com.milaboratory.core.alignment

Class MultiAlignmentHelper

java.lang.Object

com.milaboratory.core.alignment.MultiAlignmentHelper

public class MultiAlignmentHelper
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MultiAlignmentHelper.Settings

Field Summary

Fields

Modifier and Type	Field and Description
static MultiAlignmentHelper.Settings	DEFAULT_SETTINGS
static MultiAlignmentHelper.Settings	DOT_MATCH_SETTINGS

Method Summary

Methods

Modifier and Type	Method and Description
MultiAlignmentHelper	addAnnotationString(String title, String string)
MultiAlignmentHelper	addSubjectQuality(String title, SequenceQuality quality)
static void	alignPositions(MultiAlignmentHelper[] helpers)
static <S extends Sequence<S>> MultiAlignmentHelper	build(MultiAlignmentHelper.Settings settings, Range subjectRange, Alignment<S>... alignments)
static <S extends Sequence<S>> MultiAlignmentHelper	build(MultiAlignmentHelper.Settings settings, Range subjectRange, S subject, Alignment<S>... alignments)
int	getAbsQueryPositionAt(int index, int position)
int	getAbsSubjectPositionAt(int position)
int	getActualPositionWidth()
int	getQueryFrom(int index)
String	getQueryLeftTitle(int i)
int	getQueryPositionAt(int index, int position)
String	getQueryRightTitle(int i)
int	getQueryTo(int index)
MultiAlignmentHelper	getRange(int from, int to)
int	getSubjectFrom()
String	getSubjectLeftTitle()
int	getSubjectLength()
int	getSubjectPositionAt(int position)
String	getSubjectRightTitle()
int	getSubjectTo()
void	setMinimalPositionWidth(int minimalPositionWidth)
MultiAlignmentHelper	setQueryLeftTitle(int id, String queryLeftTitle)
MultiAlignmentHelper	setQueryRightTitle(int id, String queryRightTitle)
MultiAlignmentHelper	setSubjectLeftTitle(String subjectLeftTitle)
MultiAlignmentHelper	setSubjectRightTitle(String subjectRightTitle)
int	size()
MultiAlignmentHelper[]	split(int length)
MultiAlignmentHelper[]	split(int length, boolean eqPositionWidth)
int	subjectToAlignmentPosition(int subjectPosition)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_SETTINGS

public static final MultiAlignmentHelper.Settings DEFAULT_SETTINGS

DOT_MATCH_SETTINGS

public static final MultiAlignmentHelper.Settings DOT_MATCH_SETTINGS

Method Detail

getSubjectLeftTitle

public String getSubjectLeftTitle()

getSubjectRightTitle

public String getSubjectRightTitle()

getQueryLeftTitle

public String getQueryLeftTitle(int i)

getQueryRightTitle

public String getQueryRightTitle(int i)

getActualPositionWidth

public int getActualPositionWidth()

setMinimalPositionWidth

public void setMinimalPositionWidth(int minimalPositionWidth)

setSubjectLeftTitle

public MultiAlignmentHelper setSubjectLeftTitle(String subjectLeftTitle)

addSubjectQuality

public MultiAlignmentHelper addSubjectQuality(String title,
                                     SequenceQuality quality)

setSubjectRightTitle

public MultiAlignmentHelper setSubjectRightTitle(String subjectRightTitle)

addAnnotationString

public MultiAlignmentHelper addAnnotationString(String title,
                                       String string)

setQueryLeftTitle

public MultiAlignmentHelper setQueryLeftTitle(int id,
                                     String queryLeftTitle)

setQueryRightTitle

public MultiAlignmentHelper setQueryRightTitle(int id,
                                      String queryRightTitle)

getSubjectPositionAt

public int getSubjectPositionAt(int position)

subjectToAlignmentPosition

public int subjectToAlignmentPosition(int subjectPosition)

getQueryPositionAt

public int getQueryPositionAt(int index,
                     int position)

getAbsSubjectPositionAt

public int getAbsSubjectPositionAt(int position)

getAbsQueryPositionAt

public int getAbsQueryPositionAt(int index,
                        int position)

getSubjectFrom

public int getSubjectFrom()

getSubjectTo

public int getSubjectTo()

getSubjectLength

public int getSubjectLength()

getQueryFrom

public int getQueryFrom(int index)

getQueryTo

public int getQueryTo(int index)

size

public int size()

getRange

public MultiAlignmentHelper getRange(int from,
                            int to)

split

public MultiAlignmentHelper[] split(int length)

split

public MultiAlignmentHelper[] split(int length,
                           boolean eqPositionWidth)

toString

public String toString()

Overrides:

toString in class Object

build

public static <S extends Sequence<S>> MultiAlignmentHelper build(MultiAlignmentHelper.Settings settings,
                                                 Range subjectRange,
                                                 Alignment<S>... alignments)

build

public static <S extends Sequence<S>> MultiAlignmentHelper build(MultiAlignmentHelper.Settings settings,
                                                 Range subjectRange,
                                                 S subject,
                                                 Alignment<S>... alignments)

alignPositions

public static void alignPositions(MultiAlignmentHelper[] helpers)