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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.BioSequence.SeqFeatureLocation
public class SeqFeatureLocation
The location of the SeqFeature annotation.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasSubregions |
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HasSubregions.Subregions_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 SequencePosition |
coordinate
At which base pairs or amino acid this SeqFeature begins and ends. |
protected java.util.List |
subregions
Regions within the SeqFeature. |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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SeqFeatureLocation()
Default constructor. |
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SeqFeatureLocation(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToSubregions(int position,
SeqFeatureLocation seqFeatureLocation)
Method to add SeqFeatureLocation at position to Subregions_list |
void |
addToSubregions(SeqFeatureLocation seqFeatureLocation)
Method to add SeqFeatureLocation to Subregions_list |
boolean |
emptyMAGEobject()
|
SequencePosition |
getCoordinate()
Get method for coordinate |
SeqFeatureLocation |
getFromSubregions(int position)
Method to get SeqFeatureLocation from Subregions_list |
java.lang.String |
getModelClassName()
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java.lang.String |
getStrandType()
Get method for strandType |
HasSubregions.Subregions_list |
getSubregions()
Get method for subregions |
void |
removeElementAtFromSubregions(int position)
Method to remove by position from Subregions_list |
void |
removeFromSubregions(SeqFeatureLocation seqFeatureLocation)
Method to remove first SeqFeatureLocation from Subregions_list |
void |
setCoordinate(SequencePosition coordinate)
Set method for coordinate |
void |
setStrandType(java.lang.String strandType)
Set method for strandType |
void |
setSubregions(HasSubregions.Subregions_list subregions)
Set method for subregions |
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 java.util.List subregions
protected SequencePosition coordinate
Constructor Detail |
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public SeqFeatureLocation()
public SeqFeatureLocation(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 void setStrandType(java.lang.String strandType)
value
- to setpublic java.lang.String getStrandType()
public java.lang.String getModelClassName()
getModelClassName
in class Extendable
public void setSubregions(HasSubregions.Subregions_list subregions)
setSubregions
in interface HasSubregions
value
- to setpublic HasSubregions.Subregions_list getSubregions()
getSubregions
in interface HasSubregions
public void addToSubregions(SeqFeatureLocation seqFeatureLocation)
addToSubregions
in interface HasSubregions
public void addToSubregions(int position, SeqFeatureLocation seqFeatureLocation)
addToSubregions
in interface HasSubregions
public SeqFeatureLocation getFromSubregions(int position)
getFromSubregions
in interface HasSubregions
public void removeElementAtFromSubregions(int position)
removeElementAtFromSubregions
in interface HasSubregions
public void removeFromSubregions(SeqFeatureLocation seqFeatureLocation)
removeFromSubregions
in interface HasSubregions
public void setCoordinate(SequencePosition coordinate)
setCoordinate
in interface HasCoordinate
value
- to setpublic SequencePosition getCoordinate()
getCoordinate
in interface HasCoordinate
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