding methods in Style.java to set/get some variable--it's getting annoying.
boolean	addSyntenyResultMenuItem() Whether to add a menu item to the result popup menu that will bring up the selected feature as the other species in synteny
boolean	addSyntenySpeciesNumDropdown() Whether to add link query radio buttons to synteny adap gui
void	addTranscriptComment(java.lang.String comment) Add a canned transcript comment.
static void	askRenameGameConfig(java.lang.String oldname, java.lang.String newname) 7/2005: Special backwards-compatibility hand-holding: game.style and game.tiers were recently renamed fly.style (which imports game.style) and fly.tiers, but some users may still have a private game.style or game.tiers in their .apollo directory.
boolean	checkBoolean(java.lang.String value, java.lang.String variableName)
boolean	checkValidColor(java.lang.String colorStr, java.lang.String variableName)
boolean	colorAllAnnotsByOwner()
void	complain(java.lang.String message) Print message to stderr
boolean	databaseHasStyle(java.lang.String db) Returns true if have style for db
boolean	doUserTranscriptColouring()
java.lang.String	getAllStyleFilesString() Returns a string of all the style files used to create this file
java.awt.Color	getAnnotationBackground()
java.awt.Color	getAnnotationColor(java.lang.String username) Retrieve color for user name; if no color use defaultAnnotationColor.
java.util.Vector	getAnnotationComments()
java.awt.Color	getAnnotationLabelColor()
java.lang.String	getBandUrl()
java.lang.String	getBlixemLocation()
java.util.Vector	getChromosomes() Returns a vector of chromosome names as strings, null if none given
java.awt.Color	getCoordBackground()
java.awt.Color	getCoordForeground()
java.awt.Color	getCoordRevcompColor()
boolean	getDashSets()
java.util.Vector	getDatabaseList() If no DatabaseList set in style, defaults to a list of just the DatabaseDefault (which defaults to gadfly if not set)
java.util.Vector	getDatabaseList(java.lang.String queryType) Get list of databases with changes possible based on queryType.
java.lang.String	getDatabaseURLField() Field in url to replace with database selection
java.lang.String	getDefaultDatabase() Used for navigation bar db (for game), also if no database list is provided, getDatabaseList defaults to a list of default db.
int	getDefaultPadding()
java.lang.String	getDefaultSyntenyDataAdapterString() String of class name for default synteny data adapter to use if none are specified in style file - default is null
protected DisplayPrefsI	getDisplayPrefs()
boolean	getDraw3D()
boolean	getDrawOutline()
java.awt.Color	getEdgematchColor()
int	getEdgematchWidth()
java.lang.String	getErrors()
int	getEvidencePanelHeight()
java.awt.Font	getExonDetailEditorSequenceFont() Font for amino and dna sequence in EDE
java.awt.Color	getFeatureBackground()
java.awt.Color	getFeatureLabelColor()
int	getFeatureLoadSize()
java.lang.String	getFileName()
int	getGeneticCodeNumber()
java.lang.String	getGeneUrl()
java.awt.Color	getHighlightColor()
boolean	getInitialSitesVisibility() Initial state for sites visibility (view menu item)
java.lang.String	getLayoutIniFile()
int	getLinkPanelSize()
boolean	getNaiveCrossSpeciesDataLoading() This indicates whether a composite adapter UI is to load cross-species data simply - that is, just read the adapters for each species & the compara sets in turn, and not propagate information from one read to the other.
java.lang.String	getNameAdapter()
boolean	getNoStripes()
int	getNumberOfSpecies() How many species to display in synteny - default is 1
int	getNumberOfSyntenySpecies()
java.awt.Color	getOutlineColor() Edgematch color is also used for generic outlines around features
java.lang.String	getOverlapDefinition()
java.lang.String	getPadLeftURLField() Field in url to replace with padding int
java.lang.String	getPadRightURLField()
java.lang.String	getParameter(java.lang.String name) Returns the last value (even if there are many)
java.util.Vector	getParameterMulti(java.lang.String name) Returns the whole vector of values for this parameter
java.util.Hashtable	getParameters() Returns hash with only one string for each key.
java.util.Hashtable	getParametersMulti() Returns hash of Parameter vectors.
java.lang.String	getProjectName(java.lang.String username)
PropertyScheme	getPropertyScheme()
java.lang.String	getRangeUrl()
java.util.Vector	getResultTag(java.lang.String result_type)
java.util.Hashtable	getResultTags()
java.lang.String	getScaffoldUrl()
java.awt.Color	getSelectionColor()
java.awt.Color	getSeqErrorColor() Return color for showing genomic sequencing errors or frameshifts
java.awt.Color	getSeqGapColor()
java.awt.Color	getSequenceColor()
java.lang.String	getSeqUrl()
boolean	getShowAnnotations()
boolean	getShowResults()
int	getSingleSpeciesPanelSize()
Style	getStyleForDb(java.lang.String db) Returns null if cant make style for db
java.lang.String	getSyntenyDatabaseForSpecies(java.lang.String species) Database species maps to as proscribed by SpeciesToDatabase entries.
java.util.List	getSyntenyLinkOrder()
java.util.List	getSyntenySpeciesAndLinkOrder() List of Strings which are the species/names/tags of sub-adapters.
java.util.HashMap	getSyntenySpeciesNames() Maps names (Name.Mouse) to adapter label/logical name (Mus Musculus).
java.util.List	getSyntenySpeciesOrder() Same as syntenySpeciesAndLinkOrder(Strings) minus links(denoted by "Compara") eg "Name.Mouse", "Name.Human" If synteny species names not explicitly set(ensj,gff), and useGenericSyntenySpecies is true, make a generic list up to getNumberOfSpecies (Species1,Species2,...SpeciesN) (game)
java.util.HashMap	getSyntenySpeciesProperties() This maps these kinds of strings from the style file: "Species.Mouse.DataAdapter" -> "apollo.dataadapter.ensj.AnnotationEnsJAdapter" So basically its where the dataadapter is
java.lang.String	getSyntenySpeciesString(int i)
java.awt.Color	getTaggedColor() Return color for boxing tagged results
java.lang.String	getTiersFile()
java.util.Vector	getTranscriptComments()
boolean	getTranscriptSymbolEditable() Whether transcript symbol/name is editable in annot info, default true
boolean	igbHttpConnectionEnabled()
boolean	initialLockedScrolling() Whether synteny's initial state is to lock scrolling.
boolean	initialShiftForLockedZooming() Whether synteny should lock zooming with a shift or vice versa, initially.
boolean	internalMode()
boolean	isEditingEnabled()
boolean	isSuperUser(java.lang.String name)
boolean	queryForNamesOnSplit() added BY TAIR someday we may need to change this to something more fitting than a boolean, but for now it is binary
void	readStyle(java.io.File styleFile) Saves error messages for later checking
void	readStyle(java.lang.String styleFilename)
void	removeParameter(java.lang.String key)
void	replaceParameter(java.lang.String key, java.lang.String value)
boolean	seqErrorEditingIsEnabled()
void	setAnnotationBackground(java.awt.Color color)
void	setAnnotationLabelColor(java.awt.Color col)
void	setCoordBackground(java.awt.Color col)
void	setCoordForeground(java.awt.Color col)
void	setCoordRevcompColor(java.awt.Color col)
void	setDraw3D(boolean state)
void	setDrawOutline(boolean state)
void	setEdgematchColor(java.awt.Color col)
void	setEditingEnabled(boolean editingEnabled)
void	setFeatureBackground(java.awt.Color col)
void	setFeatureLabelColor(java.awt.Color col)
void	setLocalNavigationManagerEnabled(java.lang.Boolean enable)
void	setSequenceColor(java.awt.Color col)
void	setShowAnnotations(boolean showAnnotations)
void	setShowResults(boolean showResults)
void	setStyleFile(java.lang.String name)
void	setTiersFile(java.lang.String tiersFile)
boolean	showDbXRefTable() Whether to show db cross reference table in annot info
boolean	showEvalOfPeptide()
boolean	showFinishedCheckbox() Whether to show/use finished checkbox in annot info transcript panel
boolean	showIdField() Whether gene id field is displayed in annot info
boolean	showIsDicistronicCheckbox() Whether to show, and therefore use, the "Is Dicistronic?" checkbox in annot info editor
boolean	showIsProbCheckbox()
boolean	showOwnershipAnnotMenuItem()
boolean	showReplaceStopCheckbox()
boolean	showTranscriptFinishedAnnotMenuItem()
boolean	syntenyLinksAreGeneToGene()
java.lang.String	toString()
boolean	transactionsAreInGameFile()
boolean	translationalFrameShiftEditingIsEnabled()
boolean	useOpaqueLinks() If the links between individual species' features are drawn opaquely then rendering of the panels as a whole will be faster.
boolean	writeStyle(java.io.File styleFile) Writes the style data to a file.
void	writeStyle(java.lang.String styleFilename) Writes the style data to a file.

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

parameters

protected java.util.Hashtable parameters

General way to store config variables. We could start replacing the special-purpose variables and methods with add/getProperty.

Constructor Detail

Style

public Style(java.lang.String styleFileString)

Method Detail

setStyleFile

public void setStyleFile(java.lang.String name)

getAllStyleFilesString

public java.lang.String getAllStyleFilesString()

Returns a string of all the style files used to create this file

readStyle

public void readStyle(java.lang.String styleFilename)

readStyle

public void readStyle(java.io.File styleFile)

Saves error messages for later checking

writeStyle

public void writeStyle(java.lang.String styleFilename)

Writes the style data to a file.

Parameters:

styleFilename - - String for the name of the style file to write to

writeStyle

public boolean writeStyle(java.io.File styleFile)

Writes the style data to a file.

Parameters:

styleFile - - File for the style file to write to

Returns:

true if successful

complain

public void complain(java.lang.String message)

Print message to stderr

getErrors

public java.lang.String getErrors()

queryForNamesOnSplit

public boolean queryForNamesOnSplit()

added BY TAIR someday we may need to change this to something more fitting than a boolean, but for now it is binary

askRenameGameConfig

public static void askRenameGameConfig(java.lang.String oldname,
                                       java.lang.String newname)

7/2005: Special backwards-compatibility hand-holding: game.style and game.tiers were recently renamed fly.style (which imports game.style) and fly.tiers, but some users may still have a private game.style or game.tiers in their .apollo directory. Ask if they want to rename it to the new name.

checkValidColor

public boolean checkValidColor(java.lang.String colorStr,
                               java.lang.String variableName)

getBlixemLocation

public java.lang.String getBlixemLocation()

checkBoolean

public boolean checkBoolean(java.lang.String value,
                            java.lang.String variableName)

getTiersFile

public java.lang.String getTiersFile()

setTiersFile

public void setTiersFile(java.lang.String tiersFile)

getLayoutIniFile

public java.lang.String getLayoutIniFile()

getShowAnnotations

public boolean getShowAnnotations()

setShowAnnotations

public void setShowAnnotations(boolean showAnnotations)

getShowResults

public boolean getShowResults()

setShowResults

public void setShowResults(boolean showResults)

getEdgematchWidth

public int getEdgematchWidth()

doUserTranscriptColouring

public boolean doUserTranscriptColouring()

colorAllAnnotsByOwner

public boolean colorAllAnnotsByOwner()

getDraw3D

public boolean getDraw3D()

setDraw3D

public void setDraw3D(boolean state)

getNoStripes

public boolean getNoStripes()

getEvidencePanelHeight

public int getEvidencePanelHeight()

isEditingEnabled

public boolean isEditingEnabled()

setEditingEnabled

public void setEditingEnabled(boolean editingEnabled)

setLocalNavigationManagerEnabled

public void setLocalNavigationManagerEnabled(java.lang.Boolean enable)

getChromosomes

public java.util.Vector getChromosomes()

Returns a vector of chromosome names as strings, null if none given

getDrawOutline

public boolean getDrawOutline()

setDrawOutline

public void setDrawOutline(boolean state)

getDatabaseList

public java.util.Vector getDatabaseList()

If no DatabaseList set in style, defaults to a list of just the DatabaseDefault (which defaults to gadfly if not set)

getDatabaseList

public java.util.Vector getDatabaseList(java.lang.String queryType)

Get list of databases with changes possible based on queryType. FOR NOW, database list for sequence queries doesn't include database r3.2

getDefaultDatabase

public java.lang.String getDefaultDatabase()

Used for navigation bar db (for game), also if no database list is provided, getDatabaseList defaults to a list of default db. defaultDatabase defaults to "gadfly" if not provided.

getAnnotationComments

public java.util.Vector getAnnotationComments()

getTranscriptComments

public java.util.Vector getTranscriptComments()

addAnnotationComment

public void addAnnotationComment(java.lang.String comment)

Add a canned annotation comment.

Parameters:

comment - - String to be added

addTranscriptComment

public void addTranscriptComment(java.lang.String comment)

Add a canned transcript comment.

Parameters:

comment - - String to be added

internalMode

public boolean internalMode()

getProjectName

public java.lang.String getProjectName(java.lang.String username)

getAnnotationColor

public java.awt.Color getAnnotationColor(java.lang.String username)

Retrieve color for user name; if no color use defaultAnnotationColor. Note that this is called only if doUserTranscriptColouring is true and we're in internal (not public) mode.

getTaggedColor

public java.awt.Color getTaggedColor()

Return color for boxing tagged results

getSeqErrorColor

public java.awt.Color getSeqErrorColor()

Return color for showing genomic sequencing errors or frameshifts

getFeatureLoadSize

public int getFeatureLoadSize()

getGeneUrl

public java.lang.String getGeneUrl()

getBandUrl

public java.lang.String getBandUrl()

getScaffoldUrl

public java.lang.String getScaffoldUrl()

getSeqUrl

public java.lang.String getSeqUrl()

getRangeUrl

public java.lang.String getRangeUrl()

getDashSets

public boolean getDashSets()

getAnnotationBackground

public java.awt.Color getAnnotationBackground()

setAnnotationBackground

public void setAnnotationBackground(java.awt.Color color)

getFeatureBackground

public java.awt.Color getFeatureBackground()

setFeatureBackground

public void setFeatureBackground(java.awt.Color col)

getEdgematchColor

public java.awt.Color getEdgematchColor()

setEdgematchColor

public void setEdgematchColor(java.awt.Color col)

getOutlineColor

public java.awt.Color getOutlineColor()

Edgematch color is also used for generic outlines around features

getFeatureLabelColor

public java.awt.Color getFeatureLabelColor()

setFeatureLabelColor

public void setFeatureLabelColor(java.awt.Color col)

getAnnotationLabelColor

public java.awt.Color getAnnotationLabelColor()

setAnnotationLabelColor

public void setAnnotationLabelColor(java.awt.Color col)

getCoordBackground

public java.awt.Color getCoordBackground()

setCoordBackground

public void setCoordBackground(java.awt.Color col)

getCoordForeground

public java.awt.Color getCoordForeground()

setCoordForeground

public void setCoordForeground(java.awt.Color col)

getCoordRevcompColor

public java.awt.Color getCoordRevcompColor()

setCoordRevcompColor

public void setCoordRevcompColor(java.awt.Color col)

getSequenceColor

public java.awt.Color getSequenceColor()

setSequenceColor

public void setSequenceColor(java.awt.Color col)

getHighlightColor

public java.awt.Color getHighlightColor()

getSelectionColor

public java.awt.Color getSelectionColor()

getSeqGapColor

public java.awt.Color getSeqGapColor()

getDisplayPrefs

protected DisplayPrefsI getDisplayPrefs()

getNameAdapter

public java.lang.String getNameAdapter()

getOverlapDefinition

public java.lang.String getOverlapDefinition()

getFileName

public java.lang.String getFileName()

getExonDetailEditorSequenceFont

public java.awt.Font getExonDetailEditorSequenceFont()

Font for amino and dna sequence in EDE

getResultTag

public java.util.Vector getResultTag(java.lang.String result_type)

getResultTags

public java.util.Hashtable getResultTags()

getDatabaseURLField

public java.lang.String getDatabaseURLField()

Field in url to replace with database selection

getPadLeftURLField

public java.lang.String getPadLeftURLField()

Field in url to replace with padding int

getPadRightURLField

public java.lang.String getPadRightURLField()

getDefaultPadding

public int getDefaultPadding()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

isSuperUser

public boolean isSuperUser(java.lang.String name)

getPropertyScheme

public PropertyScheme getPropertyScheme()

getSingleSpeciesPanelSize

public int getSingleSpeciesPanelSize()

getLinkPanelSize

public int getLinkPanelSize()

getInitialSitesVisibility

public boolean getInitialSitesVisibility()

Initial state for sites visibility (view menu item)

addSyntenySpeciesNumDropdown

public boolean addSyntenySpeciesNumDropdown()

Whether to add link query radio buttons to synteny adap gui

addSyntenyResultMenuItem

public boolean addSyntenyResultMenuItem()

Whether to add a menu item to the result popup menu that will bring up the selected feature as the other species in synteny

syntenyLinksAreGeneToGene

public boolean syntenyLinksAreGeneToGene()

initialShiftForLockedZooming

public boolean initialShiftForLockedZooming()

Whether synteny should lock zooming with a shift or vice versa, initially. Default: true

initialLockedScrolling

public boolean initialLockedScrolling()

Whether synteny's initial state is to lock scrolling. Default false

getNaiveCrossSpeciesDataLoading

public boolean getNaiveCrossSpeciesDataLoading()

This indicates whether a composite adapter UI is to load cross-species data simply - that is, just read the adapters for each species & the compara sets in turn, and not propagate information from one read to the other.

useOpaqueLinks

public boolean useOpaqueLinks()

If the links between individual species' features are drawn opaquely then rendering of the panels as a whole will be faster.

getDefaultSyntenyDataAdapterString

public java.lang.String getDefaultSyntenyDataAdapterString()

String of class name for default synteny data adapter to use if none are specified in style file - default is null

getNumberOfSpecies

public int getNumberOfSpecies()

How many species to display in synteny - default is 1

getSyntenySpeciesNames

public java.util.HashMap getSyntenySpeciesNames()

Maps names (Name.Mouse) to adapter label/logical name (Mus Musculus). if useGenericSyntenySpecies is true just maps "Species1" -> "Species1", "Species2" -> "Species2", ... to work with SyntenyAdapter

getSyntenySpeciesProperties

public java.util.HashMap getSyntenySpeciesProperties()

This maps these kinds of strings from the style file: "Species.Mouse.DataAdapter" -> "apollo.dataadapter.ensj.AnnotationEnsJAdapter" So basically its where the dataadapter is

getSyntenySpeciesOrder

public java.util.List getSyntenySpeciesOrder()

Same as syntenySpeciesAndLinkOrder(Strings) minus links(denoted by "Compara") eg "Name.Mouse", "Name.Human" If synteny species names not explicitly set(ensj,gff), and useGenericSyntenySpecies is true, make a generic list up to getNumberOfSpecies (Species1,Species2,...SpeciesN) (game)

getSyntenyLinkOrder

public java.util.List getSyntenyLinkOrder()

getSyntenySpeciesString

public java.lang.String getSyntenySpeciesString(int i)

getNumberOfSyntenySpecies

public int getNumberOfSyntenySpecies()

getSyntenySpeciesAndLinkOrder

public java.util.List getSyntenySpeciesAndLinkOrder()

List of Strings which are the species/names/tags of sub-adapters. This is not a list of the adapters themselves. (eg "Name.Species1","Name.Species2",...) If UseGenericSyntenySpecies is true, just return the generic getSyntenySpeciesOrder Species1 thru SpeciesN with no link names (assume no link adapters - game)

getSyntenyDatabaseForSpecies

public java.lang.String getSyntenyDatabaseForSpecies(java.lang.String species)

Database species maps to as proscribed by SpeciesToDatabase entries. This is for synteny links to other species (used in game synteny). Returns null (and prints err msg) if no such mapping.

databaseHasStyle

public boolean databaseHasStyle(java.lang.String db)

Returns true if have style for db

getStyleForDb

public Style getStyleForDb(java.lang.String db)

Returns null if cant make style for db

showIdField

public boolean showIdField()

Whether gene id field is displayed in annot info

getTranscriptSymbolEditable

public boolean getTranscriptSymbolEditable()

Whether transcript symbol/name is editable in annot info, default true

showIsDicistronicCheckbox

public boolean showIsDicistronicCheckbox()

Whether to show, and therefore use, the "Is Dicistronic?" checkbox in annot info editor

showEvalOfPeptide

public boolean showEvalOfPeptide()

showIsProbCheckbox

public boolean showIsProbCheckbox()

showFinishedCheckbox

public boolean showFinishedCheckbox()

Whether to show/use finished checkbox in annot info transcript panel

showDbXRefTable

public boolean showDbXRefTable()

Whether to show db cross reference table in annot info

showReplaceStopCheckbox

public boolean showReplaceStopCheckbox()

translationalFrameShiftEditingIsEnabled

public boolean translationalFrameShiftEditingIsEnabled()

seqErrorEditingIsEnabled

public boolean seqErrorEditingIsEnabled()

showOwnershipAnnotMenuItem

public boolean showOwnershipAnnotMenuItem()

showTranscriptFinishedAnnotMenuItem

public boolean showTranscriptFinishedAnnotMenuItem()

igbHttpConnectionEnabled

public boolean igbHttpConnectionEnabled()

transactionsAreInGameFile

public boolean transactionsAreInGameFile()

getGeneticCodeNumber

public int getGeneticCodeNumber()

addParameter

public void addParameter(java.lang.String name,
                         java.lang.String value)

Whenever we add a new parameter to the style file, we've been adding methods in Style.java to set/get some variable--it's getting annoying. Parameters give us a general-purpose, extensible way to set key=value(s) pairs in the style. The default can be set here (which, of course, means we can't set it for brand-new parameters that are not yet known) or by the caller. For case-insensitivity, keys are stored as lowercase and getParameter converts the request to lowercase before looking for it.

removeParameter

public void removeParameter(java.lang.String key)

replaceParameter

public void replaceParameter(java.lang.String key,
                             java.lang.String value)

getParameter

public java.lang.String getParameter(java.lang.String name)

Returns the last value (even if there are many)

getParameterMulti

public java.util.Vector getParameterMulti(java.lang.String name)

Returns the whole vector of values for this parameter

getParameters

public java.util.Hashtable getParameters()

Returns hash with only one string for each key.

getParametersMulti

public java.util.Hashtable getParametersMulti()

Returns hash of Parameter vectors.