apollo.config
Class TierProperty

java.lang.Object
  apollo.config.TierProperty

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

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

TierProperty holds a list of FeatureProperties. This corresponds to a "Tier" in the tiers file. Tiers are what is displayed in the Types panel (should probably be called TiersPanel, you have to right click on a tier you see all of its types/feature properties) A Tier holds a bunch of "Types" (visual types), a Type is captured by a FeatureProperty. Each FeatureProperty can have a different color, etc... A "Tier" is the unit for collapsing and hiding, all FeatureProperties in a Tier expand and collapse together, hide and show together. TierProperty is an Observable so it does a setChanged() and notifyObservers() when its changed. Observers add themselves with addObserver. PropertyScheme observes TierProperties. Thats now changed. Observer stuff replaced with PropSchemeChangeEvent.

See Also:

Serialized Form

Field Summary

protected CaseInsensitiveStringHash	analysis_types
protected java.util.Vector	comments
protected boolean	curated
protected boolean	expanded
protected boolean	isFirstTier
protected java.lang.String	label
protected boolean	labeled
protected int	maxRow
static boolean	NOT_VISIBLE
protected boolean	sorted
protected boolean	visible
static boolean	VISIBLE
protected boolean	warnOnEdit warnOnEdit can be set at the Tier level (here) or at the individual FeatureProperty level

Constructor Summary

TierProperty()

TierProperty(java.lang.String label)

TierProperty(java.lang.String label, boolean visible)

TierProperty(java.lang.String label, boolean visible, boolean expanded)

TierProperty(java.lang.String label, boolean visible, boolean expanded, boolean sorted)

TierProperty(java.lang.String label, boolean visible, boolean expanded, boolean sorted, int maxRow)

TierProperty(java.lang.String label, boolean visible, boolean expanded, boolean sorted, int maxRow, boolean labeled)

TierProperty(TierProperty from)

Method Summary

void	addAnalysisType(FeatureProperty fp, java.lang.String analysis)
protected void	addComment(java.lang.String comment)
void	addFeatureProperty(FeatureProperty fp)
java.lang.Object	clone()
FeatureProperty	featureForAnalysisType(java.lang.String analysis_type)
java.awt.Color	getColour()
protected java.util.Vector	getComments()
java.util.Vector	getFeatureProperties()
FeatureProperty	getFeatureProperty(java.lang.String type)
java.lang.String	getLabel()
int	getMaxRow()
java.lang.String	getTypesAsString()
boolean	holdsType(java.lang.String type)
boolean	isCurated()
boolean	isExpanded()
boolean	isFirstTier()
boolean	isLabeled()
boolean	isLabeled(boolean checkExpanded)
boolean	isProtein() Default is false
boolean	isSorted()
boolean	isVisible()
boolean	labelEquals(java.lang.String name)
protected java.lang.String	quoteIfSpace(java.lang.String str)
void	setCurated(boolean curated) Whether this tier represents curated annotations (to be shown in the annotation view rather than result view).
void	setExpanded(boolean expanded)
void	setExpanded(boolean expanded, boolean isTemporary)
protected void	setIsFirstTier(boolean firstTier)
void	setLabel(java.lang.String label)
void	setLabeled(boolean labeled)
void	setLabeled(boolean labeled, boolean isTemporary)
void	setMaxRow(int maxRow)
void	setSorted(boolean sorted)
void	setVisible(boolean visible)
void	setVisible(boolean visible, boolean isTemporary)
void	setWarnOnEdit(boolean warn) Whether the user should be warned if they try to edit features of a given type.
java.lang.String	toString()
boolean	warnOnEdit()

Methods inherited from class java.lang.Object

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

Field Detail

label

protected java.lang.String label

expanded

protected boolean expanded

visible

protected boolean visible

sorted

protected boolean sorted

labeled

protected boolean labeled

maxRow

protected int maxRow

curated

protected boolean curated

warnOnEdit

protected boolean warnOnEdit

warnOnEdit can be set at the Tier level (here) or at the individual FeatureProperty level

comments

protected java.util.Vector comments

analysis_types

protected CaseInsensitiveStringHash analysis_types

VISIBLE

public static boolean VISIBLE

NOT_VISIBLE

public static boolean NOT_VISIBLE

isFirstTier

protected boolean isFirstTier

Constructor Detail

TierProperty

public TierProperty()

TierProperty

public TierProperty(java.lang.String label,
                    boolean visible,
                    boolean expanded,
                    boolean sorted,
                    int maxRow,
                    boolean labeled)

TierProperty

public TierProperty(java.lang.String label,
                    boolean visible,
                    boolean expanded,
                    boolean sorted,
                    int maxRow)

TierProperty

public TierProperty(java.lang.String label,
                    boolean visible,
                    boolean expanded,
                    boolean sorted)

TierProperty

public TierProperty(java.lang.String label,
                    boolean visible,
                    boolean expanded)

TierProperty

public TierProperty(java.lang.String label,
                    boolean visible)

TierProperty

public TierProperty(java.lang.String label)

TierProperty

public TierProperty(TierProperty from)

Method Detail

setLabel

public void setLabel(java.lang.String label)

getLabel

public java.lang.String getLabel()

setVisible

public void setVisible(boolean visible,
                       boolean isTemporary)

setVisible

public void setVisible(boolean visible)

isVisible

public boolean isVisible()

setExpanded

public void setExpanded(boolean expanded,
                        boolean isTemporary)

setExpanded

public void setExpanded(boolean expanded)

isExpanded

public boolean isExpanded()

setSorted

public void setSorted(boolean sorted)

isSorted

public boolean isSorted()

setMaxRow

public void setMaxRow(int maxRow)

getMaxRow

public int getMaxRow()

setLabeled

public void setLabeled(boolean labeled,
                       boolean isTemporary)

setLabeled

public void setLabeled(boolean labeled)

isLabeled

public boolean isLabeled()

isLabeled

public boolean isLabeled(boolean checkExpanded)

setCurated

public void setCurated(boolean curated)

Whether this tier represents curated annotations (to be shown in the annotation view rather than result view). Default is false.

isCurated

public boolean isCurated()

setWarnOnEdit

public void setWarnOnEdit(boolean warn)

Whether the user should be warned if they try to edit features of a given type. Default is false. Applies to all types belonging to this tier; can be overridden by individual types.

warnOnEdit

public boolean warnOnEdit()

quoteIfSpace

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

clone

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

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

getFeatureProperty

public FeatureProperty getFeatureProperty(java.lang.String type)

getFeatureProperties

public java.util.Vector getFeatureProperties()

addFeatureProperty

public void addFeatureProperty(FeatureProperty fp)

addAnalysisType

public void addAnalysisType(FeatureProperty fp,
                            java.lang.String analysis)

featureForAnalysisType

public FeatureProperty featureForAnalysisType(java.lang.String analysis_type)

getTypesAsString

public java.lang.String getTypesAsString()

labelEquals

public boolean labelEquals(java.lang.String name)

holdsType

public boolean holdsType(java.lang.String type)

getColour

public java.awt.Color getColour()

isProtein

public boolean isProtein()

Default is false

addComment

protected void addComment(java.lang.String comment)

getComments

protected java.util.Vector getComments()

setIsFirstTier

protected void setIsFirstTier(boolean firstTier)

isFirstTier

public boolean isFirstTier()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object