apollo.config
Class PropertyScheme

java.lang.Object
  apollo.config.PropertyScheme

All Implemented Interfaces:

java.io.Serializable

public class PropertyScheme
extends java.lang.Object
implements java.io.Serializable

PropertyScheme is basically the java version of the tiers file. Changed from static/singleton to instance as we now have different instances of tiers for different data adapters Holds a list of TierProperties, TierProperties hold FeatureProperties Fires PropSchemeChangeEvent (to controller) when anything changes.

See Also:

Serialized Form

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

PropertyScheme()
Parses tiers file returned by Config.getTiersFile(), which returns the current Style's tiers file.

PropertyScheme(java.lang.String tiersFile)
Parses and creates prop scheme from tiers file passed in

Method Summary

void	addPropSchemeChangeListener(PropSchemeChangeListener pcl)
void	addTierType(TierProperty tierProp)
FeatureProperty	createDefaultFeatureProperty()
void	expandAllTiers(boolean state)
void	firePropSchemeChangeEvent()
java.util.Vector	getAllTiers()
java.util.Enumeration	getAnalNames()
java.util.Vector	getAnnotationFeatureProps() Moved from Style
java.util.Vector	getCopyOfTiers(java.util.Vector source)
FeatureProperty	getFeatureProperty(java.lang.String analysis_type) Returns the FeatureProperty associated with analysis_type.
FeatureProperty	getFeatureProperty(java.lang.String analysis_type, boolean createProperty) Returns the FeatureProperty associated with analysis_type.
FeatureProperty	getLinkedFeatProp(int i)
int	getLinkedFeatPropsSize()
TierProperty	getLinkedTierProp(int i)
java.util.List	getLinkedTierProps()
java.util.List	getSyntenyLinkedFeatProps() Retrieves all feature props that are synteny links At some point we may want to include species as a parameter and only retrieve links between specified species.
int	getTierInd(java.lang.String label)
TierProperty	getTierProperty(java.lang.String type)
TierProperty	getTierProperty(java.lang.String type, boolean dig) Returns the TierProperty associated with either label or analysis_type.
java.util.Enumeration	getTypes()
boolean	isAnnotationTier(java.lang.String tier) Returns true if this tiername contains annotations rather than results.
boolean	isTypeSyntenyLink(java.lang.String type) by type we mean apollo feature type not result/analysis type
static void	main(java.lang.String[] Args)
void	moveTier(java.lang.String fromTier, java.lang.String toTier)
void	setAllTiersVisible(boolean state)
void	setDefaultFeatureProperty(FeatureProperty fp)
int	size()
void	write(java.io.File file)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

PropertyScheme

public PropertyScheme()
               throws java.io.IOException,
                      java.io.FileNotFoundException

Parses tiers file returned by Config.getTiersFile(), which returns the current Style's tiers file.

Throws:

java.io.IOException

java.io.FileNotFoundException

PropertyScheme

public PropertyScheme(java.lang.String tiersFile)
               throws java.io.IOException,
                      java.io.FileNotFoundException

Parses and creates prop scheme from tiers file passed in

Throws:

java.io.IOException

java.io.FileNotFoundException

Method Detail

addPropSchemeChangeListener

public void addPropSchemeChangeListener(PropSchemeChangeListener pcl)

firePropSchemeChangeEvent

public void firePropSchemeChangeEvent()

size

public int size()

addTierType

public void addTierType(TierProperty tierProp)

expandAllTiers

public void expandAllTiers(boolean state)

setAllTiersVisible

public void setAllTiersVisible(boolean state)

moveTier

public void moveTier(java.lang.String fromTier,
                     java.lang.String toTier)

getTypes

public java.util.Enumeration getTypes()

getAnalNames

public java.util.Enumeration getAnalNames()

getFeatureProperty

public FeatureProperty getFeatureProperty(java.lang.String analysis_type,
                                          boolean createProperty)

Returns the FeatureProperty associated with analysis_type.

The FeatureProperty will be the registered property if type is known. Otherwise, if createProperty is true, it will create a new FeatureProperty object with the default values, otherwise it will return null.

Parameters:

type - the String type of a feature

createProperty - - whether to create a new property if not found

Returns:

the FeatureProperty object for that type, or null

Throws:

java.lang.NullPointerException - if type is null

getFeatureProperty

public FeatureProperty getFeatureProperty(java.lang.String analysis_type)

Returns the FeatureProperty associated with analysis_type.

The FeatureProperty will be the registered property if type is known, and null otherwise.

Parameters:

type - the String type of a feature

Returns:

the FeatureProperty object for that type, or null

Throws:

java.lang.NullPointerException - if type is null

getTierProperty

public TierProperty getTierProperty(java.lang.String type,
                                    boolean dig)

Returns the TierProperty associated with either label or analysis_type.

The FeatureProperty will be the registered property if type is known, and null otherwise.

Parameters:

type - the String type of a feature

Returns:

the FeatureProperty object for that type, or null

Throws:

java.lang.NullPointerException - if type is null

getTierProperty

public TierProperty getTierProperty(java.lang.String type)

getTierInd

public int getTierInd(java.lang.String label)

getAllTiers

public java.util.Vector getAllTiers()

getCopyOfTiers

public java.util.Vector getCopyOfTiers(java.util.Vector source)

setDefaultFeatureProperty

public void setDefaultFeatureProperty(FeatureProperty fp)

createDefaultFeatureProperty

public FeatureProperty createDefaultFeatureProperty()

getSyntenyLinkedFeatProps

public java.util.List getSyntenyLinkedFeatProps()

Retrieves all feature props that are synteny links At some point we may want to include species as a parameter and only retrieve links between specified species.

getLinkedFeatPropsSize

public int getLinkedFeatPropsSize()

getLinkedFeatProp

public FeatureProperty getLinkedFeatProp(int i)

isTypeSyntenyLink

public boolean isTypeSyntenyLink(java.lang.String type)

by type we mean apollo feature type not result/analysis type

getLinkedTierProps

public java.util.List getLinkedTierProps()

getLinkedTierProp

public TierProperty getLinkedTierProp(int i)

write

public void write(java.io.File file)
           throws java.io.IOException

Throws:

java.io.IOException

getAnnotationFeatureProps

public java.util.Vector getAnnotationFeatureProps()

Moved from Style

isAnnotationTier

public boolean isAnnotationTier(java.lang.String tier)

Returns true if this tiername contains annotations rather than results. We check this by looking in the vector of annotationFeatureProps, which was filled in by a previous call to getAnnotationFeatureProps. Note: this doesn't seem to actually get called! yes it does by FeatProp

main

public static void main(java.lang.String[] Args)
                 throws java.lang.Exception

Throws:

java.lang.Exception