compbio.data.sequence
Enum SMERFSConstraints

java.lang.Object
  java.lang.Enum<SMERFSConstraints>
      compbio.data.sequence.SMERFSConstraints

All Implemented Interfaces:

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

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

Enumeration defining two constraints for SMERFS columns score calculation. MAX_SCORE gives the highest core of all the windows the column belongs to. MID_SCORE gives the window score to the column in the middle.

Author:

Agnieszka Golicz & Peter Troshin

Enum Constant Summary

MAX_SCORE

MID_SCORE

Field Summary

static SMERFSConstraints	DEFAULT_COLUMN_SCORE Default column scoring schema
static double	DEFAULT_GAP_THRESHOLD Default gap threshold value for SMERFS algorithm
static int	DEFAULT_WINDOW_SIZE Default window size value for SMERFS algorithm

Method Summary

static SMERFSConstraints	getSMERFSColumnScore(java.lang.String score)
static SMERFSConstraints	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static SMERFSConstraints[]	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

MAX_SCORE

public static final SMERFSConstraints MAX_SCORE

MID_SCORE

public static final SMERFSConstraints MID_SCORE

Field Detail

DEFAULT_COLUMN_SCORE

public static final SMERFSConstraints DEFAULT_COLUMN_SCORE

Default column scoring schema

DEFAULT_WINDOW_SIZE

public static final int DEFAULT_WINDOW_SIZE

Default window size value for SMERFS algorithm

See Also:

Constant Field Values

DEFAULT_GAP_THRESHOLD

public static final double DEFAULT_GAP_THRESHOLD

Default gap threshold value for SMERFS algorithm

See Also:

Constant Field Values

Method Detail

values

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

Returns:

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

valueOf

public static SMERFSConstraints 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

getSMERFSColumnScore

public static SMERFSConstraints getSMERFSColumnScore(java.lang.String score)