-SMERFSConstraints -

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- -compbio.data.sequence -
-Enum SMERFSConstraints

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

All Implemented Interfaces:: Serializable, Comparable<SMERFSConstraints>

public enum SMERFSConstraints
extends Enum<SMERFSConstraints>
extends Enum<SMERFSConstraints>

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-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. -

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Author:: Agnieszka Golicz & Peter Troshin

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-Enum Constant Summary
MAX_SCORE - -
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MID_SCORE - -
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-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
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-Method Summary
-static SMERFSConstraints getSMERFSColumnScore(String score) - -
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-static SMERFSConstraints valueOf(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.
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Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
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Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
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-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(String score)` - - -
-`static SMERFSConstraints`	`valueOf(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`

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-Enum Constant Detail
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-MAX_SCORE

-public static final SMERFSConstraints MAX_SCORE

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-MID_SCORE

-public static final SMERFSConstraints MID_SCORE

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-Field Detail

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-DEFAULT_COLUMN_SCORE

-public static final SMERFSConstraints DEFAULT_COLUMN_SCORE

Default column scoring schema -

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-DEFAULT_WINDOW_SIZE

-public static final int DEFAULT_WINDOW_SIZE

Default window size value for SMERFS algorithm -

See Also:: Constant Field Values

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-DEFAULT_GAP_THRESHOLD

-public static final double DEFAULT_GAP_THRESHOLD

Default gap threshold value for SMERFS algorithm -

See Also:: Constant Field Values

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-Method Detail

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

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-valueOf

-public static SMERFSConstraints valueOf(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: -: IllegalArgumentException - if this enum type has no constant -with the specified name -; NullPointerException - if the argument is null

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-getSMERFSColumnScore

-public static SMERFSConstraints getSMERFSColumnScore(String score)

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Overview

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Use

Tree

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Index

Help

- -

- PREV CLASS - NEXT CLASS

- FRAMES - NO FRAMES - - - - -

- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD

-DETAIL: ENUM CONSTANTS | FIELD | METHOD

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- -compbio.data.sequence - -Enum SMERFSConstraints

-MAX_SCORE

-MID_SCORE

-DEFAULT_COLUMN_SCORE

-DEFAULT_WINDOW_SIZE

-DEFAULT_GAP_THRESHOLD

-values

-valueOf

-getSMERFSColumnScore

- -compbio.data.sequence -
-Enum SMERFSConstraints