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java.lang.Objectorg.biomage.DesignElement.DesignElement_package
public class DesignElement_package
The classes of this package are the contained classes of the ArrayDesign and describe through the DesignElements what is intended to be at each location of the Array. The Feature describes an intended location on the Array, the Reporter the Oligo, Clone, PCR Product that is on a Feature and the CompositeSequence which combines Reporters or CompositeSequences into what the child DesignElements are meant to represent biologically, e.g. a Gene, Exon, SpliceVariant, etc.
Nested Class Summary | |
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class |
DesignElement_package.CompositeCompositeMap_list
Inner list class for holding multiple entries for attribute compositeCompositeMap. |
class |
DesignElement_package.CompositeSequence_list
Inner list class for holding multiple entries for attribute compositeSequence. |
class |
DesignElement_package.FeatureReporterMap_list
Inner list class for holding multiple entries for attribute featureReporterMap. |
class |
DesignElement_package.Reporter_list
Inner list class for holding multiple entries for attribute reporter. |
class |
DesignElement_package.ReporterCompositeMap_list
Inner list class for holding multiple entries for attribute reporterCompositeMap. |
Field Summary | |
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DesignElement_package.CompositeCompositeMap_list |
compositeCompositeMap_list
A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. |
DesignElement_package.CompositeSequence_list |
compositeSequence_list
A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence. |
DesignElement_package.FeatureReporterMap_list |
featureReporterMap_list
A FeatureReporterMap is the description of how source features are transformed into a target reporter. |
DesignElement_package.Reporter_list |
reporter_list
A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences. |
DesignElement_package.ReporterCompositeMap_list |
reporterCompositeMap_list
A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. |
Constructor Summary | |
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DesignElement_package()
Default constructor. |
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DesignElement_package(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToCompositeCompositeMap_list(CompositeCompositeMap compositeCompositeMap)
Method to add CompositeCompositeMap to CompositeCompositeMap_list |
void |
addToCompositeCompositeMap_list(int position,
CompositeCompositeMap compositeCompositeMap)
Method to add CompositeCompositeMap at position to CompositeCompositeMap_list |
void |
addToCompositeSequence_list(CompositeSequence compositeSequence)
Method to add CompositeSequence to CompositeSequence_list |
void |
addToCompositeSequence_list(int position,
CompositeSequence compositeSequence)
Method to add CompositeSequence at position to CompositeSequence_list |
void |
addToFeatureReporterMap_list(FeatureReporterMap featureReporterMap)
Method to add FeatureReporterMap to FeatureReporterMap_list |
void |
addToFeatureReporterMap_list(int position,
FeatureReporterMap featureReporterMap)
Method to add FeatureReporterMap at position to FeatureReporterMap_list |
void |
addToReporter_list(int position,
Reporter reporter)
Method to add Reporter at position to Reporter_list |
void |
addToReporter_list(Reporter reporter)
Method to add Reporter to Reporter_list |
void |
addToReporterCompositeMap_list(int position,
ReporterCompositeMap reporterCompositeMap)
Method to add ReporterCompositeMap at position to ReporterCompositeMap_list |
void |
addToReporterCompositeMap_list(ReporterCompositeMap reporterCompositeMap)
Method to add ReporterCompositeMap to ReporterCompositeMap_list |
boolean |
emptyMAGEobject()
|
DesignElement_package.CompositeCompositeMap_list |
getCompositeCompositeMap_list()
Get method for compositeCompositeMap_list |
DesignElement_package.CompositeSequence_list |
getCompositeSequence_list()
Get method for compositeSequence_list |
DesignElement_package.FeatureReporterMap_list |
getFeatureReporterMap_list()
Get method for featureReporterMap_list |
CompositeCompositeMap |
getFromCompositeCompositeMap_list(int position)
Method to get CompositeCompositeMap from CompositeCompositeMap_list |
CompositeSequence |
getFromCompositeSequence_list(int position)
Method to get CompositeSequence from CompositeSequence_list |
FeatureReporterMap |
getFromFeatureReporterMap_list(int position)
Method to get FeatureReporterMap from FeatureReporterMap_list |
Reporter |
getFromReporter_list(int position)
Method to get Reporter from Reporter_list |
ReporterCompositeMap |
getFromReporterCompositeMap_list(int position)
Method to get ReporterCompositeMap from ReporterCompositeMap_list |
java.lang.String |
getModelClassName()
|
DesignElement_package.Reporter_list |
getReporter_list()
Get method for reporter_list |
DesignElement_package.ReporterCompositeMap_list |
getReporterCompositeMap_list()
Get method for reporterCompositeMap_list |
void |
removeElementAtFromCompositeCompositeMap_list(int position)
Method to remove by position from CompositeCompositeMap_list |
void |
removeElementAtFromCompositeSequence_list(int position)
Method to remove by position from CompositeSequence_list |
void |
removeElementAtFromFeatureReporterMap_list(int position)
Method to remove by position from FeatureReporterMap_list |
void |
removeElementAtFromReporter_list(int position)
Method to remove by position from Reporter_list |
void |
removeElementAtFromReporterCompositeMap_list(int position)
Method to remove by position from ReporterCompositeMap_list |
void |
removeFromCompositeCompositeMap_list(CompositeCompositeMap compositeCompositeMap)
Method to remove first CompositeCompositeMap from CompositeCompositeMap_list |
void |
removeFromCompositeSequence_list(CompositeSequence compositeSequence)
Method to remove first CompositeSequence from CompositeSequence_list |
void |
removeFromFeatureReporterMap_list(FeatureReporterMap featureReporterMap)
Method to remove first FeatureReporterMap from FeatureReporterMap_list |
void |
removeFromReporter_list(Reporter reporter)
Method to remove first Reporter from Reporter_list |
void |
removeFromReporterCompositeMap_list(ReporterCompositeMap reporterCompositeMap)
Method to remove first ReporterCompositeMap from ReporterCompositeMap_list |
void |
setCompositeCompositeMap_list(DesignElement_package.CompositeCompositeMap_list compositeCompositeMap_list)
Set method for compositeCompositeMap_list |
void |
setCompositeSequence_list(DesignElement_package.CompositeSequence_list compositeSequence_list)
Set method for compositeSequence_list |
void |
setFeatureReporterMap_list(DesignElement_package.FeatureReporterMap_list featureReporterMap_list)
Set method for featureReporterMap_list |
void |
setReporter_list(DesignElement_package.Reporter_list reporter_list)
Set method for reporter_list |
void |
setReporterCompositeMap_list(DesignElement_package.ReporterCompositeMap_list reporterCompositeMap_list)
Set method for reporterCompositeMap_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 DesignElement_package.CompositeSequence_list compositeSequence_list
public DesignElement_package.Reporter_list reporter_list
public DesignElement_package.CompositeCompositeMap_list compositeCompositeMap_list
public DesignElement_package.ReporterCompositeMap_list reporterCompositeMap_list
public DesignElement_package.FeatureReporterMap_list featureReporterMap_list
Constructor Detail |
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public DesignElement_package()
public DesignElement_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 setCompositeSequence_list(DesignElement_package.CompositeSequence_list compositeSequence_list)
value
- to setpublic DesignElement_package.CompositeSequence_list getCompositeSequence_list()
public void addToCompositeSequence_list(CompositeSequence compositeSequence)
public void addToCompositeSequence_list(int position, CompositeSequence compositeSequence)
public CompositeSequence getFromCompositeSequence_list(int position)
public void removeElementAtFromCompositeSequence_list(int position)
public void removeFromCompositeSequence_list(CompositeSequence compositeSequence)
public void setReporter_list(DesignElement_package.Reporter_list reporter_list)
value
- to setpublic DesignElement_package.Reporter_list getReporter_list()
public void addToReporter_list(Reporter reporter)
public void addToReporter_list(int position, Reporter reporter)
public Reporter getFromReporter_list(int position)
public void removeElementAtFromReporter_list(int position)
public void removeFromReporter_list(Reporter reporter)
public void setCompositeCompositeMap_list(DesignElement_package.CompositeCompositeMap_list compositeCompositeMap_list)
value
- to setpublic DesignElement_package.CompositeCompositeMap_list getCompositeCompositeMap_list()
public void addToCompositeCompositeMap_list(CompositeCompositeMap compositeCompositeMap)
public void addToCompositeCompositeMap_list(int position, CompositeCompositeMap compositeCompositeMap)
public CompositeCompositeMap getFromCompositeCompositeMap_list(int position)
public void removeElementAtFromCompositeCompositeMap_list(int position)
public void removeFromCompositeCompositeMap_list(CompositeCompositeMap compositeCompositeMap)
public void setReporterCompositeMap_list(DesignElement_package.ReporterCompositeMap_list reporterCompositeMap_list)
value
- to setpublic DesignElement_package.ReporterCompositeMap_list getReporterCompositeMap_list()
public void addToReporterCompositeMap_list(ReporterCompositeMap reporterCompositeMap)
public void addToReporterCompositeMap_list(int position, ReporterCompositeMap reporterCompositeMap)
public ReporterCompositeMap getFromReporterCompositeMap_list(int position)
public void removeElementAtFromReporterCompositeMap_list(int position)
public void removeFromReporterCompositeMap_list(ReporterCompositeMap reporterCompositeMap)
public void setFeatureReporterMap_list(DesignElement_package.FeatureReporterMap_list featureReporterMap_list)
value
- to setpublic DesignElement_package.FeatureReporterMap_list getFeatureReporterMap_list()
public void addToFeatureReporterMap_list(FeatureReporterMap featureReporterMap)
public void addToFeatureReporterMap_list(int position, FeatureReporterMap featureReporterMap)
public FeatureReporterMap getFromFeatureReporterMap_list(int position)
public void removeElementAtFromFeatureReporterMap_list(int position)
public void removeFromFeatureReporterMap_list(FeatureReporterMap featureReporterMap)
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