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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.Array.Array
public class Array
The physical substrate along with its features and their annotation
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasArrayManufactureDeviations |
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HasArrayManufactureDeviations.ArrayManufactureDeviations_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 ArrayDesign |
arrayDesign
The association of a physical array with its array design. |
protected ArrayGroup |
arrayGroup
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 java.util.List |
arrayManufactureDeviations
Association to classes to describe deviations from the ArrayDesign. |
protected ArrayManufacture |
information
Association between the manufactured array and the information on that manufacture. |
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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Array()
Default constructor. |
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Array(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list |
void |
addToArrayManufactureDeviations(int position,
ArrayManufactureDeviation arrayManufactureDeviation)
Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list |
boolean |
emptyMAGEobject()
|
ArrayDesign |
getArrayDesign()
Get method for arrayDesign |
ArrayGroup |
getArrayGroup()
Get method for arrayGroup |
java.lang.String |
getArrayIdentifier()
Get method for arrayIdentifier |
HasArrayManufactureDeviations.ArrayManufactureDeviations_list |
getArrayManufactureDeviations()
Get method for arrayManufactureDeviations |
java.lang.Float |
getArrayXOrigin()
Get method for arrayXOrigin |
java.lang.Float |
getArrayYOrigin()
Get method for arrayYOrigin |
ArrayManufactureDeviation |
getFromArrayManufactureDeviations(int position)
Method to get ArrayManufactureDeviation from ArrayManufactureDeviations_list |
ArrayManufacture |
getInformation()
Get method for information |
java.lang.String |
getModelClassName()
|
java.lang.String |
getOriginRelativeTo()
Get method for originRelativeTo |
void |
removeElementAtFromArrayManufactureDeviations(int position)
Method to remove by position from ArrayManufactureDeviations_list |
void |
removeFromArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
Method to remove first ArrayManufactureDeviation from ArrayManufactureDeviations_list |
void |
setArrayDesign(ArrayDesign arrayDesign)
Set method for arrayDesign |
void |
setArrayGroup(ArrayGroup arrayGroup)
Set method for arrayGroup |
void |
setArrayIdentifier(java.lang.String arrayIdentifier)
Set method for arrayIdentifier |
void |
setArrayManufactureDeviations(HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations)
Set method for arrayManufactureDeviations |
void |
setArrayXOrigin(java.lang.Float arrayXOrigin)
Set method for arrayXOrigin |
void |
setArrayYOrigin(java.lang.Float arrayYOrigin)
Set method for arrayYOrigin |
void |
setAttributes(org.xml.sax.Attributes atts)
|
void |
setInformation(ArrayManufacture information)
Set method for information |
void |
setOriginRelativeTo(java.lang.String originRelativeTo)
Set method for originRelativeTo |
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 ArrayDesign arrayDesign
protected ArrayManufacture information
protected ArrayGroup arrayGroup
protected java.util.List arrayManufactureDeviations
Constructor Detail |
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public Array()
public Array(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 setArrayIdentifier(java.lang.String arrayIdentifier)
value
- to setpublic java.lang.String getArrayIdentifier()
public void setArrayXOrigin(java.lang.Float arrayXOrigin)
value
- to setpublic java.lang.Float getArrayXOrigin()
public void setArrayYOrigin(java.lang.Float arrayYOrigin)
value
- to setpublic java.lang.Float getArrayYOrigin()
public void setOriginRelativeTo(java.lang.String originRelativeTo)
value
- to setpublic java.lang.String getOriginRelativeTo()
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setArrayDesign(ArrayDesign arrayDesign)
setArrayDesign
in interface HasArrayDesign
value
- to setpublic ArrayDesign getArrayDesign()
getArrayDesign
in interface HasArrayDesign
public void setInformation(ArrayManufacture information)
setInformation
in interface HasInformation
value
- to setpublic ArrayManufacture getInformation()
getInformation
in interface HasInformation
public void setArrayGroup(ArrayGroup arrayGroup)
setArrayGroup
in interface HasArrayGroup
value
- to setpublic ArrayGroup getArrayGroup()
getArrayGroup
in interface HasArrayGroup
public void setArrayManufactureDeviations(HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations)
setArrayManufactureDeviations
in interface HasArrayManufactureDeviations
value
- to setpublic HasArrayManufactureDeviations.ArrayManufactureDeviations_list getArrayManufactureDeviations()
getArrayManufactureDeviations
in interface HasArrayManufactureDeviations
public void addToArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
addToArrayManufactureDeviations
in interface HasArrayManufactureDeviations
public void addToArrayManufactureDeviations(int position, ArrayManufactureDeviation arrayManufactureDeviation)
addToArrayManufactureDeviations
in interface HasArrayManufactureDeviations
public ArrayManufactureDeviation getFromArrayManufactureDeviations(int position)
getFromArrayManufactureDeviations
in interface HasArrayManufactureDeviations
public void removeElementAtFromArrayManufactureDeviations(int position)
removeElementAtFromArrayManufactureDeviations
in interface HasArrayManufactureDeviations
public void removeFromArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
removeFromArrayManufactureDeviations
in interface HasArrayManufactureDeviations
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