|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectfr.orsay.lri.varna.models.templates.RNATemplate.RemovePseudoKnots
private class RNATemplate.RemovePseudoKnots
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 |
---|
private ArrayList<RNATemplate.RNATemplateHelix> helixesSeq
private ArrayList<Integer> helixesStruct
private int[] helixesStructWithoutPseudoKnots
Constructor Detail |
---|
private RNATemplate.RemovePseudoKnots()
Method Detail |
---|
private void initArrays() throws fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
private boolean isSelfCrossing()
private void removePseudoKnotsAux()
private Set<RNATemplate.RNATemplateHelix> makeSet()
public Set<RNATemplate.RNATemplateHelix> removePseudoKnots() throws fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |