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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.BioSequence.SequencePosition
org.biomage.DesignElement.CompositePosition
public class CompositePosition
The location in the compositeSequence target's sequence to which a source compositeSequence maps. The association to MismatchInformation allows the specification, usually for control purposes, of deviations from the CompositeSequence's BioMaterial.
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 CompositeSequence |
composite
A source CompositeSequence that is part of a target CompositeSequence |
protected java.util.List |
mismatchInformation
Differences in how the contained compositeSequence matches its target compositeSequence's sequence. |
Fields inherited from class org.biomage.BioSequence.SequencePosition |
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ojbConcreteClass |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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CompositePosition()
Default constructor. |
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CompositePosition(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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CompositeSequence |
getComposite()
Get method for composite |
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 |
setComposite(CompositeSequence composite)
Set method for composite |
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.BioSequence.SequencePosition |
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getEnd, getStart, setEnd, setStart |
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 CompositeSequence composite
protected java.util.List mismatchInformation
Constructor Detail |
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public CompositePosition()
public CompositePosition(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 SequencePosition
java.io.IOException
public boolean emptyMAGEobject()
emptyMAGEobject
in class SequencePosition
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class SequencePosition
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class SequencePosition
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class SequencePosition
public void setComposite(CompositeSequence composite)
setComposite
in interface HasComposite
value
- to setpublic CompositeSequence getComposite()
getComposite
in interface HasComposite
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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