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java.lang.Objectorg.biomage.ArrayDesign.ArrayDesign_package
public class ArrayDesign_package
Describes a microarray design that can be printed and then, in the case of gene expression, hybridized. An array design consists of several features (also called spots) in which reporter sequences are placed. Many features may have the same reporter replicated and a reporter may be specified in one or more array designs. The nature of the reporter's biosequence placed on a spot will depend on the technology. Two well-known technologies differ significantly-spotter arrays draw material from a well and place a spot on the array whereas in situ oligo arrays are created through the synthesis of many, short (~20-100mer) nucleotide sequences onto the features. Reporters can be grouped together into CompositeSequences, typically representing a gene or one or more splice variants in gene expression experiments. There are then two distinct ways that DesignElements are grouped. The one described in the ArrayDesign package by FeatureGroup, ReporterGroup and CompositeGroup is by technology type, that is, one might want to segregate the controls to a Group and all the non-controls to another. Or if PCR Product and Oligos are both used on an array they would likely be in different groups. The grouping described in the DesignElement package by the mappings relates the Features to the Reporter, the Reporters to CompositeSequence, and at higher levels, CompositeSequences to CompositeSequence.
Nested Class Summary | |
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class |
ArrayDesign_package.ArrayDesign_list
Inner list class for holding multiple entries for attribute arrayDesign. |
class |
ArrayDesign_package.CompositeGroup_list
Inner list class for holding multiple entries for attribute compositeGroup. |
class |
ArrayDesign_package.ReporterGroup_list
Inner list class for holding multiple entries for attribute reporterGroup. |
Field Summary | |
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ArrayDesign_package.ArrayDesign_list |
arrayDesign_list
Describes the design of an gene expression layout. |
ArrayDesign_package.CompositeGroup_list |
compositeGroup_list
Allows specification of the type of Composite Design Element. |
ArrayDesign_package.ReporterGroup_list |
reporterGroup_list
Allows specification of the type of Reporter Design Element. |
Constructor Summary | |
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ArrayDesign_package()
Default constructor. |
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ArrayDesign_package(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToArrayDesign_list(ArrayDesign arrayDesign)
Method to add ArrayDesign to ArrayDesign_list |
void |
addToArrayDesign_list(int position,
ArrayDesign arrayDesign)
Method to add ArrayDesign at position to ArrayDesign_list |
void |
addToCompositeGroup_list(CompositeGroup compositeGroup)
Method to add CompositeGroup to CompositeGroup_list |
void |
addToCompositeGroup_list(int position,
CompositeGroup compositeGroup)
Method to add CompositeGroup at position to CompositeGroup_list |
void |
addToReporterGroup_list(int position,
ReporterGroup reporterGroup)
Method to add ReporterGroup at position to ReporterGroup_list |
void |
addToReporterGroup_list(ReporterGroup reporterGroup)
Method to add ReporterGroup to ReporterGroup_list |
boolean |
emptyMAGEobject()
|
ArrayDesign_package.ArrayDesign_list |
getArrayDesign_list()
Get method for arrayDesign_list |
ArrayDesign_package.CompositeGroup_list |
getCompositeGroup_list()
Get method for compositeGroup_list |
ArrayDesign |
getFromArrayDesign_list(int position)
Method to get ArrayDesign from ArrayDesign_list |
CompositeGroup |
getFromCompositeGroup_list(int position)
Method to get CompositeGroup from CompositeGroup_list |
ReporterGroup |
getFromReporterGroup_list(int position)
Method to get ReporterGroup from ReporterGroup_list |
java.lang.String |
getModelClassName()
|
ArrayDesign_package.ReporterGroup_list |
getReporterGroup_list()
Get method for reporterGroup_list |
void |
removeElementAtFromArrayDesign_list(int position)
Method to remove by position from ArrayDesign_list |
void |
removeElementAtFromCompositeGroup_list(int position)
Method to remove by position from CompositeGroup_list |
void |
removeElementAtFromReporterGroup_list(int position)
Method to remove by position from ReporterGroup_list |
void |
removeFromArrayDesign_list(ArrayDesign arrayDesign)
Method to remove first ArrayDesign from ArrayDesign_list |
void |
removeFromCompositeGroup_list(CompositeGroup compositeGroup)
Method to remove first CompositeGroup from CompositeGroup_list |
void |
removeFromReporterGroup_list(ReporterGroup reporterGroup)
Method to remove first ReporterGroup from ReporterGroup_list |
void |
setArrayDesign_list(ArrayDesign_package.ArrayDesign_list arrayDesign_list)
Set method for arrayDesign_list |
void |
setCompositeGroup_list(ArrayDesign_package.CompositeGroup_list compositeGroup_list)
Set method for compositeGroup_list |
void |
setReporterGroup_list(ArrayDesign_package.ReporterGroup_list reporterGroup_list)
Set method for reporterGroup_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 ArrayDesign_package.ReporterGroup_list reporterGroup_list
public ArrayDesign_package.CompositeGroup_list compositeGroup_list
public ArrayDesign_package.ArrayDesign_list arrayDesign_list
Constructor Detail |
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public ArrayDesign_package()
public ArrayDesign_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 setReporterGroup_list(ArrayDesign_package.ReporterGroup_list reporterGroup_list)
value
- to setpublic ArrayDesign_package.ReporterGroup_list getReporterGroup_list()
public void addToReporterGroup_list(ReporterGroup reporterGroup)
public void addToReporterGroup_list(int position, ReporterGroup reporterGroup)
public ReporterGroup getFromReporterGroup_list(int position)
public void removeElementAtFromReporterGroup_list(int position)
public void removeFromReporterGroup_list(ReporterGroup reporterGroup)
public void setCompositeGroup_list(ArrayDesign_package.CompositeGroup_list compositeGroup_list)
value
- to setpublic ArrayDesign_package.CompositeGroup_list getCompositeGroup_list()
public void addToCompositeGroup_list(CompositeGroup compositeGroup)
public void addToCompositeGroup_list(int position, CompositeGroup compositeGroup)
public CompositeGroup getFromCompositeGroup_list(int position)
public void removeElementAtFromCompositeGroup_list(int position)
public void removeFromCompositeGroup_list(CompositeGroup compositeGroup)
public void setArrayDesign_list(ArrayDesign_package.ArrayDesign_list arrayDesign_list)
value
- to setpublic ArrayDesign_package.ArrayDesign_list getArrayDesign_list()
public void addToArrayDesign_list(ArrayDesign arrayDesign)
public void addToArrayDesign_list(int position, ArrayDesign arrayDesign)
public ArrayDesign getFromArrayDesign_list(int position)
public void removeElementAtFromArrayDesign_list(int position)
public void removeFromArrayDesign_list(ArrayDesign arrayDesign)
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