com.milaboratory.core.alignment

Class Alignment<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.alignment.Alignment<S>

All Implemented Interfaces:

Serializable

public final class Alignment<S extends Sequence<S>>
extends Object
implements Serializable

Author:

Dmitry Bolotin, Stanislav Poslavsky

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Alignment(S sequence1, Mutations<S> mutations, AlignmentScoring<S> scoring)
Alignment(S sequence1, Mutations<S> mutations, float score)
Alignment(S sequence1, Mutations<S> mutations, Range sequence1Range, Range sequence2Range, AlignmentScoring<S> scoring)
Alignment(S sequence1, Mutations<S> mutations, Range sequence1Range, Range sequence2Range, float score)

Method Summary

Methods

Modifier and Type	Method and Description
static int	aabs(int position)
int	calculateScore(AlignmentScoring<S> scoring) Calculates score for this alignment using another scoring.
int	convertToSeq1Position(int positionInSeq2) Converts specified position from sequence2 coordinates to sequence1 coordinates.
Range	convertToSeq1Range(Range rangeInSeq2) Converts range in sequence2 to range in sequence1, or returns null if input range is not fully covered by alignment
int	convertToSeq2Position(int positionInSeq1) Converts specified position from sequence1 coordinates to sequence2 coordinates.
Range	convertToSeq2Range(Range rangeInSeq1) Converts range in sequence1 to range in sequence2, or returns null if input range is not fully covered by alignment
boolean	equals(Object o)
AlignmentIteratorForward<S>	forwardIterator() Returns alignment iterator.
Mutations<S>	getAbsoluteMutations() Returns mutations in absolute (global) sequence1 coordinates.
AlignmentHelper	getAlignmentHelper() Returns alignment helper to simplify alignment output in conventional (BLAST) form.
Mutations<S>	getRelativeMutations() Returns mutations in local coordinates, relative to sequence1range.
float	getScore() Return alignment score
S	getSequence1() Return initial sequence (upper sequence in alignment).
Range	getSequence1Range() Returns aligned range of sequence1.
Range	getSequence2Range() Returns aligned range of sequence2.
int	hashCode()
Alignment<S>	invert(S sequence2) Having sequence2 creates alignment from sequence2 to sequence1
Alignment<S>	move(int offset) Returns alignment with seq2range = seq2Range.move(offset), and everything else inherited from this alignment.
AlignmentIteratorReverse<S>	reverseIterator() Returns reverse alignment iterator.
float	similarity() Returns number of matches divided by sum of number of matches and mismatches.
String	toCompactString()
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Alignment

public Alignment(S sequence1,
         Mutations<S> mutations,
         float score)

Alignment

public Alignment(S sequence1,
         Mutations<S> mutations,
         AlignmentScoring<S> scoring)

Alignment

public Alignment(S sequence1,
         Mutations<S> mutations,
         Range sequence1Range,
         Range sequence2Range,
         AlignmentScoring<S> scoring)

Alignment

public Alignment(S sequence1,
         Mutations<S> mutations,
         Range sequence1Range,
         Range sequence2Range,
         float score)

Method Detail

calculateScore

public int calculateScore(AlignmentScoring<S> scoring)

Calculates score for this alignment using another scoring.

Parameters:

scoring - scoring

Returns:

alignment score

forwardIterator

public AlignmentIteratorForward<S> forwardIterator()

Returns alignment iterator.

Returns:

alignment iterator

reverseIterator

public AlignmentIteratorReverse<S> reverseIterator()

Returns reverse alignment iterator.

Returns:

reverse alignment iterator

getSequence1

public S getSequence1()

Return initial sequence (upper sequence in alignment).

Returns:

initial sequence (upper sequence in alignment)

getAbsoluteMutations

public Mutations<S> getAbsoluteMutations()

Returns mutations in absolute (global) sequence1 coordinates.

Returns:

mutations in absolute (global) sequence1 coordinates

getRelativeMutations

public Mutations<S> getRelativeMutations()

Returns mutations in local coordinates, relative to sequence1range.

Returns:

mutations in local coordinates, relative to sequence1range

getSequence1Range

public Range getSequence1Range()

Returns aligned range of sequence1.

Returns:

aligned range of sequence1

getSequence2Range

public Range getSequence2Range()

Returns aligned range of sequence2.

Returns:

aligned range of sequence2

convertToSeq2Position

public int convertToSeq2Position(int positionInSeq1)

Converts specified position from sequence1 coordinates to sequence2 coordinates. If position is out of aligned range of sequence1, returns -1. If letter at specified position in sequence1 is removed in sequence2, than returns -2 - p, where p is a position of previous letter in sequence2.

Parameters:

positionInSeq1 - position in sequence1

Returns:

position in coordinates of sequence2, or -1 if specified position is out of aligned range of sequence1, or if letter at specified position in sequence1 is removed in sequence2 --- -2 - p where p is a position of next letter in sequence2

convertToSeq1Position

public int convertToSeq1Position(int positionInSeq2)

Converts specified position from sequence2 coordinates to sequence1 coordinates. If position is out of aligned range of sequence2, returns -1. If letter at specified position in sequence2 is removed in sequence1, than returns -2 - p, where p is a position of previous letter in sequence2.

Parameters:

positionInSeq2 - position in sequence2

Returns:

position in coordinates of sequence1, or -1 if specified position is out of aligned range of sequence2, or if letter at specified position in sequence2 is removed in sequence2 --- -2 - p where p is a position of next letter in sequence1

convertToSeq1Range

public Range convertToSeq1Range(Range rangeInSeq2)

Converts range in sequence2 to range in sequence1, or returns null if input range is not fully covered by alignment

Parameters:

rangeInSeq2 - range in sequence 2

Returns:

range in sequence1 or null if rangeInSeq2 is not fully covered by alignment

convertToSeq2Range

public Range convertToSeq2Range(Range rangeInSeq1)

Converts range in sequence1 to range in sequence2, or returns null if input range is not fully covered by alignment

Parameters:

rangeInSeq1 - range in sequence 1

Returns:

range in sequence2 or null if rangeInSeq1 is not fully covered by alignment

getScore

public float getScore()

Return alignment score

Returns:

alignment score

invert

public Alignment<S> invert(S sequence2)

Having sequence2 creates alignment from sequence2 to sequence1

Parameters:

sequence2 - sequence2

Returns:

inverted alignment

similarity

public float similarity()

Returns number of matches divided by sum of number of matches and mismatches.

Returns:

number of matches divided by sum of number of matches and mismatches

getAlignmentHelper

public AlignmentHelper getAlignmentHelper()

Returns alignment helper to simplify alignment output in conventional (BLAST) form.

Returns:

alignment helper

move

public Alignment<S> move(int offset)

Returns alignment with seq2range = seq2Range.move(offset), and everything else inherited from this alignment.

Returns:

alignment with seq2range = seq2Range.move(offset), and everything else inherited from this alignment

toString

public String toString()

Overrides:

toString in class Object

toCompactString

public String toCompactString()

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

aabs

public static int aabs(int position)