com.milaboratory.core.mutations

Class Mutation

java.lang.Object

com.milaboratory.core.mutations.Mutation

public final class Mutation
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	FROM_OFFSET
static int	LETTER_MASK
static int	MAX_POSITION_VALUE
static int	MUTATION_POSITION_MASK
static int	MUTATION_TYPE_MASK
static int	MUTATION_TYPE_OFFSET
static int	NON_MUTATION
static int	NON_MUTATION_1
static IntArrayList.IntComparator	POSITION_COMPARATOR Compares int mutations by their positions
static int	POSITION_OFFSET
static int	RAW_MUTATION_TYPE_DELETION
static int	RAW_MUTATION_TYPE_INSERTION
static int	RAW_MUTATION_TYPE_RESERVED
static int	RAW_MUTATION_TYPE_SUBSTITUTION

Method Summary

Methods

Modifier and Type	Method and Description
static int	createDeletion(int position, int from)
static int	createInsertion(int position, int to)
static int	createMutation(int rawType, int from, int to)
static int	createMutation(int rawType, int position, int from, int to)
static int	createMutation(MutationType type, int from, int to)
static int	createMutation(MutationType type, int position, int from, int to)
static int	createSubstitution(int position, int from, int to)
static String	encode(int mutation, Alphabet alphabet) Encodes single mutation in compact human-readable string, that can be decoded by method MutationsUtil.decode(String, com.milaboratory.core.sequence.Alphabet).
static String	encodeFixed(int mutation, Alphabet alphabet)
static byte	getFrom(int code)
static char	getFromSymbol(int code, Alphabet alphabet)
static int	getPosition(int code)
static int	getRawTypeCode(int code) Returns: 0x20 for substitution, 0x40 for Deletion, 0x60 for insertion.
static byte	getTo(int code)
static char	getToSymbol(int code, Alphabet alphabet)
static MutationType	getType(int code)
static boolean	isDeletion(int code)
static boolean	isInDel(int code)
static boolean	isInsertion(int code)
static boolean	isSubstitution(int code)
static int	move(int mutation, int offset)
static String	toString(Alphabet alphabet, int mutation)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

RAW_MUTATION_TYPE_SUBSTITUTION

public static final int RAW_MUTATION_TYPE_SUBSTITUTION

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Constant Field Values

RAW_MUTATION_TYPE_DELETION

public static final int RAW_MUTATION_TYPE_DELETION

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Constant Field Values

RAW_MUTATION_TYPE_INSERTION

public static final int RAW_MUTATION_TYPE_INSERTION

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Constant Field Values

RAW_MUTATION_TYPE_RESERVED

public static final int RAW_MUTATION_TYPE_RESERVED

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Constant Field Values

MUTATION_TYPE_MASK

public static final int MUTATION_TYPE_MASK

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Constant Field Values

MUTATION_POSITION_MASK

public static final int MUTATION_POSITION_MASK

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Constant Field Values

LETTER_MASK

public static final int LETTER_MASK

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Constant Field Values

FROM_OFFSET

public static final int FROM_OFFSET

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Constant Field Values

POSITION_OFFSET

public static final int POSITION_OFFSET

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Constant Field Values

MAX_POSITION_VALUE

public static final int MAX_POSITION_VALUE

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Constant Field Values

NON_MUTATION

public static final int NON_MUTATION

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Constant Field Values

NON_MUTATION_1

public static final int NON_MUTATION_1

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Constant Field Values

MUTATION_TYPE_OFFSET

public static final int MUTATION_TYPE_OFFSET

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Constant Field Values

POSITION_COMPARATOR

public static IntArrayList.IntComparator POSITION_COMPARATOR

Compares int mutations by their positions

Method Detail

createInsertion

public static int createInsertion(int position,
                  int to)

createDeletion

public static int createDeletion(int position,
                 int from)

createSubstitution

public static int createSubstitution(int position,
                     int from,
                     int to)

createMutation

public static int createMutation(MutationType type,
                 int from,
                 int to)

createMutation

public static int createMutation(int rawType,
                 int from,
                 int to)

createMutation

public static int createMutation(MutationType type,
                 int position,
                 int from,
                 int to)

createMutation

public static int createMutation(int rawType,
                 int position,
                 int from,
                 int to)

getPosition

public static int getPosition(int code)

getFrom

public static byte getFrom(int code)

getFromSymbol

public static char getFromSymbol(int code,
                 Alphabet alphabet)

getTo

public static byte getTo(int code)

getToSymbol

public static char getToSymbol(int code,
               Alphabet alphabet)

getRawTypeCode

public static int getRawTypeCode(int code)

Returns: 0x20 for substitution, 0x40 for Deletion, 0x60 for insertion.

Parameters:

code - mutation code form mutations array returned by Aligner.alignGlobal(AlignmentScoring, com.milaboratory.core.sequence.Sequence, com.milaboratory.core.sequence.Sequence) method.

Returns:

0x20 for substitution, 0x40 for Deletion, 0x60 for insertion

getType

public static MutationType getType(int code)

isSubstitution

public static boolean isSubstitution(int code)

isInsertion

public static boolean isInsertion(int code)

isDeletion

public static boolean isDeletion(int code)

isInDel

public static boolean isInDel(int code)

move

public static int move(int mutation,
       int offset)

toString

public static String toString(Alphabet alphabet,
              int mutation)

encode

public static String encode(int mutation,
            Alphabet alphabet)

Encodes single mutation in compact human-readable string, that can be decoded by method MutationsUtil.decode(String, com.milaboratory.core.sequence.Alphabet).

The format is following:

• Substitution: starts with S then nucleotide in initial sequence encoded in one letter (from) then position then resulting nucleotide (to) encoded in one letter. (Example: SA12T = substitution from A to T at position 12).
• Deletion: starts with D then nucleotide that was deleted encoded in one letter (from) then position. (Example: DG43 = G deleted at position 43).
• Insertion: starts with I then position then inserted letter to. (Example: I54C = C inserted before letter at position 54).

Parameters:

mutation - mutation to encode

Returns:

mutation in a human-readable format

encodeFixed

public static String encodeFixed(int mutation,
                 Alphabet alphabet)