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java.lang.Objectfr.orsay.lri.varna.models.templates.RNATemplateMapping
public class RNATemplateMapping
A RNATemplateMapping is a mapping between bases in an RNA sequence and elements in a RNA template. A base is mapped to only one template element but a template element can be mapped to several bases. This class is designed to be similar to the Mapping class.
Field Summary | |
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private double |
distance
Alignment distance. |
private Map<RNATemplate.RNATemplateElement,ArrayList<Integer>> |
invmap
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private Map<Integer,RNATemplate.RNATemplateElement> |
map
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Constructor Summary | |
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RNATemplateMapping()
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Method Summary | |
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void |
addCouple(int baseIndex,
RNATemplate.RNATemplateElement templateElement)
Tell this mapping object that this base index and this element are mapped with each other. |
ArrayList<Integer> |
getAncestor(RNATemplate.RNATemplateElement templateElement)
If the given template element is in the mapping, return an ArrayList containing the corresponding base indexes, otherwise return null. |
double |
getDistance()
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RNATemplate.RNATemplateElement |
getPartner(int baseIndex)
If the given base index is in the mapping, return the corresponding template element, otherwise return null. |
Set<Integer> |
getSourceElemsAsSet()
Return a set containing all the base indexes in the mapping. |
Set<RNATemplate.RNATemplateElement> |
getTargetElemsAsSet()
Return a set containing all the template elements in the mapping. |
void |
setDistance(double distance)
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String |
showCompact(RNA r)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private Map<Integer,RNATemplate.RNATemplateElement> map
private Map<RNATemplate.RNATemplateElement,ArrayList<Integer>> invmap
private double distance
Constructor Detail |
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public RNATemplateMapping()
Method Detail |
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public double getDistance()
public void setDistance(double distance)
public void addCouple(int baseIndex, RNATemplate.RNATemplateElement templateElement) throws RNATemplateMappingException
RNATemplateMappingException
public String showCompact(RNA r)
public RNATemplate.RNATemplateElement getPartner(int baseIndex)
public ArrayList<Integer> getAncestor(RNATemplate.RNATemplateElement templateElement)
public Set<Integer> getSourceElemsAsSet()
public Set<RNATemplate.RNATemplateElement> getTargetElemsAsSet()
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