public final class FilterUtil
extends java.lang.Object
FilterUtil
contains static methods for constructing
marker filters.Modifier and Type | Method and Description |
---|---|
static Filter<Marker> |
idFilter(java.util.Collection<java.lang.String> exclude)
Returns a filter that accepts all markers which do not have an
identifier or chromomsome position present in the specified
collection.
|
static Filter<Marker> |
markerFilter(java.io.File excludeMarkersFile)
Returns a filter that excludes markers that have an identifier
or genome coordinates that matches a line of the specified file,
or returns
null if the excludeMarkersFile parameter is
null . |
static boolean |
markerIsInSet(Marker marker,
java.util.Set<java.lang.String> set)
Returns
true if the specified marker has an identifier
is in the specified set, or if ("marker.chrom()" + ":" + "marker.pos()")
is in the specified set, and returns false otherwise. |
static Filter<java.lang.String> |
sampleFilter(java.io.File excludeSamplesFile)
Returns a filter that excludes samples that have an identifier
that matches a line of the specified file, or returns
null if
the excludeSamplesFile parameter is null |
public static Filter<Marker> markerFilter(java.io.File excludeMarkersFile)
null
if the excludeMarkersFile
parameter is
null
. Genome coordinates must be in "CHROM:POS" format.excludeMarkersFile
- a file that contains an identifier
or genome coordinate of one excluded marker on each linenull
if the excludeMarkersFile
parameter is
null
java.lang.IllegalArgumentException
- if the specified file does not existjava.lang.IllegalArgumentException
- if the specified file is a directoryjava.lang.IllegalArgumentException
- if any line of the specified
file contains two non-white-space characters separated by one or
more white-space characterspublic static Filter<java.lang.String> sampleFilter(java.io.File excludeSamplesFile)
null
if
the excludeSamplesFile
parameter is null
excludeSamplesFile
- a file which contains an identifier
of one excluded sample on each linenull
if
the excludeSamplesFile
parameter is null
java.lang.IllegalArgumentException
- if the specified file does not existjava.lang.IllegalArgumentException
- if the specified file is a directoryjava.lang.IllegalArgumentException
- if any line of the specified
file contains two non-white-space characters separated by one or
more white-space characterspublic static boolean markerIsInSet(Marker marker, java.util.Set<java.lang.String> set)
true
if the specified marker has an identifier
is in the specified set, or if ("marker.chrom()" + ":" + "marker.pos()")
is in the specified set, and returns false
otherwise.marker
- a markerset
- a set of marker identifiers and chromosome positions in
"CHROM:POS" formattrue
if the specified marker has an identifier
is in the specified set or if ("marker.chrom()" + ":" + "marker.pos()")
is in the specified setjava.lang.NullPointerException
- if marker == null || set == null
public static Filter<Marker> idFilter(java.util.Collection<java.lang.String> exclude)
exclude.contains(marker.id(j)) == true
for any 0 <= j < marker.nIds()
or if
exclude.contains(marker.chrom() + ":" + marker.pos()) == true
.exclude
- a collection of marker identifiers and chromosome
positions in "CHROM:POS" formatjava.lang.NullPointerException
- if exclude == null