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SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD | DETAIL: ENUM CONSTANTS | FIELD | METHOD |
java.lang.Objectjava.lang.Enum<Loop>
Loop
public enum Loop
Enumeration of RNA structural loop elements. This enumeration only contains stack loops. A loop consists of a left and a right base pair. The first two letters represent the left base pair and the last two letters represent the second base pair (notice that the second base pair is upside down).
GCAU = 5'-G-U- 3' | | 3'-C-A- 5'Each loop has a free energy which have been retrieved from the program RNAfold.
See also http://2008.igem.org/Team:TUDelft/Temperature_software
BasePair
,
Nucleotide
Enum Constant Summary | |
---|---|
AUAU
|
|
AUCG
|
|
AUGC
|
|
AUGU
|
|
AUUA
|
|
AUUG
|
|
CGAU
|
|
CGCG
|
|
CGGC
|
|
CGGU
|
|
CGUA
|
|
CGUG
|
|
GCAU
|
|
GCCG
|
|
GCGC
|
|
GCGU
|
|
GCUA
|
|
GCUG
|
|
GUAU
|
|
GUCG
|
|
GUGC
|
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GUGU
|
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GUUA
|
|
GUUG
|
|
UAAU
|
|
UACG
|
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UAGC
|
|
UAGU
|
|
UAUA
|
|
UAUG
|
|
UGAU
|
|
UGCG
|
|
UGGC
|
|
UGGU
|
|
UGUA
|
|
UGUG
|
Method Summary | |
---|---|
int |
getEnergy()
Returns the free energy of the loop. |
BasePair |
getLeft()
Returns the left base pair. |
static java.util.ArrayList<Loop> |
getLoops(java.lang.String template,
int lowerBound,
int upperBound)
This method returns all the Loops that 'fit' the given template and have an energy value in between the given upper and lower bound. |
BasePair |
getRight()
Returns the right base pair. |
int |
getSize()
Returns the size of the loop. |
java.lang.String |
toString()
Returns a string representation of the loop. |
static Loop |
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name. |
static Loop[] |
values()
Returns an array containing the constants of this enum type, in the order they are declared. |
Methods inherited from class java.lang.Enum |
---|
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, valueOf |
Methods inherited from class java.lang.Object |
---|
getClass, notify, notifyAll, wait, wait, wait |
Enum Constant Detail |
---|
public static final Loop CGCG
public static final Loop CGGC
public static final Loop CGGU
public static final Loop CGUG
public static final Loop CGAU
public static final Loop CGUA
public static final Loop GCCG
public static final Loop GCGC
public static final Loop GCGU
public static final Loop GCUG
public static final Loop GCAU
public static final Loop GCUA
public static final Loop GUCG
public static final Loop GUGC
public static final Loop GUGU
public static final Loop GUUG
public static final Loop GUAU
public static final Loop GUUA
public static final Loop UGCG
public static final Loop UGGC
public static final Loop UGGU
public static final Loop UGUG
public static final Loop UGAU
public static final Loop UGUA
public static final Loop AUCG
public static final Loop AUGC
public static final Loop AUGU
public static final Loop AUUG
public static final Loop AUAU
public static final Loop AUUA
public static final Loop UACG
public static final Loop UAGC
public static final Loop UAGU
public static final Loop UAUG
public static final Loop UAAU
public static final Loop UAUA
Method Detail |
---|
public static Loop[] values()
for (Loop c : Loop.values()) System.out.println(c);
public static Loop valueOf(java.lang.String name)
name
- the name of the enum constant to be returned.
java.lang.IllegalArgumentException
- if this enum type has no constant
with the specified name
java.lang.NullPointerException
- if the argument is nullpublic static java.util.ArrayList<Loop> getLoops(java.lang.String template, int lowerBound, int upperBound)
template
- Template which should fit the loop.lowerBound
- Minimal allowed free energy.upperBound
- Maximal allowed free erergy.
public int getEnergy()
public int getSize()
public BasePair getLeft()
public BasePair getRight()
public java.lang.String toString()
toString
in class java.lang.Enum<Loop>
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