Package org.snpeff.interval
Class Markers
- java.lang.Object
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- org.snpeff.interval.Markers
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Iterable<Marker>
,java.util.Collection<Marker>
public class Markers extends java.lang.Object implements java.io.Serializable, java.util.Collection<Marker>
A collection of markers- Author:
- pcingola
- See Also:
- Serialized Form
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
add(Marker marker)
Add an interval to the collectionMarkers
add(Markers markersToAdd)
Add all intervalsboolean
addAll(java.util.Collection<? extends Marker> mm)
Add all markers in this collectionvoid
clear()
boolean
contains(java.lang.Object o)
boolean
containsAll(java.util.Collection<?> c)
boolean
equals(Markers intervals)
Are all intervals equal?Marker
get(int i)
java.util.List<Marker>
getMarkers()
int
getMedian()
Calculate the median point in this set of markersjava.lang.String
getName()
Markers
intersect()
Perform the intersection of all overlapping sub-intervalsMarkers
intersect(Marker marker)
Intersection between 'marker' and all sub-intervalsboolean
isEmpty()
java.util.Iterator<Marker>
iterator()
void
load(java.lang.String fileName)
void
load(java.lang.String fileName, Genome genome)
Markers
merge()
Merge overlapping intervals This is the same as 'union()' method, but the algorithm is more efficientMarkers
minus(Marker interval)
Calculate 'set minus' using one intervalMarkers
minus(Markers intervals)
Returns the result of this set minus 'intervals'Interval
rand()
Return a random interval within this collectionstatic Markers
readMarkers(java.lang.String fileName)
Read markers from a file Supported formats: BED, BigBed, VCF, TXTboolean
remove(java.lang.Object o)
boolean
removeAll(java.util.Collection<?> c)
boolean
retainAll(java.util.Collection<?> c)
void
save(java.lang.String fileName)
Save to a file using a serializervoid
save(java.lang.String fileName, java.lang.String chr)
Save to a file using a serializer Only save one chromosome ('chr') Note: This is used to save only markers related to one chromosome (e.g.void
setName(java.lang.String name)
int
size()
Markers
sort()
Sort intervalsMarkers
sort(boolean byEnd, boolean reverse)
Sort intervalsMarker[]
toArray()
<T> T[]
toArray(T[] a)
java.lang.String
toString()
java.lang.String
toStringAsciiArt(int maxLen)
Show all intervals as an ASCII artjava.lang.String
toStringTxt()
Markers
union()
Perform the union of all overlapping intervalsMarkers
unique()
Remove duplicated markers-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Field Detail
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markers
protected java.util.ArrayList<Marker> markers
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name
protected java.lang.String name
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Constructor Detail
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Markers
public Markers()
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Markers
public Markers(java.util.Collection otherMarkers)
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Markers
public Markers(Markers otherMarkers)
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Markers
public Markers(java.lang.String name)
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Method Detail
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readMarkers
public static Markers readMarkers(java.lang.String fileName)
Read markers from a file Supported formats: BED, BigBed, VCF, TXT
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add
public boolean add(Marker marker)
Add an interval to the collection- Specified by:
add
in interfacejava.util.Collection<Marker>
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addAll
public boolean addAll(java.util.Collection<? extends Marker> mm)
Add all markers in this collection- Specified by:
addAll
in interfacejava.util.Collection<Marker>
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clear
public void clear()
- Specified by:
clear
in interfacejava.util.Collection<Marker>
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contains
public boolean contains(java.lang.Object o)
- Specified by:
contains
in interfacejava.util.Collection<Marker>
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containsAll
public boolean containsAll(java.util.Collection<?> c)
- Specified by:
containsAll
in interfacejava.util.Collection<Marker>
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equals
public boolean equals(Markers intervals)
Are all intervals equal?
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get
public Marker get(int i)
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getMarkers
public java.util.List<Marker> getMarkers()
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getMedian
public int getMedian()
Calculate the median point in this set of markers
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getName
public java.lang.String getName()
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setName
public void setName(java.lang.String name)
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intersect
public Markers intersect()
Perform the intersection of all overlapping sub-intervalsFor each marker, calculate all overlapping markers and create a new marker that contains them all. Return a set of those new markers.
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intersect
public Markers intersect(Marker marker)
Intersection between 'marker' and all sub-intervals
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isEmpty
public boolean isEmpty()
- Specified by:
isEmpty
in interfacejava.util.Collection<Marker>
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iterator
public java.util.Iterator<Marker> iterator()
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load
public void load(java.lang.String fileName)
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load
public void load(java.lang.String fileName, Genome genome)
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merge
public Markers merge()
Merge overlapping intervals This is the same as 'union()' method, but the algorithm is more efficient
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minus
public Markers minus(Marker interval)
Calculate 'set minus' using one interval- Parameters:
interval
-- Returns:
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minus
public Markers minus(Markers intervals)
Returns the result of this set minus 'intervals'WARNING: This method should only be used for debugging (or in very small collections) since it is extremely inefficient.
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rand
public Interval rand()
Return a random interval within this collection
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remove
public boolean remove(java.lang.Object o)
- Specified by:
remove
in interfacejava.util.Collection<Marker>
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removeAll
public boolean removeAll(java.util.Collection<?> c)
- Specified by:
removeAll
in interfacejava.util.Collection<Marker>
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retainAll
public boolean retainAll(java.util.Collection<?> c)
- Specified by:
retainAll
in interfacejava.util.Collection<Marker>
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save
public void save(java.lang.String fileName)
Save to a file using a serializer
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save
public void save(java.lang.String fileName, java.lang.String chr)
Save to a file using a serializer Only save one chromosome ('chr') Note: This is used to save only markers related to one chromosome (e.g. when saving GenomicSequences)
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size
public int size()
- Specified by:
size
in interfacejava.util.Collection<Marker>
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sort
public Markers sort()
Sort intervals
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sort
public Markers sort(boolean byEnd, boolean reverse)
Sort intervals- Parameters:
byEnd
- : If true, sort by end. Otherwise sort by startreverse
- : Reverse order
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toArray
public <T> T[] toArray(T[] a)
- Specified by:
toArray
in interfacejava.util.Collection<Marker>
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toStringAsciiArt
public java.lang.String toStringAsciiArt(int maxLen)
Show all intervals as an ASCII art
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toStringTxt
public java.lang.String toStringTxt()
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union
public Markers union()
Perform the union of all overlapping intervalsFor each marker, calculate all overlapping markers and create a new marker that contains them all. Return a set of those new markers.
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unique
public Markers unique()
Remove duplicated markers- Returns:
- this object
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