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java.lang.Objectfr.orsay.lri.varna.models.treealign.RNANodeValue2
public class RNANodeValue2
In this model, nodes are either: 1. a couple of paired bases, and in that case they may have children, in this case singleNode is true 2. a single base that comes from a broken base pair (broken during planarization), without children, in this case singleNode is true 3. a list of consecutive non-paired bases, without children. in this case singleNode is false Note that case 2 happens only if original sequences contained pseudoknots, otherwise this case can be ignored.
Field Summary | |
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private RNANodeValue |
node
Defined if singleNode is true. |
private List<RNANodeValue> |
nodes
Defined if singleNode is false; |
private boolean |
singleNode
Says whether we have a single node or a list of nodes. |
Constructor Summary | |
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RNANodeValue2(boolean singleNode)
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Method Summary | |
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char[] |
computeSequence()
In case of multiple nodes, return the sequence of nucleotides. |
RNANodeValue |
getNode()
In case of a single node, return it. |
List<RNANodeValue> |
getNodes()
In case of multiple nodes, return them. |
boolean |
isSingleNode()
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void |
setNode(RNANodeValue node)
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void |
setNodes(List<RNANodeValue> nodes)
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String |
toGraphvizNodeName()
Returns a string that will be displayed on the node by graphviz. |
String |
toString()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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private boolean singleNode
private RNANodeValue node
private List<RNANodeValue> nodes
Constructor Detail |
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public RNANodeValue2(boolean singleNode)
Method Detail |
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public RNANodeValue getNode()
public void setNode(RNANodeValue node)
public List<RNANodeValue> getNodes()
public char[] computeSequence()
public void setNodes(List<RNANodeValue> nodes)
public boolean isSingleNode()
public String toString()
toString
in class Object
public String toGraphvizNodeName()
GraphvizDrawableNodeValue
toGraphvizNodeName
in interface GraphvizDrawableNodeValue
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