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java.lang.Objectorg.biomage.Array.Array_package
public class Array_package
Describes the process of creating arrays from array designs. Includes information on how arrays are grouped together, if relevant, how an array deviates from its array design both in layout and per feature and potentially contains references to LIMS data that might contain more detail on the BioMaterial used to create the reporters.
Nested Class Summary | |
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class |
Array_package.Array_list
Inner list class for holding multiple entries for attribute array. |
class |
Array_package.ArrayGroup_list
Inner list class for holding multiple entries for attribute arrayGroup. |
class |
Array_package.ArrayManufacture_list
Inner list class for holding multiple entries for attribute arrayManufacture. |
Field Summary | |
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Array_package.Array_list |
array_list
The physical substrate along with its features and their annotation |
Array_package.ArrayGroup_list |
arrayGroup_list
An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. |
Array_package.ArrayManufacture_list |
arrayManufacture_list
Describes the process by which arrays are produced. |
Constructor Summary | |
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Array_package()
Default constructor. |
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Array_package(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToArray_list(Array array)
Method to add Array to Array_list |
void |
addToArray_list(int position,
Array array)
Method to add Array at position to Array_list |
void |
addToArrayGroup_list(ArrayGroup arrayGroup)
Method to add ArrayGroup to ArrayGroup_list |
void |
addToArrayGroup_list(int position,
ArrayGroup arrayGroup)
Method to add ArrayGroup at position to ArrayGroup_list |
void |
addToArrayManufacture_list(ArrayManufacture arrayManufacture)
Method to add ArrayManufacture to ArrayManufacture_list |
void |
addToArrayManufacture_list(int position,
ArrayManufacture arrayManufacture)
Method to add ArrayManufacture at position to ArrayManufacture_list |
boolean |
emptyMAGEobject()
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Array_package.Array_list |
getArray_list()
Get method for array_list |
Array_package.ArrayGroup_list |
getArrayGroup_list()
Get method for arrayGroup_list |
Array_package.ArrayManufacture_list |
getArrayManufacture_list()
Get method for arrayManufacture_list |
Array |
getFromArray_list(int position)
Method to get Array from Array_list |
ArrayGroup |
getFromArrayGroup_list(int position)
Method to get ArrayGroup from ArrayGroup_list |
ArrayManufacture |
getFromArrayManufacture_list(int position)
Method to get ArrayManufacture from ArrayManufacture_list |
java.lang.String |
getModelClassName()
|
void |
removeElementAtFromArray_list(int position)
Method to remove by position from Array_list |
void |
removeElementAtFromArrayGroup_list(int position)
Method to remove by position from ArrayGroup_list |
void |
removeElementAtFromArrayManufacture_list(int position)
Method to remove by position from ArrayManufacture_list |
void |
removeFromArray_list(Array array)
Method to remove first Array from Array_list |
void |
removeFromArrayGroup_list(ArrayGroup arrayGroup)
Method to remove first ArrayGroup from ArrayGroup_list |
void |
removeFromArrayManufacture_list(ArrayManufacture arrayManufacture)
Method to remove first ArrayManufacture from ArrayManufacture_list |
void |
setArray_list(Array_package.Array_list array_list)
Set method for array_list |
void |
setArrayGroup_list(Array_package.ArrayGroup_list arrayGroup_list)
Set method for arrayGroup_list |
void |
setArrayManufacture_list(Array_package.ArrayManufacture_list arrayManufacture_list)
Set method for arrayManufacture_list |
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 java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public Array_package.ArrayGroup_list arrayGroup_list
public Array_package.Array_list array_list
public Array_package.ArrayManufacture_list arrayManufacture_list
Constructor Detail |
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public Array_package()
public Array_package(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void writeMAGEML(java.io.Writer out) throws java.io.IOException
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
java.io.IOException
public java.lang.String getModelClassName()
public void setArrayGroup_list(Array_package.ArrayGroup_list arrayGroup_list)
value
- to setpublic Array_package.ArrayGroup_list getArrayGroup_list()
public void addToArrayGroup_list(ArrayGroup arrayGroup)
public void addToArrayGroup_list(int position, ArrayGroup arrayGroup)
public ArrayGroup getFromArrayGroup_list(int position)
public void removeElementAtFromArrayGroup_list(int position)
public void removeFromArrayGroup_list(ArrayGroup arrayGroup)
public void setArray_list(Array_package.Array_list array_list)
value
- to setpublic Array_package.Array_list getArray_list()
public void addToArray_list(Array array)
public void addToArray_list(int position, Array array)
public Array getFromArray_list(int position)
public void removeElementAtFromArray_list(int position)
public void removeFromArray_list(Array array)
public void setArrayManufacture_list(Array_package.ArrayManufacture_list arrayManufacture_list)
value
- to setpublic Array_package.ArrayManufacture_list getArrayManufacture_list()
public void addToArrayManufacture_list(ArrayManufacture arrayManufacture)
public void addToArrayManufacture_list(int position, ArrayManufacture arrayManufacture)
public ArrayManufacture getFromArrayManufacture_list(int position)
public void removeElementAtFromArrayManufacture_list(int position)
public void removeFromArrayManufacture_list(ArrayManufacture arrayManufacture)
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