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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.DesignElement.FeatureInformation
public class FeatureInformation
As part of the map information, allows the association of one or more differences in the BioMaterial on a feature from the BioMaterial of the Reporter. Useful for control purposes such as in Affymetrix probe pairs.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasMismatchInformation |
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HasMismatchInformation.MismatchInformation_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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protected Feature |
feature
The feature the FeatureInformation is supplying information for. |
protected java.util.List |
mismatchInformation
Differences in how the feature matches the reporter's sequence, typical examples is the Affymetrix probe pair where one of the features is printed with a mismatch to the other feature's perfect match. |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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FeatureInformation()
Default constructor. |
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FeatureInformation(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToMismatchInformation(int position,
MismatchInformation mismatchInformation)
Method to add MismatchInformation at position to MismatchInformation_list |
void |
addToMismatchInformation(MismatchInformation mismatchInformation)
Method to add MismatchInformation to MismatchInformation_list |
boolean |
emptyMAGEobject()
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Feature |
getFeature()
Get method for feature |
MismatchInformation |
getFromMismatchInformation(int position)
Method to get MismatchInformation from MismatchInformation_list |
HasMismatchInformation.MismatchInformation_list |
getMismatchInformation()
Get method for mismatchInformation |
java.lang.String |
getModelClassName()
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void |
removeElementAtFromMismatchInformation(int position)
Method to remove by position from MismatchInformation_list |
void |
removeFromMismatchInformation(MismatchInformation mismatchInformation)
Method to remove first MismatchInformation from MismatchInformation_list |
void |
setFeature(Feature feature)
Set method for feature |
void |
setMismatchInformation(HasMismatchInformation.MismatchInformation_list mismatchInformation)
Set method for mismatchInformation |
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 org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setAttributes, setId, setIsEditable, setPropertySets, setSecuredElementId, toString |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected Feature feature
protected java.util.List mismatchInformation
Constructor Detail |
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public FeatureInformation()
public FeatureInformation(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
writeMAGEML
in class Extendable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Extendable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Extendable
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Extendable
public void setFeature(Feature feature)
setFeature
in interface HasFeature
value
- to setpublic Feature getFeature()
getFeature
in interface HasFeature
public void setMismatchInformation(HasMismatchInformation.MismatchInformation_list mismatchInformation)
setMismatchInformation
in interface HasMismatchInformation
value
- to setpublic HasMismatchInformation.MismatchInformation_list getMismatchInformation()
getMismatchInformation
in interface HasMismatchInformation
public void addToMismatchInformation(MismatchInformation mismatchInformation)
addToMismatchInformation
in interface HasMismatchInformation
public void addToMismatchInformation(int position, MismatchInformation mismatchInformation)
addToMismatchInformation
in interface HasMismatchInformation
public MismatchInformation getFromMismatchInformation(int position)
getFromMismatchInformation
in interface HasMismatchInformation
public void removeElementAtFromMismatchInformation(int position)
removeElementAtFromMismatchInformation
in interface HasMismatchInformation
public void removeFromMismatchInformation(MismatchInformation mismatchInformation)
removeFromMismatchInformation
in interface HasMismatchInformation
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