fr.orsay.lri.varna.models.templates
Class RNATemplate.RemovePseudoKnots

java.lang.Object
  fr.orsay.lri.varna.models.templates.RNATemplate.RemovePseudoKnots

Enclosing class:

RNATemplate

private class RNATemplate.RemovePseudoKnots
extends Object

Field Summary

private ArrayList<RNATemplate.RNATemplateHelix>	helixesSeq The elements of the template as an array, in the order of the RNA sequence.
private ArrayList<Integer>	helixesStruct For any i, j = helixesStruct[i] is the index in helixesSeq where the same helix also appears.
private int[]	helixesStructWithoutPseudoKnots The same as helixesStruct, but without the pseudoknots, ie.

Constructor Summary

private

RNATemplate.RemovePseudoKnots()

Method Summary

private void	initArrays()
private boolean	isSelfCrossing() Tells whether there is a pseudoknot.
private Set<RNATemplate.RNATemplateHelix>	makeSet()
Set<RNATemplate.RNATemplateHelix>	removePseudoKnots()
private void	removePseudoKnotsAux() We compute helixesStructWithoutPseudoKnots from helixesStruct by replacing values by -1 for the helixes we cut (the bases are become non-paired).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

helixesSeq

private ArrayList<RNATemplate.RNATemplateHelix> helixesSeq

The elements of the template as an array, in the order of the RNA sequence. Note that helixes will appear twice, and non-paired sequences don't appear.

helixesStruct

private ArrayList<Integer> helixesStruct

For any i, j = helixesStruct[i] is the index in helixesSeq where the same helix also appears. It means we have for all i: helixesSeq[helixesStruct[i]] == helixesSeq[i]

helixesStructWithoutPseudoKnots

private int[] helixesStructWithoutPseudoKnots

The same as helixesStruct, but without the pseudoknots, ie. helixesStructWithoutPseudoKnots[i] may be -1 even though helixesStruct[i] != -1 .

Constructor Detail

RNATemplate.RemovePseudoKnots

private RNATemplate.RemovePseudoKnots()

Method Detail

initArrays

private void initArrays()
                 throws fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate

Throws:

fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate

isSelfCrossing

private boolean isSelfCrossing()

Tells whether there is a pseudoknot. Adapted from RNAMLParser.isSelfCrossing()

removePseudoKnotsAux

private void removePseudoKnotsAux()

We compute helixesStructWithoutPseudoKnots from helixesStruct by replacing values by -1 for the helixes we cut (the bases are become non-paired). We try to cut as few base pairs as possible.

makeSet

private Set<RNATemplate.RNATemplateHelix> makeSet()

removePseudoKnots

public Set<RNATemplate.RNATemplateHelix> removePseudoKnots()
                                                    throws fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate

Throws:

fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate