contextFold.rnaFolding
Interface StructureRecognizer

All Superinterfaces:
java.io.Serializable
All Known Implementing Classes:
StructureRecognizerImpl

public interface StructureRecognizer
extends java.io.Serializable


Field Summary
static int MIN_HAIRPIN_LENGTH
           
static int UNPAIRED_BASE
           
 
Method Summary
 java.lang.String elementToString(int[] element)
           
 java.util.Collection<int[]> getCombinedElements(int[] fold)
           
 java.lang.String getElementName(int elementType)
           
 int getFirstBasepairType()
           
 int getFirstBaseType()
           
 int getFirstLengthType()
           
 int getLastBasepairType()
           
 int getLastBaseType()
           
 int getLastLengthType()
           
 boolean isBasepairType(int type)
           
 boolean isBaseType(int type)
           
 boolean isLengthType(int type)
           
 int numTypes()
           
 void sortElements(java.util.List<int[]> elements)
           
 

Field Detail

UNPAIRED_BASE

static final int UNPAIRED_BASE
See Also:
Constant Field Values

MIN_HAIRPIN_LENGTH

static final int MIN_HAIRPIN_LENGTH
Method Detail

numTypes

int numTypes()

isBaseType

boolean isBaseType(int type)

isBasepairType

boolean isBasepairType(int type)

isLengthType

boolean isLengthType(int type)

getFirstBaseType

int getFirstBaseType()

getLastBaseType

int getLastBaseType()

getFirstBasepairType

int getFirstBasepairType()

getLastBasepairType

int getLastBasepairType()

getFirstLengthType

int getFirstLengthType()

getLastLengthType

int getLastLengthType()

getCombinedElements

java.util.Collection<int[]> getCombinedElements(int[] fold)

getElementName

java.lang.String getElementName(int elementType)

elementToString

java.lang.String elementToString(int[] element)

sortElements

void sortElements(java.util.List<int[]> elements)