contextFold.rnaFolding
Class StructureRecognizerImpl
java.lang.Object
contextFold.rnaFolding.StructureRecognizerImpl
- All Implemented Interfaces:
- StructureRecognizer, java.io.Serializable
public class StructureRecognizerImpl
- extends java.lang.Object
- implements StructureRecognizer
This class defines the structural elements which are considered by the
Folder class.
Base-pairs elements:
--------------------
Base-pair elements are oriented and are considered with respect to the
loop they terminate. Each base-pair (i,j) induces two "loop termination"
elements: one for the loop it "closes" (including i+1 and j-1), and one for
the loop it "opens" (including i-1 and j+1). In addition, there are specific
base-pair elements for short hairpin, internal, and bulge loops (each short
loop length induces its unique element).
Loop types: hairpin (HP), stem, internal loop (IL), left bulge (LB), right
bulge (RB), multi-loop (ML), external loop (XL).
Unpaired base elements:
-----------------------
Every unpaired base induces an element which depends in the loop within it
is enclosed. These elements allow linear score expressions with respect to
loop lengths.
Base types: HP_BASE, IL_BASE, ML_BASE, BLG_BASE, XI_BASE_5 (a base in an
external interval at the 5` end of the string), XI_BASE_3 (the same, at the
3` end of the string), and XI_BASE_MID (the same, but neither at the 5` nor
3` end).
Length elements:
----------------
Loops and external intervals induce length elements. The score of such elements
is usually a correction to the linear score which is obtained by the unpaired
bases. For bulges and internal loops, length elements are only induced by medium
length loops, where for longer loops the score is linear with respect to the length
(for multi-loop, the score is always linear).
Length element types: HP_LENGTH, IL_LENGTH (the summation of lengths of both unpaired
regions of the loop), IL_ASYM (the absolute difference between the lengths of the two
unpaired regions), BLG_LENGTH, XI_LENGTH_5 (XI = external interval), XI_LENGTH_3,
XI_LENGTH_MID.
- See Also:
- Serialized Form
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
FIRST_BASE_TYPE
public final int FIRST_BASE_TYPE
LAST_BASE_TYPE
public final int LAST_BASE_TYPE
BASE_TYPES_NUM
public final int BASE_TYPES_NUM
HP_BASE
public final int HP_BASE
IL_BASE
public final int[][] IL_BASE
ML_BASE
public final int ML_BASE
XI_BASE_5
public final int XI_BASE_5
XI_BASE_3
public final int XI_BASE_3
XI_BASE_MID
public final int XI_BASE_MID
IL_MEDIUM
public final int[] IL_MEDIUM
IL_LONG
public final int[] IL_LONG
IL_MEDIUM_MAX_TOTAL_LENGTH
public final int IL_MEDIUM_MAX_TOTAL_LENGTH
FIRST_LOOP_TERMINATION_TYPE
public final int FIRST_LOOP_TERMINATION_TYPE
LAST_LOOP_TERMINATION_TYPE
public final int LAST_LOOP_TERMINATION_TYPE
LOOP_TERMINATION_TYPES_NUM
public final int LOOP_TERMINATION_TYPES_NUM
HP_CLOSE
public final int[] HP_CLOSE
IL_CLOSE
public final int[][] IL_CLOSE
IL_OPEN
public final int[][] IL_OPEN
ML_CLOSE
public final int ML_CLOSE
ML_OPEN
public final int ML_OPEN
XL_OPEN
public final int XL_OPEN
HP_MAX_IX
public final int HP_MAX_IX
IL_SHORT_MAX_IX
public final int IL_SHORT_MAX_IX
IL_MAX_IX
public final int IL_MAX_IX
FIRST_LENGTH_TYPE
public final int FIRST_LENGTH_TYPE
LAST_LENGTH_TYPE
public final int LAST_LENGTH_TYPE
LENGTH_TYPES_NUM
public final int LENGTH_TYPES_NUM
HP_LENGTH
public final int HP_LENGTH
IL_MEDIUM_LENGTH
public final int[] IL_MEDIUM_LENGTH
XI_LENGTH_5
public final int XI_LENGTH_5
XI_LENGTH_3
public final int XI_LENGTH_3
XI_LENGTH_MID
public final int XI_LENGTH_MID
StructureRecognizerImpl
public StructureRecognizerImpl(int hpShortMaxLength,
int[] ilLong,
int[] ilMedium)
StructureRecognizerImpl
public StructureRecognizerImpl()
numTypes
public int numTypes()
- Specified by:
numTypes
in interface StructureRecognizer
getCombinedElements
public java.util.Collection<int[]> getCombinedElements(int[] fold)
- Specified by:
getCombinedElements
in interface StructureRecognizer
isBaseType
public boolean isBaseType(int type)
- Specified by:
isBaseType
in interface StructureRecognizer
isBasepairType
public boolean isBasepairType(int type)
- Specified by:
isBasepairType
in interface StructureRecognizer
isLengthType
public boolean isLengthType(int type)
- Specified by:
isLengthType
in interface StructureRecognizer
getFirstBaseType
public int getFirstBaseType()
- Specified by:
getFirstBaseType
in interface StructureRecognizer
getLastBaseType
public int getLastBaseType()
- Specified by:
getLastBaseType
in interface StructureRecognizer
getFirstBasepairType
public int getFirstBasepairType()
- Specified by:
getFirstBasepairType
in interface StructureRecognizer
getLastBasepairType
public int getLastBasepairType()
- Specified by:
getLastBasepairType
in interface StructureRecognizer
getFirstLengthType
public int getFirstLengthType()
- Specified by:
getFirstLengthType
in interface StructureRecognizer
getLastLengthType
public int getLastLengthType()
- Specified by:
getLastLengthType
in interface StructureRecognizer
getElementName
public java.lang.String getElementName(int elementType)
- Specified by:
getElementName
in interface StructureRecognizer
sortElements
public void sortElements(java.util.List<int[]> elements)
- Specified by:
sortElements
in interface StructureRecognizer
elementToString
public java.lang.String elementToString(int[] element)
- Specified by:
elementToString
in interface StructureRecognizer
elementsString
public java.lang.String elementsString(int[] fold)