compbio.conservation

Enum Format

java.lang.Object

java.lang.Enum<Format>

compbio.conservation.Format

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<Format>

public enum Format
extends java.lang.Enum<Format>

Conservation output Format.

Author:

Agnieszka Golicz & Peter Troshin

Enum Constant Summary

Enum Constants

Enum Constant and Description
RESULT_NO_ALIGNMENT Output the conservation scores and the alignment The alignment is saved in FASTA format prior to the conservation scores.
RESULT_WITH_ALIGNMENT Output just the conservation scores, but no alignment in the following format: #Method name scores For example:

Method Summary

Modifier and Type	Method and Description
static Format	getFormat(java.lang.String format) Converts from String format name to enum Format
static Format	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static Format[]	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, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

RESULT_WITH_ALIGNMENT

public static final Format RESULT_WITH_ALIGNMENT

Output just the conservation scores, but no alignment in the following format:
#Method name scores
For example:

 #SANDER 0 0.345 0.543 0.667 1 0.2
 #SMERFS 1 1 1 1 1 1 1 1 1 1 
 

RESULT_NO_ALIGNMENT

public static final Format RESULT_NO_ALIGNMENT

Output the conservation scores and the alignment The alignment is saved in FASTA format prior to the conservation scores. The scores themselves are saved in the same format as with RESULT_WITH_ALIGNMENT

Method Detail

values

public static Format[] 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 (Format c : Format.values())
    System.out.println(c);

Returns:

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

valueOf

public static Format 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

getFormat

public static Format getFormat(java.lang.String format)

Converts from String format name to enum Format

Parameters:

format - the format to parse

Returns:

the Format Enum value