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java.lang.Objectorg.biomage.BioAssay.BioAssay_package
public class BioAssay_package
Provides classes that contain information and annotation on the event of joining an Array with a BioMaterial preparation, the acquisition of images and the extraction of data on a per feature basis from those images. The derived classes of BioAssay represent the base PhysicalBioAssays which lead to the production of Images, the MeasuredBioAssay which is associated with the set of quantitations produced by FeatureExtraction, and DerivedBioAssay (see BioAssayData package) which groups together BioAssays that have been analyzed together to produce further refinement of the quantitations. The design of this package and the related BioAssayData package was driven by the following query considerations and the desire to return as little data as necessary to satisfy a query. Often, the first set of queries for experiments below the Experiment level will want to discover the why of an experiment and this is captured in the BioAssay class through its FactorValue, BioEvent and Description associations. This separates it from the data but allows an overview of the experiment hierarchy. The BioAssayData class association to BioDataValues is optional only to allow queries on them to discover the how of the experiment through the association to the transformation and mappings of the three BioAssayData dimensions and the protocols used. Once a researcher, for instance, has narrowed down the experiments of interest then the actual data, represented by the BioDataValues, can be downloaded. Because these data can be in the hundreds of megabytes to gigabytes range, it was considered desirable to be able to return information and annotation on the experiment without the data.
Nested Class Summary | |
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class |
BioAssay_package.BioAssay_list
Inner list class for holding multiple entries for attribute bioAssay. |
class |
BioAssay_package.Channel_list
Inner list class for holding multiple entries for attribute channel. |
Field Summary | |
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BioAssay_package.BioAssay_list |
bioAssay_list
An abstract class which represents both physical and computational groupings of arrays and biomaterials. |
BioAssay_package.Channel_list |
channel_list
A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength. |
Constructor Summary | |
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BioAssay_package()
Default constructor. |
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BioAssay_package(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToBioAssay_list(BioAssay bioAssay)
Method to add BioAssay to BioAssay_list |
void |
addToBioAssay_list(int position,
BioAssay bioAssay)
Method to add BioAssay at position to BioAssay_list |
void |
addToChannel_list(Channel channel)
Method to add Channel to Channel_list |
void |
addToChannel_list(int position,
Channel channel)
Method to add Channel at position to Channel_list |
boolean |
emptyMAGEobject()
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BioAssay_package.BioAssay_list |
getBioAssay_list()
Get method for bioAssay_list |
BioAssay_package.Channel_list |
getChannel_list()
Get method for channel_list |
BioAssay |
getFromBioAssay_list(int position)
Method to get BioAssay from BioAssay_list |
Channel |
getFromChannel_list(int position)
Method to get Channel from Channel_list |
java.lang.String |
getModelClassName()
|
void |
removeElementAtFromBioAssay_list(int position)
Method to remove by position from BioAssay_list |
void |
removeElementAtFromChannel_list(int position)
Method to remove by position from Channel_list |
void |
removeFromBioAssay_list(BioAssay bioAssay)
Method to remove first BioAssay from BioAssay_list |
void |
removeFromChannel_list(Channel channel)
Method to remove first Channel from Channel_list |
void |
setBioAssay_list(BioAssay_package.BioAssay_list bioAssay_list)
Set method for bioAssay_list |
void |
setChannel_list(BioAssay_package.Channel_list channel_list)
Set method for channel_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 BioAssay_package.Channel_list channel_list
public BioAssay_package.BioAssay_list bioAssay_list
Constructor Detail |
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public BioAssay_package()
public BioAssay_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 setChannel_list(BioAssay_package.Channel_list channel_list)
value
- to setpublic BioAssay_package.Channel_list getChannel_list()
public void addToChannel_list(Channel channel)
public void addToChannel_list(int position, Channel channel)
public Channel getFromChannel_list(int position)
public void removeElementAtFromChannel_list(int position)
public void removeFromChannel_list(Channel channel)
public void setBioAssay_list(BioAssay_package.BioAssay_list bioAssay_list)
value
- to setpublic BioAssay_package.BioAssay_list getBioAssay_list()
public void addToBioAssay_list(BioAssay bioAssay)
public void addToBioAssay_list(int position, BioAssay bioAssay)
public BioAssay getFromBioAssay_list(int position)
public void removeElementAtFromBioAssay_list(int position)
public void removeFromBioAssay_list(BioAssay bioAssay)
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