|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectfr.orsay.lri.varna.models.templates.RNATemplateAlign
public class RNATemplateAlign
This class is about the alignment between a tree of RNANodeValue2 and a tree of RNANodeValueTemplate.
Constructor Summary | |
---|---|
RNATemplateAlign()
|
Method Summary | |
---|---|
static TreeAlignResult<RNANodeValue2,RNANodeValueTemplate> |
alignRNAWithTemplate(RNA rna,
RNATemplate template)
Align the given RNA with the given RNA template. |
private static boolean |
canBePartOfABrokenHelix(RNANodeValue2 leftNodeValue)
|
private static boolean |
canBePartOfAnHelix(RNANodeValue2 leftNodeValue)
|
private static boolean |
canBePartOfASequence(RNANodeValue2 leftNodeValue)
|
static int[] |
intArrayFromList(List<Integer> l)
Convert a list of integers into an array of integers. |
static RNATemplateMapping |
makeTemplateMapping(TreeAlignResult<RNANodeValue2,RNANodeValueTemplate> alignResult,
RNA rna)
This method takes an alignment between a tree of RNANodeValue2 of RNANodeValue and a tree of RNANodeValue2 of RNANodeValueTemplate, and the original RNA object that was used to create the first tree in the alignment. |
static RNATemplateMapping |
mapRNAWithTemplate(RNA rna,
RNATemplate template)
Map an RNA with an RNATemplate using tree alignment. |
static void |
printIntArray(int[] A)
Print an integer array. |
static void |
printIntArrayList(ArrayList<Integer> A)
Print an integer ArrayList. |
static void |
printMapping(RNATemplateMapping mapping,
RNATemplate template,
String sequence)
|
static void |
printShortMatrix(short[][] M)
Print an matrix of shorts. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public RNATemplateAlign()
Method Detail |
---|
private static boolean canBePartOfAnHelix(RNANodeValue2 leftNodeValue)
private static boolean canBePartOfASequence(RNANodeValue2 leftNodeValue)
private static boolean canBePartOfABrokenHelix(RNANodeValue2 leftNodeValue)
public static RNATemplateMapping makeTemplateMapping(TreeAlignResult<RNANodeValue2,RNANodeValueTemplate> alignResult, RNA rna) throws RNATemplateMappingException
RNATemplateMappingException
public static void printMapping(RNATemplateMapping mapping, RNATemplate template, String sequence)
public static TreeAlignResult<RNANodeValue2,RNANodeValueTemplate> alignRNAWithTemplate(RNA rna, RNATemplate template) throws RNATemplateDrawingAlgorithmException
RNATemplateDrawingAlgorithmException
public static RNATemplateMapping mapRNAWithTemplate(RNA rna, RNATemplate template) throws RNATemplateDrawingAlgorithmException
RNATemplateDrawingAlgorithmException
public static void printIntArray(int[] A)
public static void printIntArrayList(ArrayList<Integer> A)
public static void printShortMatrix(short[][] M)
public static int[] intArrayFromList(List<Integer> l)
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |