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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.BioSequence.SeqFeature
public class SeqFeature
Represents, in general, what would be a GenBank Feature Table annotation for a sequence.
Nested Class Summary | |
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class |
SeqFeature.Basis
Inner class for the enumeration values that the attribute basis can assume. |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasRegions |
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HasRegions.Regions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_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 java.util.List |
regions
Association to classes that describe the location with the sequence of the SeqFeature. |
Fields inherited from class org.biomage.Common.Describable |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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SeqFeature()
Default constructor. |
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SeqFeature(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToRegions(int position,
SeqFeatureLocation seqFeatureLocation)
Method to add SeqFeatureLocation at position to Regions_list |
void |
addToRegions(SeqFeatureLocation seqFeatureLocation)
Method to add SeqFeatureLocation to Regions_list |
boolean |
emptyMAGEobject()
|
SeqFeature.Basis |
getBasis()
Get method for basis |
SeqFeatureLocation |
getFromRegions(int position)
Method to get SeqFeatureLocation from Regions_list |
java.lang.String |
getModelClassName()
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java.lang.String |
getNameBasis()
Return the current name of the Enumeration type of Basis. |
java.lang.String |
getNameByValueBasis(int val)
For Basis get the Name of the Enumeration type by passing a Value to it. |
HasRegions.Regions_list |
getRegions()
Get method for regions |
int |
getValueBasis()
Return the currrent value of the Enumeration type of Basis. |
int |
getValueByNameBasis(java.lang.String name)
For Basis get the Value of the Enumeration type by passing a Name to it. |
void |
removeElementAtFromRegions(int position)
Method to remove by position from Regions_list |
void |
removeFromRegions(SeqFeatureLocation seqFeatureLocation)
Method to remove first SeqFeatureLocation from Regions_list |
void |
setBasis(SeqFeature.Basis basis)
Set method for basis |
java.lang.String |
setNameByValueBasis(int val)
For Basis set the Name of the Enumeration type by passing a value (int) |
void |
setRegions(HasRegions.Regions_list regions)
Set method for regions |
int |
setValueByNameBasis(java.lang.String name)
For Basis set the Value of the Enumeration type by passing a Name to it. |
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.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAttributes, setAuditTrail, setDescriptions, setSecurity |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, 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 regions
Constructor Detail |
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public SeqFeature()
public SeqFeature(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 Describable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Describable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Describable
java.io.IOException
public void setBasis(SeqFeature.Basis basis)
value
- to setpublic SeqFeature.Basis getBasis()
public java.lang.String setNameByValueBasis(int val)
int
- value The value to be mapped to the namepublic int setValueByNameBasis(java.lang.String name)
String
- name The name to be mapped to a valuepublic java.lang.String getNameByValueBasis(int val)
int
- val The value for which the Mapped String will be returned.public int getValueByNameBasis(java.lang.String name)
String
- name The name to be mapped to a value.public java.lang.String getNameBasis()
public int getValueBasis()
public java.lang.String getModelClassName()
getModelClassName
in class Describable
public void setRegions(HasRegions.Regions_list regions)
setRegions
in interface HasRegions
value
- to setpublic HasRegions.Regions_list getRegions()
getRegions
in interface HasRegions
public void addToRegions(SeqFeatureLocation seqFeatureLocation)
addToRegions
in interface HasRegions
public void addToRegions(int position, SeqFeatureLocation seqFeatureLocation)
addToRegions
in interface HasRegions
public SeqFeatureLocation getFromRegions(int position)
getFromRegions
in interface HasRegions
public void removeElementAtFromRegions(int position)
removeElementAtFromRegions
in interface HasRegions
public void removeFromRegions(SeqFeatureLocation seqFeatureLocation)
removeFromRegions
in interface HasRegions
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