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java.lang.Objectorg.biomage.BioSequence.BioSequence_package
public class BioSequence_package
Describes a known gene or sequence. BioAssays typically seek to identify what BioSequences are expressed in a BioMaterial after treatments, the expression level measured from the association between the BioMaterial and the Array. The Array's Features typically provide known locations for this association to occur. Most often, the Reporter and CompositeSequence are known and the presence or absence of a particular BioSequence in the BioMaterial is based on whether there as been an association to the DesignElement targeted for it. Some other experiments may not know the DesignElement's target but can discover it with known properties of the BioSequences in the BioMaterial.
Nested Class Summary | |
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class |
BioSequence_package.BioSequence_list
Inner list class for holding multiple entries for attribute bioSequence. |
Field Summary | |
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BioSequence_package.BioSequence_list |
bioSequence_list
A BioSequence is a representation of a DNA, RNA, or protein sequence. |
Constructor Summary | |
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BioSequence_package()
Default constructor. |
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BioSequence_package(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToBioSequence_list(BioSequence bioSequence)
Method to add BioSequence to BioSequence_list |
void |
addToBioSequence_list(int position,
BioSequence bioSequence)
Method to add BioSequence at position to BioSequence_list |
boolean |
emptyMAGEobject()
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BioSequence_package.BioSequence_list |
getBioSequence_list()
Get method for bioSequence_list |
BioSequence |
getFromBioSequence_list(int position)
Method to get BioSequence from BioSequence_list |
java.lang.String |
getModelClassName()
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void |
removeElementAtFromBioSequence_list(int position)
Method to remove by position from BioSequence_list |
void |
removeFromBioSequence_list(BioSequence bioSequence)
Method to remove first BioSequence from BioSequence_list |
void |
setBioSequence_list(BioSequence_package.BioSequence_list bioSequence_list)
Set method for bioSequence_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 BioSequence_package.BioSequence_list bioSequence_list
Constructor Detail |
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public BioSequence_package()
public BioSequence_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 setBioSequence_list(BioSequence_package.BioSequence_list bioSequence_list)
value
- to setpublic BioSequence_package.BioSequence_list getBioSequence_list()
public void addToBioSequence_list(BioSequence bioSequence)
public void addToBioSequence_list(int position, BioSequence bioSequence)
public BioSequence getFromBioSequence_list(int position)
public void removeElementAtFromBioSequence_list(int position)
public void removeFromBioSequence_list(BioSequence bioSequence)
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