com.milaboratory.core.alignment

Class AlignmentHelper

java.lang.Object

com.milaboratory.core.alignment.AlignmentHelper

All Implemented Interfaces:

Serializable

public final class AlignmentHelper
extends Object
implements Serializable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected String	markup
protected BitArray	match
protected int	offset
protected int[]	seq1Position
protected String	seq1String
protected int[]	seq2Position
protected String	seq2String

Constructor Summary

Constructors

Constructor and Description
AlignmentHelper(String seq1String, String seq2String, int[] seq1Position, int[] seq2Position, BitArray match)
AlignmentHelper(String seq1String, String seq2String, int[] seq1Position, int[] seq2Position, BitArray match, int offset)

Method Summary

Methods

Modifier and Type	Method and Description
String	getLine1() Gets the first line of formatted alignment (query sequence)
String	getLine1Compact()
String	getLine2() Gets the second line of formatted alignment (alignment markup)
String	getLine3() Gets the third line of formatted alignment (subject sequence)
String	getLine3Compact()
String	getMarkup() Get the alignment markup line
AlignmentHelper	getRange(int from, int to)
AlignmentHelper	getRange(int from, int to, int offset)
String	getSeq1String() Get the aligned query sequence
String	getSeq2String() Get the aligned subject sequence
int	getSequence1PositionAt(int i)
int	getSequence2PositionAt(int i)
double	identity() Gets the identity of alignment, i.e.
int	size() Gets the size of aligned region
AlignmentHelper[]	split(int length)
AlignmentHelper[]	split(int length, int offset)
String	toCompactString() Gets the alignment string in contact format (no markup line, mismatches shown by lower-case characters)
String	toString()
String	toStringWithSeq2Quality(SequenceQuality quality)

Methods inherited from class java.lang.Object

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

Field Detail

seq1String

protected final String seq1String

seq2String

protected final String seq2String

markup

protected final String markup

seq1Position

protected final int[] seq1Position

seq2Position

protected final int[] seq2Position

match

protected final BitArray match

offset

protected final int offset

Constructor Detail

AlignmentHelper

public AlignmentHelper(String seq1String,
               String seq2String,
               int[] seq1Position,
               int[] seq2Position,
               BitArray match)

AlignmentHelper

public AlignmentHelper(String seq1String,
               String seq2String,
               int[] seq1Position,
               int[] seq2Position,
               BitArray match,
               int offset)

Method Detail

getRange

public AlignmentHelper getRange(int from,
                       int to)

getRange

public AlignmentHelper getRange(int from,
                       int to,
                       int offset)

split

public AlignmentHelper[] split(int length)

split

public AlignmentHelper[] split(int length,
                      int offset)

identity

public double identity()

Gets the identity of alignment, i.e. ratio of matching nucleotides in the aligned region

size

public int size()

Gets the size of aligned region

getSequence1PositionAt

public int getSequence1PositionAt(int i)

getSequence2PositionAt

public int getSequence2PositionAt(int i)

getSeq1String

public String getSeq1String()

Get the aligned query sequence

getSeq2String

public String getSeq2String()

Get the aligned subject sequence

getMarkup

public String getMarkup()

Get the alignment markup line

getLine1

public String getLine1()

Gets the first line of formatted alignment (query sequence)

getLine1Compact

public String getLine1Compact()

getLine2

public String getLine2()

Gets the second line of formatted alignment (alignment markup)

getLine3

public String getLine3()

Gets the third line of formatted alignment (subject sequence)

toStringWithSeq2Quality

public String toStringWithSeq2Quality(SequenceQuality quality)

getLine3Compact

public String getLine3Compact()

toString

public String toString()

Overrides:

toString in class Object

toCompactString

public String toCompactString()

Gets the alignment string in contact format (no markup line, mismatches shown by lower-case characters)