Enum Loop

java.lang.Object
  extended by java.lang.Enum<Loop>
      extended by Loop
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<Loop>

public enum Loop
extends java.lang.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

Author:
Bastiaan van den Berg
See Also:
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
           
GUGU
           
GUUA
           
GUUG
           
UAAU
           
UACG
           
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

CGCG

public static final Loop CGCG

CGGC

public static final Loop CGGC

CGGU

public static final Loop CGGU

CGUG

public static final Loop CGUG

CGAU

public static final Loop CGAU

CGUA

public static final Loop CGUA

GCCG

public static final Loop GCCG

GCGC

public static final Loop GCGC

GCGU

public static final Loop GCGU

GCUG

public static final Loop GCUG

GCAU

public static final Loop GCAU

GCUA

public static final Loop GCUA

GUCG

public static final Loop GUCG

GUGC

public static final Loop GUGC

GUGU

public static final Loop GUGU

GUUG

public static final Loop GUUG

GUAU

public static final Loop GUAU

GUUA

public static final Loop GUUA

UGCG

public static final Loop UGCG

UGGC

public static final Loop UGGC

UGGU

public static final Loop UGGU

UGUG

public static final Loop UGUG

UGAU

public static final Loop UGAU

UGUA

public static final Loop UGUA

AUCG

public static final Loop AUCG

AUGC

public static final Loop AUGC

AUGU

public static final Loop AUGU

AUUG

public static final Loop AUUG

AUAU

public static final Loop AUAU

AUUA

public static final Loop AUUA

UACG

public static final Loop UACG

UAGC

public static final Loop UAGC

UAGU

public static final Loop UAGU

UAUG

public static final Loop UAUG

UAAU

public static final Loop UAAU

UAUA

public static final Loop UAUA
Method Detail

values

public static Loop[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
for (Loop c : Loop.values())
    System.out.println(c);

Returns:
an array containing the constants of this enum type, in the order they are declared

valueOf

public static Loop valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:
name - the name of the enum constant to be returned.
Returns:
the enum constant with the specified name
Throws:
java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
java.lang.NullPointerException - if the argument is null

getLoops

public 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. Template has length 4 and contains [cgua.] and lowerbound < upperbound.

Parameters:
template - Template which should fit the loop.
lowerBound - Minimal allowed free energy.
upperBound - Maximal allowed free erergy.
Returns:
List with loops that meet the requirements.

getEnergy

public int getEnergy()
Returns the free energy of the loop.

Returns:
Free energy of the loop.

getSize

public int getSize()
Returns the size of the loop.

Returns:
Size of the loop.

getLeft

public BasePair getLeft()
Returns the left base pair.

Returns:
Left base pair.

getRight

public BasePair getRight()
Returns the right base pair.

Returns:
Right base pair.

toString

public java.lang.String toString()
Returns a string representation of the loop.

Overrides:
toString in class java.lang.Enum<Loop>