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java.lang.Objectorg.biomage.BioMaterial.BioMaterial_package
public class BioMaterial_package
The classes in this package describe how a BioSource is treated to obtain the BioMaterial (typically a LabeledExtract) that is used by a BioAssayCreation in combination with an Array to produce a PhysicalBioAssay. A set of treatments are typically linear in time but can form a Directed Acyclic Graph.
Nested Class Summary | |
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class |
BioMaterial_package.BioMaterial_list
Inner list class for holding multiple entries for attribute bioMaterial. |
class |
BioMaterial_package.Compound_list
Inner list class for holding multiple entries for attribute compound. |
Field Summary | |
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BioMaterial_package.BioMaterial_list |
bioMaterial_list
BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... |
BioMaterial_package.Compound_list |
compound_list
A Compound can be a simple compound such as SDS (sodium dodecyl sulfate). |
Constructor Summary | |
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BioMaterial_package()
Default constructor. |
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BioMaterial_package(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToBioMaterial_list(BioMaterial bioMaterial)
Method to add BioMaterial to BioMaterial_list |
void |
addToBioMaterial_list(int position,
BioMaterial bioMaterial)
Method to add BioMaterial at position to BioMaterial_list |
void |
addToCompound_list(Compound compound)
Method to add Compound to Compound_list |
void |
addToCompound_list(int position,
Compound compound)
Method to add Compound at position to Compound_list |
boolean |
emptyMAGEobject()
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BioMaterial_package.BioMaterial_list |
getBioMaterial_list()
Get method for bioMaterial_list |
BioMaterial_package.Compound_list |
getCompound_list()
Get method for compound_list |
BioMaterial |
getFromBioMaterial_list(int position)
Method to get BioMaterial from BioMaterial_list |
Compound |
getFromCompound_list(int position)
Method to get Compound from Compound_list |
java.lang.String |
getModelClassName()
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void |
removeElementAtFromBioMaterial_list(int position)
Method to remove by position from BioMaterial_list |
void |
removeElementAtFromCompound_list(int position)
Method to remove by position from Compound_list |
void |
removeFromBioMaterial_list(BioMaterial bioMaterial)
Method to remove first BioMaterial from BioMaterial_list |
void |
removeFromCompound_list(Compound compound)
Method to remove first Compound from Compound_list |
void |
setBioMaterial_list(BioMaterial_package.BioMaterial_list bioMaterial_list)
Set method for bioMaterial_list |
void |
setCompound_list(BioMaterial_package.Compound_list compound_list)
Set method for compound_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 BioMaterial_package.Compound_list compound_list
public BioMaterial_package.BioMaterial_list bioMaterial_list
Constructor Detail |
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public BioMaterial_package()
public BioMaterial_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 setCompound_list(BioMaterial_package.Compound_list compound_list)
value
- to setpublic BioMaterial_package.Compound_list getCompound_list()
public void addToCompound_list(Compound compound)
public void addToCompound_list(int position, Compound compound)
public Compound getFromCompound_list(int position)
public void removeElementAtFromCompound_list(int position)
public void removeFromCompound_list(Compound compound)
public void setBioMaterial_list(BioMaterial_package.BioMaterial_list bioMaterial_list)
value
- to setpublic BioMaterial_package.BioMaterial_list getBioMaterial_list()
public void addToBioMaterial_list(BioMaterial bioMaterial)
public void addToBioMaterial_list(int position, BioMaterial bioMaterial)
public BioMaterial getFromBioMaterial_list(int position)
public void removeElementAtFromBioMaterial_list(int position)
public void removeFromBioMaterial_list(BioMaterial bioMaterial)
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