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java.lang.Objectfr.orsay.lri.varna.models.templates.RNATemplate
public class RNATemplate
A model for RNA templates. A template is a way to display an RNA secondary structure.
Nested Class Summary | |
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private class |
RNATemplate.ConvertToTree
|
private class |
RNATemplate.ConvertToXml
|
static class |
RNATemplate.EdgeEndPointPosition
Position of an endpoint on an endpoint. |
static class |
RNATemplate.In1Is
For an helix, tells us whether IN1/OUT1 is the 5' strand (the first strand we meet if we follow the RNA sequence) or the 3' strand (the second we meet if we follow the RNA sequence). |
private class |
RNATemplate.LoadFromXml
|
private class |
RNATemplate.MakeEdgeList
|
private class |
RNATemplate.RemovePseudoKnots
|
private class |
RNATemplate.RNAIterator
To get an iterator of this class, use rnaIterator(). |
class |
RNATemplate.RNATemplateElement
An endpoint of an RNA template, it can be an helix or a sequence of non-paired bases. |
class |
RNATemplate.RNATemplateHelix
An helix in an RNA template. |
class |
RNATemplate.RNATemplateUnpairedSequence
A sequence of non-paired bases in an RNA template. |
private class |
RNATemplate.VertexIterator
|
Field Summary | |
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private Collection<RNATemplate.RNATemplateElement> |
elements
The list of template elements. |
private static int |
NEXT_ID
|
private RNATemplate |
template
Variable containing "this", used by the internal class to access this object. |
Constructor Summary | |
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RNATemplate()
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Method Summary | |
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void |
checkIsValidTemplate()
Checks whether this template is a valid RNA template, ie. |
Iterator<RNATemplate.RNATemplateElement> |
classicIterator()
Iterates over all elements (each endpoint is given only once) in an arbitrary order. |
void |
computeIn1Is()
For each helix, compute the in1Is field. |
boolean |
connectedComponentIsCyclic(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
Tells whether the connected component to which endPoint belongs to is cyclic. |
static RNATemplate |
fromXMLDocument(Document xmlDocument)
|
static RNATemplate |
fromXMLFile(File file)
|
RNATemplate.RNATemplateElement |
getAny()
Return an arbitrary element of the template, null if empty. |
RNATemplate.RNATemplateElement.EdgeEndPoint |
getAnyEndPoint()
Return an arbitrary endpoint of the template, null if empty. |
RNATemplate.RNATemplateElement |
getFirst()
The first endpoint (in sequence order) of the template. |
RNATemplate.RNATemplateElement.EdgeEndPoint |
getFirstEndPoint()
The first endpoint edge endpoint (in sequence order) of the template. |
boolean |
isConnected()
Tells whether the template elements are all connected, ie. |
boolean |
isEmpty()
Tells whether the template contains elements. |
List<RNATemplate.RNATemplateElement.EdgeEndPoint> |
makeEdgeList()
Return over all edges in an arbitrary order. |
boolean |
removeElement(RNATemplate.RNATemplateElement element)
Remove the element from the template. |
Iterator<RNATemplate.RNATemplateElement> |
rnaIterator()
Iterates over the elements of the template, in the sequence order. |
RNA |
toRNA()
Generate an RNA sequence that exactly matches the template. |
Tree<RNANodeValueTemplate> |
toTree()
Make a tree of the template. |
Document |
toXMLDocument()
|
void |
toXMLFile(File file)
|
Iterator<RNATemplate.RNATemplateElement.EdgeEndPoint> |
vertexIterator()
Iterates over the elements edge endpoints of the template, in the sequence order. |
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 Collection<RNATemplate.RNATemplateElement> elements
private final RNATemplate template
private static int NEXT_ID
Constructor Detail |
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public RNATemplate()
Method Detail |
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public boolean isEmpty()
public RNATemplate.RNATemplateElement getFirst()
public RNATemplate.RNATemplateElement.EdgeEndPoint getFirstEndPoint()
public RNATemplate.RNATemplateElement getAny()
public RNATemplate.RNATemplateElement.EdgeEndPoint getAnyEndPoint()
public Iterator<RNATemplate.RNATemplateElement> rnaIterator()
public Iterator<RNATemplate.RNATemplateElement> classicIterator()
public Iterator<RNATemplate.RNATemplateElement.EdgeEndPoint> vertexIterator()
public List<RNATemplate.RNATemplateElement.EdgeEndPoint> makeEdgeList()
public boolean connectedComponentIsCyclic(RNATemplate.RNATemplateElement.EdgeEndPoint endPoint)
public boolean isConnected()
public void checkIsValidTemplate() throws fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
public Tree<RNANodeValueTemplate> toTree() throws fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
public RNA toRNA() throws fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
public void toXMLFile(File file) throws fr.orsay.lri.varna.exceptions.ExceptionXMLGeneration, fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionXMLGeneration
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
public Document toXMLDocument() throws fr.orsay.lri.varna.exceptions.ExceptionXMLGeneration, fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionXMLGeneration
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
public static RNATemplate fromXMLFile(File file) throws fr.orsay.lri.varna.exceptions.ExceptionXmlLoading
fr.orsay.lri.varna.exceptions.ExceptionXmlLoading
public static RNATemplate fromXMLDocument(Document xmlDocument) throws fr.orsay.lri.varna.exceptions.ExceptionXmlLoading
fr.orsay.lri.varna.exceptions.ExceptionXmlLoading
public void computeIn1Is() throws fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
public boolean removeElement(RNATemplate.RNATemplateElement element) throws fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
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