com.pacbio.secondary.vis.data.marker

Class MarkerCollection

java.lang.Object

com.pacbio.secondary.vis.data.marker.MarkerCollection

public class MarkerCollection
extends java.lang.Object

A collection of genomic markers.

Field Summary

Fields

Modifier and Type	Field and Description
protected BaseDataModel.eDataType	data_type
protected java.util.LinkedList<java.lang.String>	filename
protected java.util.ArrayList<Marker>	markers

Constructor Summary

Constructors

Constructor and Description
MarkerCollection()
MarkerCollection(BaseDataModel.eDataType data_type)
MarkerCollection(java.util.LinkedList<java.lang.String> name) Gives the MarkerCollection a name.

Method Summary

Methods

Modifier and Type	Method and Description
void	add(Marker marker) Adds a marker to the collection
void	clear()
java.util.List<Marker>	find(Interval interval) Find all markers intercepting specific interval; Used during drawing
protected int[]	findBin(Interval interval) returns a bin to use for fast searching intercepting markers
protected int[]	findBin(long bp) returns a bin to use for fast searching intercepting markers
Marker	findNearest(long bp) Finds the marker lying nearest to the given bp position
int	findNearestIndex(long bp) Find nearest marker index with orientation.
int	findNearestIndexFast(long bp) Find nearest marker index this is called every time users click on a view...
Marker	findNeighbour(Marker target, boolean forward) Find nearest marker, used to search next/previous markers
java.util.List<Marker>	findSlow(Interval interval)
BaseDataModel.eDataType	getDataType()
java.lang.String	getDataTypeAsString()
Marker	getMarker(int marker_index)
java.util.List<Marker>	getMarkers()
java.util.LinkedList<java.lang.String>	getName()
java.lang.String	getNameAsString()
boolean	isGeneType() returns true if this is modifications type
boolean	isMarkerType() returns true if this is modifications type
boolean	isModificationsType() returns true if this is modifications type
boolean	isReadsType() returns true if this is reads type
boolean	isSummaryType() returns true if this is summary type
boolean	isVariantsType() returns true if this is variants or vcf data type
void	setDataType(BaseDataModel.eDataType d)
void	setName(java.util.LinkedList<java.lang.String> name)
int	size()

Methods inherited from class java.lang.Object

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

Field Detail

markers

protected java.util.ArrayList<Marker> markers

filename

protected java.util.LinkedList<java.lang.String> filename

data_type

protected BaseDataModel.eDataType data_type

Constructor Detail

MarkerCollection

public MarkerCollection()

MarkerCollection

public MarkerCollection(BaseDataModel.eDataType data_type)

MarkerCollection

public MarkerCollection(java.util.LinkedList<java.lang.String> name)

Gives the MarkerCollection a name.

Parameters:

name -

Method Detail

add

public void add(Marker marker)

Adds a marker to the collection

Parameters:

marker -

getMarkers

public java.util.List<Marker> getMarkers()

getMarker

public Marker getMarker(int marker_index)

getDataType

public BaseDataModel.eDataType getDataType()

setDataType

public void setDataType(BaseDataModel.eDataType d)

clear

public void clear()

getName

public java.util.LinkedList<java.lang.String> getName()

getNameAsString

public java.lang.String getNameAsString()

setName

public void setName(java.util.LinkedList<java.lang.String> name)

size

public int size()

getDataTypeAsString

public java.lang.String getDataTypeAsString()

isReadsType

public boolean isReadsType()

returns true if this is reads type

Parameters:

data -

Returns:

isVariantsType

public boolean isVariantsType()

returns true if this is variants or vcf data type

Parameters:

data -

Returns:

isSummaryType

public boolean isSummaryType()

returns true if this is summary type

Parameters:

data -

Returns:

isModificationsType

public boolean isModificationsType()

returns true if this is modifications type

Parameters:

data -

Returns:

isMarkerType

public boolean isMarkerType()

returns true if this is modifications type

Parameters:

data -

Returns:

isGeneType

public boolean isGeneType()

returns true if this is modifications type

Parameters:

data -

Returns:

findSlow

public java.util.List<Marker> findSlow(Interval interval)

Parameters:

interval -

Returns:

A LinkedList with all markers which intersect the given interval.

findNearest

public Marker findNearest(long bp)

Finds the marker lying nearest to the given bp position

Parameters:

bp - location to search

Returns:

A pointer to the marker or null if nothing was found.

findNearestIndex

public int findNearestIndex(long bp)

Find nearest marker index with orientation.

Parameters:

bp -

right_side -

Returns:

Index of the nearest marker.

findNeighbour

public Marker findNeighbour(Marker target,
                   boolean forward)

Find nearest marker, used to search next/previous markers

Parameters:

target - the marker to start the search from

forward - direction to search, fwd/rev

Returns:

The nearest marker

findNearestIndexFast

public int findNearestIndexFast(long bp)

Find nearest marker index this is called every time users click on a view...

Parameters:

bp -

Returns:

Index of the nearest marker.

find

public java.util.List<Marker> find(Interval interval)

Find all markers intercepting specific interval; Used during drawing

Parameters:

interval - genomic interval to search

Returns:

list of markers matching criteria

findBin

protected int[] findBin(Interval interval)

returns a bin to use for fast searching intercepting markers

Parameters:

interval -

Returns:

start/end index in list

findBin

protected int[] findBin(long bp)

returns a bin to use for fast searching intercepting markers

Parameters:

interval -

Returns:

start/end index in list