apollo.config
Class FeatureProperty

java.lang.Object
  apollo.config.FeatureProperty

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public class FeatureProperty
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable

FeatureProperty comes from "Types" in the tiers file. All the configurations of Types in the tiers file are reflected here (color, score threshold, glyph...). FeatureProperties are grouped into TierProperties, which are for expanding and hiding and such In the types panel Types/FeatureProperties of the displayed tiers can be seen by right clicking on the tier. When something changes tell TierProperty to fire PropSchemeChangeEvent (TP then tells PropScheme to fire PSCE). This replaces Observable which ended up firing a PSCE after doing a bunch of notifyObservers.

See Also:

Serialized Form

Field Summary

protected java.util.Vector	analysis_types
static java.awt.Color	blueGreen
static java.awt.Color	brown
protected java.awt.Color	colour
static java.util.Hashtable	colourHash
protected java.util.Vector	columns
protected java.util.Vector	comments
static java.awt.Color	DEFAULT_COLOR
static java.util.Vector	default_columns
static java.lang.String	DEFAULT_STYLE
protected java.lang.Integer	groupFlag
protected boolean	groupFlagSet
static java.util.Hashtable	groupTypes
static java.lang.Integer	GRP_GENE
static java.lang.Integer	GRP_HOMOLOGY
static java.lang.Integer	GRP_SINGLE
protected static org.apache.log4j.Logger	logger
protected float	maxScore
static java.awt.Color	midBlue
static java.awt.Color	midRed
protected float	minScore
protected int	minWidth
protected java.util.Date	recentDate
protected boolean	reverseSort
protected java.lang.String	sortProperty
protected java.lang.String	style
protected float	thresholdScore
protected TierProperty	tier
protected java.lang.String	tiername
protected java.lang.String	type
protected java.lang.String	URLString
protected boolean	usescore

Constructor Summary

FeatureProperty()

FeatureProperty(FeatureProperty from)

FeatureProperty(FeatureProperty from, boolean cloneTier)

FeatureProperty(TierProperty tier, java.lang.String type, java.util.Vector anal_types)

FeatureProperty(TierProperty tier, java.lang.String type, java.util.Vector anal_types, java.awt.Color colour)

FeatureProperty(TierProperty tier, java.lang.String type, java.util.Vector anal_types, java.awt.Color colour, java.lang.String style)

FeatureProperty(TierProperty tier, java.lang.String type, java.util.Vector anal_types, java.awt.Color colour, java.lang.String style, boolean usescore, float min, float max)

Method Summary

void	addAnalysisType(java.lang.String analysis)
void	addColumn(ColumnProperty column)
protected void	addComment(java.lang.String comment)
java.lang.Object	clone() this needs to be a deep clone not a shallow one
protected java.lang.Object	createClassFromName(java.lang.String str)
ApolloNameAdapterI	createNameAdapter()
java.lang.String	createNameFromClass(java.lang.Object cl) Given a class, e.g.
java.lang.String	getAnalysisType(int i)
java.util.Vector	getAnalysisTypes() An analysis type is what comes from "datatype" in the tiers file.
int	getAnalysisTypesSize()
java.lang.String	getAnnotType() Type of annotation this result creates, by default
java.lang.String	getChromosomeFormat() Get chromosome Prefix
java.awt.Color	getColour()
java.lang.String	getColourAsString()
java.lang.String	getColourAsString(java.awt.Color colour)
java.util.Vector	getColumns()
java.util.Vector	getColumns(boolean use_default)
protected java.util.Vector	getComments()
static java.lang.String	getDefaultAnnotType() Making default annotType "gene".
java.lang.String	getDisplayType()
java.awt.Color	getFinishedColor()
java.lang.Integer	getGroupFlag()
java.lang.String	getGroupFlagAsString()
java.lang.String	getIdFormat() Regular expression that describes format for ID, null if not set
java.lang.String	getIdPrefix() Get the id prefix
java.lang.String	getKeyFromValue(java.util.Hashtable table, java.lang.Object value)
java.lang.String	getLinkSpecies1()
java.lang.String	getLinkSpecies2()
LinkType	getLinkType() Return LinkType - default LinkType.NO_LINK (not linked) LinkType describes how FeatureProperty links to other species
float	getMaxScore()
float	getMinScore()
int	getMinWidth()
java.lang.String	getNameAdapterString()
int	getNumberOfLevels()
OverlapI	getOverlapper()
java.awt.Color	getProblematicColor()
java.util.Date	getRecentDate()
boolean	getReverseSort()
boolean	getSizeByScore()
java.lang.String	getSortProperty()
java.lang.String	getStyle()
float	getThreshold()
TierProperty	getTier()
protected java.lang.String	getTierName()
java.lang.String	getURLString()
java.awt.Color	getUtrColor() For DrawableGeneSeqFeature that colors utrs
boolean	hasNonDefaultNameAdapter() Has nameadapter if this is an annotation tier
boolean	hasOverlapper() Has overlapper if this is an annotation tier
void	inheritWarnOnEdit(boolean warn) Initially, the value of warnonedit is inherited from the parent tier--may later be overridden.
boolean	isAnnotationType()
boolean	isOneLevel()
boolean	isSyntenyLinked() Return true if feat prop is a synteny link to another species
static java.awt.Color	parseColour(java.lang.String colourStr)
protected java.lang.String	quoteIfSpace(java.lang.String str)
protected void	setAnalysisTypes(java.util.Vector anal_types)
void	setAnnotType(java.lang.String annot_type) Type of annotation this result creates, by default
void	setChromosomeFormat(java.lang.String chromosomeFormat) Set chromosome Format This is a regular expression to get the chromosome number.
void	setColour(java.awt.Color colour)
void	setColour(java.awt.Color colour, boolean temporary)
void	setColumns(java.util.Vector columns)
void	setDisplayType(java.lang.String type)
void	setDisplayType(java.lang.String type, boolean temporary)
void	setGroupFlag(java.lang.String grpStr)
void	setIdFormat(java.lang.String idFormat) Set regular expression String that describes id format for type
void	setIdPrefix(java.lang.String idPrefix) id prefix is not a regular expression Set String which describe id prefix for the type used by ChadoJdbcNameAdapter
void	setMaxScore(float max)
void	setMaxScore(float max, boolean isTemporary)
void	setMinScore(float min)
void	setMinScore(float min, boolean isTemporary)
void	setMinWidth(int min)
void	setOverlapper(java.lang.String str) Return null if no tiername or tiername is not "annotation"
void	setOverlapperIfNotSet(java.lang.String str)
void	setRecentDate(java.lang.String dateString)
void	setReverseSort(boolean reverse)
void	setSizeByScore(boolean usescore)
void	setSizeByScore(boolean usescore, boolean isTemporary)
void	setSortProperty(java.lang.String sort_by)
void	setStyle(java.lang.String style)
void	setStyle(java.lang.String style, boolean isTemporary)
void	setThreshold(float thresh)
protected void	setTier(TierProperty tier)
protected void	setTierName(java.lang.String tier)
void	setURLString(java.lang.String str)
void	setUtrColor(java.awt.Color color)
void	setWarnOnEdit(boolean warn)
static java.awt.Color	toColour(java.lang.String colourStr)
static java.awt.Color	toColour(java.lang.String colourStr, java.awt.Color defaultColour)
java.lang.String	toString()
boolean	typeEquals(java.lang.String typeName)
boolean	warnOnEdit()
void	write(java.io.PrintWriter out)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

DEFAULT_COLOR

public static java.awt.Color DEFAULT_COLOR

DEFAULT_STYLE

public static java.lang.String DEFAULT_STYLE

midBlue

public static java.awt.Color midBlue

midRed

public static java.awt.Color midRed

blueGreen

public static java.awt.Color blueGreen

brown

public static java.awt.Color brown

GRP_GENE

public static final java.lang.Integer GRP_GENE

GRP_HOMOLOGY

public static final java.lang.Integer GRP_HOMOLOGY

GRP_SINGLE

public static final java.lang.Integer GRP_SINGLE

groupTypes

public static java.util.Hashtable groupTypes

columns

protected java.util.Vector columns

default_columns

public static java.util.Vector default_columns

sortProperty

protected java.lang.String sortProperty

reverseSort

protected boolean reverseSort

colourHash

public static java.util.Hashtable colourHash

type

protected java.lang.String type

tiername

protected java.lang.String tiername

tier

protected TierProperty tier

analysis_types

protected java.util.Vector analysis_types

style

protected java.lang.String style

colour

protected java.awt.Color colour

usescore

protected boolean usescore

minScore

protected float minScore

maxScore

protected float maxScore

minWidth

protected int minWidth

thresholdScore

protected float thresholdScore

URLString

protected java.lang.String URLString

groupFlag

protected java.lang.Integer groupFlag

recentDate

protected java.util.Date recentDate

comments

protected java.util.Vector comments

groupFlagSet

protected boolean groupFlagSet

Constructor Detail

FeatureProperty

public FeatureProperty(TierProperty tier,
                       java.lang.String type,
                       java.util.Vector anal_types,
                       java.awt.Color colour,
                       java.lang.String style,
                       boolean usescore,
                       float min,
                       float max)

FeatureProperty

public FeatureProperty(TierProperty tier,
                       java.lang.String type,
                       java.util.Vector anal_types)

FeatureProperty

public FeatureProperty(FeatureProperty from)

FeatureProperty

public FeatureProperty(FeatureProperty from,
                       boolean cloneTier)
                throws java.lang.CloneNotSupportedException

Throws:

java.lang.CloneNotSupportedException

FeatureProperty

public FeatureProperty(TierProperty tier,
                       java.lang.String type,
                       java.util.Vector anal_types,
                       java.awt.Color colour,
                       java.lang.String style)

FeatureProperty

public FeatureProperty(TierProperty tier,
                       java.lang.String type,
                       java.util.Vector anal_types,
                       java.awt.Color colour)

FeatureProperty

public FeatureProperty()

Method Detail

setTierName

protected void setTierName(java.lang.String tier)

getTierName

protected java.lang.String getTierName()

setTier

protected void setTier(TierProperty tier)

getTier

public TierProperty getTier()

isAnnotationType

public boolean isAnnotationType()

getSizeByScore

public boolean getSizeByScore()

setSizeByScore

public void setSizeByScore(boolean usescore,
                           boolean isTemporary)

setSizeByScore

public void setSizeByScore(boolean usescore)

getThreshold

public float getThreshold()

setThreshold

public void setThreshold(float thresh)

setDisplayType

public void setDisplayType(java.lang.String type)

setDisplayType

public void setDisplayType(java.lang.String type,
                           boolean temporary)

getDisplayType

public java.lang.String getDisplayType()

getRecentDate

public java.util.Date getRecentDate()

setRecentDate

public void setRecentDate(java.lang.String dateString)

inheritWarnOnEdit

public void inheritWarnOnEdit(boolean warn)

Initially, the value of warnonedit is inherited from the parent tier--may later be overridden.

warnOnEdit

public boolean warnOnEdit()

setWarnOnEdit

public void setWarnOnEdit(boolean warn)

setIdFormat

public void setIdFormat(java.lang.String idFormat)

Set regular expression String that describes id format for type

getIdFormat

public java.lang.String getIdFormat()

Regular expression that describes format for ID, null if not set

setIdPrefix

public void setIdPrefix(java.lang.String idPrefix)

id prefix is not a regular expression Set String which describe id prefix for the type used by ChadoJdbcNameAdapter

getIdPrefix

public java.lang.String getIdPrefix()

Get the id prefix

setChromosomeFormat

public void setChromosomeFormat(java.lang.String chromosomeFormat)

Set chromosome Format This is a regular expression to get the chromosome number. used by ChadoJdbcNameAdapter

getChromosomeFormat

public java.lang.String getChromosomeFormat()

Get chromosome Prefix

setAnnotType

public void setAnnotType(java.lang.String annot_type)

Type of annotation this result creates, by default

getAnnotType

public java.lang.String getAnnotType()

Type of annotation this result creates, by default

getDefaultAnnotType

public static java.lang.String getDefaultAnnotType()

Making default annotType "gene". It actually already sort of is in that feats with null annotTypes end up as genes (due to a default in AnnotatedFeature). And null makes no sense as an annotType unless tiers io requires an annot type or annot editor disallows making an annot with no annot type, neither of which are the case MG 9.19.05 - this could be configurable?

setAnalysisTypes

protected void setAnalysisTypes(java.util.Vector anal_types)

addAnalysisType

public void addAnalysisType(java.lang.String analysis)

getAnalysisTypes

public java.util.Vector getAnalysisTypes()

An analysis type is what comes from "datatype" in the tiers file. There can be more than one data/analysis type per FeatProp. These map to SeqFeatures feature types. perhaps this should be renamed getFeatureTypes?

getAnalysisTypesSize

public int getAnalysisTypesSize()

getAnalysisType

public java.lang.String getAnalysisType(int i)

setStyle

public void setStyle(java.lang.String style,
                     boolean isTemporary)

setStyle

public void setStyle(java.lang.String style)

getStyle

public java.lang.String getStyle()

setColour

public void setColour(java.awt.Color colour,
                      boolean temporary)

setColour

public void setColour(java.awt.Color colour)

setUtrColor

public void setUtrColor(java.awt.Color color)

toColour

public static java.awt.Color toColour(java.lang.String colourStr)

toColour

public static java.awt.Color toColour(java.lang.String colourStr,
                                      java.awt.Color defaultColour)

parseColour

public static java.awt.Color parseColour(java.lang.String colourStr)
                                  throws java.lang.NumberFormatException

Throws:

java.lang.NumberFormatException

getGroupFlagAsString

public java.lang.String getGroupFlagAsString()

getColourAsString

public java.lang.String getColourAsString()

getColourAsString

public java.lang.String getColourAsString(java.awt.Color colour)

getKeyFromValue

public java.lang.String getKeyFromValue(java.util.Hashtable table,
                                        java.lang.Object value)

getColour

public java.awt.Color getColour()

getUtrColor

public java.awt.Color getUtrColor()

For DrawableGeneSeqFeature that colors utrs

getProblematicColor

public java.awt.Color getProblematicColor()

getFinishedColor

public java.awt.Color getFinishedColor()

getColumns

public java.util.Vector getColumns()

getColumns

public java.util.Vector getColumns(boolean use_default)

setColumns

public void setColumns(java.util.Vector columns)

addColumn

public void addColumn(ColumnProperty column)

getSortProperty

public java.lang.String getSortProperty()

setSortProperty

public void setSortProperty(java.lang.String sort_by)

getReverseSort

public boolean getReverseSort()

setReverseSort

public void setReverseSort(boolean reverse)

setMaxScore

public void setMaxScore(float max,
                        boolean isTemporary)

setMaxScore

public void setMaxScore(float max)

setMinScore

public void setMinScore(float min,
                        boolean isTemporary)

setMinScore

public void setMinScore(float min)

setMinWidth

public void setMinWidth(int min)

setURLString

public void setURLString(java.lang.String str)

setGroupFlag

public void setGroupFlag(java.lang.String grpStr)

getGroupFlag

public java.lang.Integer getGroupFlag()

getURLString

public java.lang.String getURLString()

getMaxScore

public float getMaxScore()

getMinScore

public float getMinScore()

getMinWidth

public int getMinWidth()

write

public void write(java.io.PrintWriter out)
           throws java.io.IOException

Throws:

java.io.IOException

quoteIfSpace

protected java.lang.String quoteIfSpace(java.lang.String str)

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

this needs to be a deep clone not a shallow one

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

typeEquals

public boolean typeEquals(java.lang.String typeName)

addComment

protected void addComment(java.lang.String comment)

getComments

protected java.util.Vector getComments()

getNameAdapterString

public java.lang.String getNameAdapterString()

createNameAdapter

public ApolloNameAdapterI createNameAdapter()

hasNonDefaultNameAdapter

public boolean hasNonDefaultNameAdapter()

Has nameadapter if this is an annotation tier

setOverlapper

public void setOverlapper(java.lang.String str)

Return null if no tiername or tiername is not "annotation"

setOverlapperIfNotSet

public void setOverlapperIfNotSet(java.lang.String str)

hasOverlapper

public boolean hasOverlapper()

Has overlapper if this is an annotation tier

getOverlapper

public OverlapI getOverlapper()

createClassFromName

protected java.lang.Object createClassFromName(java.lang.String str)

createNameFromClass

public java.lang.String createNameFromClass(java.lang.Object cl)

Given a class, e.g. apollo.config.FlyNameAdapter@1b5a5cf, return the simple string that names that class (FlyNameAdapter)

isSyntenyLinked

public boolean isSyntenyLinked()

Return true if feat prop is a synteny link to another species

getLinkType

public LinkType getLinkType()

Return LinkType - default LinkType.NO_LINK (not linked) LinkType describes how FeatureProperty links to other species

getLinkSpecies1

public java.lang.String getLinkSpecies1()

getLinkSpecies2

public java.lang.String getLinkSpecies2()

getNumberOfLevels

public int getNumberOfLevels()

isOneLevel

public boolean isOneLevel()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object