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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.Array.ArrayGroup
public class ArrayGroup
An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. several arrays that can be hybridized on a single microscope slide) or a virtual grouping together of arrays. The array package that has been manufactured has information about where certain artifacts about the array are located for scanning and feature extraction purposes.
Nested Class Summary | |
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class |
ArrayGroup.OrientationMarkPosition
Inner class for the enumeration values that the attribute orientationMarkPosition can assume. |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasArrays |
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HasArrays.Arrays_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFiducials |
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HasFiducials.Fiducials_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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protected java.util.List |
arrays
Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide. |
protected DistanceUnit |
distanceUnit
The unit of the measurement attributes. |
protected java.util.List |
fiducials
Association to the marks on the Array for alignment for the scanner. |
protected OntologyEntry |
substrateType
Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case. |
Fields inherited from class org.biomage.Common.Describable |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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ArrayGroup()
Default constructor. |
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ArrayGroup(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToArrays(Array array)
Method to add Array to Arrays_list |
void |
addToArrays(int position,
Array array)
Method to add Array at position to Arrays_list |
void |
addToFiducials(Fiducial fiducial)
Method to add Fiducial to Fiducials_list |
void |
addToFiducials(int position,
Fiducial fiducial)
Method to add Fiducial at position to Fiducials_list |
boolean |
emptyMAGEobject()
|
HasArrays.Arrays_list |
getArrays()
Get method for arrays |
java.lang.Float |
getArraySpacingX()
Get method for arraySpacingX |
java.lang.Float |
getArraySpacingY()
Get method for arraySpacingY |
java.lang.String |
getBarcode()
Get method for barcode |
DistanceUnit |
getDistanceUnit()
Get method for distanceUnit |
HasFiducials.Fiducials_list |
getFiducials()
Get method for fiducials |
Array |
getFromArrays(int position)
Method to get Array from Arrays_list |
Fiducial |
getFromFiducials(int position)
Method to get Fiducial from Fiducials_list |
java.lang.Float |
getLength()
Get method for length |
java.lang.String |
getModelClassName()
|
java.lang.String |
getNameByValueOrientationMarkPosition(int val)
For OrientationMarkPosition get the Name of the Enumeration type by passing a Value to it. |
java.lang.String |
getNameOrientationMarkPosition()
Return the current name of the Enumeration type of OrientationMarkPosition. |
java.lang.Integer |
getNumArrays()
Get method for numArrays |
java.lang.String |
getOrientationMark()
Get method for orientationMark |
ArrayGroup.OrientationMarkPosition |
getOrientationMarkPosition()
Get method for orientationMarkPosition |
OntologyEntry |
getSubstrateType()
Get method for substrateType |
int |
getValueByNameOrientationMarkPosition(java.lang.String name)
For OrientationMarkPosition get the Value of the Enumeration type by passing a Name to it. |
int |
getValueOrientationMarkPosition()
Return the currrent value of the Enumeration type of OrientationMarkPosition. |
java.lang.Float |
getWidth()
Get method for width |
void |
removeElementAtFromArrays(int position)
Method to remove by position from Arrays_list |
void |
removeElementAtFromFiducials(int position)
Method to remove by position from Fiducials_list |
void |
removeFromArrays(Array array)
Method to remove first Array from Arrays_list |
void |
removeFromFiducials(Fiducial fiducial)
Method to remove first Fiducial from Fiducials_list |
void |
setArrays(HasArrays.Arrays_list arrays)
Set method for arrays |
void |
setArraySpacingX(java.lang.Float arraySpacingX)
Set method for arraySpacingX |
void |
setArraySpacingY(java.lang.Float arraySpacingY)
Set method for arraySpacingY |
void |
setAttributes(org.xml.sax.Attributes atts)
|
void |
setBarcode(java.lang.String barcode)
Set method for barcode |
void |
setDistanceUnit(DistanceUnit distanceUnit)
Set method for distanceUnit |
void |
setFiducials(HasFiducials.Fiducials_list fiducials)
Set method for fiducials |
void |
setLength(java.lang.Float length)
Set method for length |
java.lang.String |
setNameByValueOrientationMarkPosition(int val)
For OrientationMarkPosition set the Name of the Enumeration type by passing a value (int) |
void |
setNameOrientationMarkPosition(java.lang.String name)
Return the current name of the Enumeration type of OrientationMarkPosition. |
void |
setNumArrays(java.lang.Integer numArrays)
Set method for numArrays |
void |
setOrientationMark(java.lang.String orientationMark)
Set method for orientationMark |
void |
setOrientationMarkPosition(ArrayGroup.OrientationMarkPosition orientationMarkPosition)
Set method for orientationMarkPosition |
void |
setSubstrateType(OntologyEntry substrateType)
Set method for substrateType |
int |
setValueByNameOrientationMarkPosition(java.lang.String name)
For OrientationMarkPosition set the Value of the Enumeration type by passing a Name to it. |
void |
setWidth(java.lang.Float width)
Set method for width |
void |
writeAssociations(java.io.Writer out)
writeAssociations This method is responsible for assembling the association data into XML. |
void |
writeAttributes(java.io.Writer out)
writeAttributes This method is responsible for assembling the attribute data into XML. |
void |
writeMAGEML(java.io.Writer out)
writeMAGEML This method is responsible for assembling the attribute and association data into XML. |
Methods inherited from class org.biomage.Common.Identifiable |
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getIdentifier, getName, setIdentifier, setName, toString |
Methods inherited from class org.biomage.Common.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected java.util.List fiducials
protected java.util.List arrays
protected OntologyEntry substrateType
protected DistanceUnit distanceUnit
Constructor Detail |
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public ArrayGroup()
public ArrayGroup(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class Identifiable
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Identifiable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Identifiable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Identifiable
java.io.IOException
public void setBarcode(java.lang.String barcode)
value
- to setpublic java.lang.String getBarcode()
public void setArraySpacingX(java.lang.Float arraySpacingX)
value
- to setpublic java.lang.Float getArraySpacingX()
public void setArraySpacingY(java.lang.Float arraySpacingY)
value
- to setpublic java.lang.Float getArraySpacingY()
public void setNumArrays(java.lang.Integer numArrays)
value
- to setpublic java.lang.Integer getNumArrays()
public void setOrientationMark(java.lang.String orientationMark)
value
- to setpublic java.lang.String getOrientationMark()
public void setOrientationMarkPosition(ArrayGroup.OrientationMarkPosition orientationMarkPosition)
value
- to setpublic ArrayGroup.OrientationMarkPosition getOrientationMarkPosition()
public java.lang.String setNameByValueOrientationMarkPosition(int val)
int
- value The value to be mapped to the namepublic int setValueByNameOrientationMarkPosition(java.lang.String name)
String
- name The name to be mapped to a valuepublic java.lang.String getNameByValueOrientationMarkPosition(int val)
int
- val The value for which the Mapped String will be returned.public int getValueByNameOrientationMarkPosition(java.lang.String name)
String
- name The name to be mapped to a value.public java.lang.String getNameOrientationMarkPosition()
public void setNameOrientationMarkPosition(java.lang.String name)
public int getValueOrientationMarkPosition()
public void setWidth(java.lang.Float width)
value
- to setpublic java.lang.Float getWidth()
public void setLength(java.lang.Float length)
value
- to setpublic java.lang.Float getLength()
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setFiducials(HasFiducials.Fiducials_list fiducials)
setFiducials
in interface HasFiducials
value
- to setpublic HasFiducials.Fiducials_list getFiducials()
getFiducials
in interface HasFiducials
public void addToFiducials(Fiducial fiducial)
addToFiducials
in interface HasFiducials
public void addToFiducials(int position, Fiducial fiducial)
addToFiducials
in interface HasFiducials
public Fiducial getFromFiducials(int position)
getFromFiducials
in interface HasFiducials
public void removeElementAtFromFiducials(int position)
removeElementAtFromFiducials
in interface HasFiducials
public void removeFromFiducials(Fiducial fiducial)
removeFromFiducials
in interface HasFiducials
public void setArrays(HasArrays.Arrays_list arrays)
setArrays
in interface HasArrays
value
- to setpublic HasArrays.Arrays_list getArrays()
getArrays
in interface HasArrays
public void addToArrays(Array array)
addToArrays
in interface HasArrays
public void addToArrays(int position, Array array)
addToArrays
in interface HasArrays
public Array getFromArrays(int position)
getFromArrays
in interface HasArrays
public void removeElementAtFromArrays(int position)
removeElementAtFromArrays
in interface HasArrays
public void removeFromArrays(Array array)
removeFromArrays
in interface HasArrays
public void setSubstrateType(OntologyEntry substrateType)
setSubstrateType
in interface HasSubstrateType
value
- to setpublic OntologyEntry getSubstrateType()
getSubstrateType
in interface HasSubstrateType
public void setDistanceUnit(DistanceUnit distanceUnit)
setDistanceUnit
in interface HasDistanceUnit
value
- to setpublic DistanceUnit getDistanceUnit()
getDistanceUnit
in interface HasDistanceUnit
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