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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.DesignElement.MismatchInformation
public class MismatchInformation
Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary |
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Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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MismatchInformation()
Default constructor. |
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MismatchInformation(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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boolean |
emptyMAGEobject()
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java.lang.String |
getModelClassName()
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java.lang.String |
getNewSequence()
Get method for newSequence |
java.lang.Integer |
getReplacedLength()
Get method for replacedLength |
java.lang.Integer |
getStartCoord()
Get method for startCoord |
void |
setNewSequence(java.lang.String newSequence)
Set method for newSequence |
void |
setReplacedLength(java.lang.Integer replacedLength)
Set method for replacedLength |
void |
setStartCoord(java.lang.Integer startCoord)
Set method for startCoord |
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 |
Constructor Detail |
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public MismatchInformation()
public MismatchInformation(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 setStartCoord(java.lang.Integer startCoord)
value
- to setpublic java.lang.Integer getStartCoord()
public void setNewSequence(java.lang.String newSequence)
value
- to setpublic java.lang.String getNewSequence()
public void setReplacedLength(java.lang.Integer replacedLength)
value
- to setpublic java.lang.Integer getReplacedLength()
public java.lang.String getModelClassName()
getModelClassName
in class Extendable
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