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Guava ranges for genomics.
/*
ngs-range Guava ranges for genomics.
Copyright (c) 2014 National Marrow Donor Program (NMDP)
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.gnu.org/licenses/lgpl.html
*/
package org.nmdp.ngs.range.rtree;
import static com.google.common.base.Preconditions.checkNotNull;
import com.github.davidmoten.rtree.geometry.Geometries;
import com.github.davidmoten.rtree.geometry.Point;
import com.github.davidmoten.rtree.geometry.Rectangle;
import com.google.common.collect.BoundType;
import com.google.common.collect.Range;
/**
* Geometries for use in building R-Trees and R*-Trees from Guava ranges.
*
*
* import static org.nmdp.ngs.range.rtree.RangeGeometries.*;
*
* RTree<String> rtree = RTree.create();
* rtree = rtree.add("foo", closed(10, 20));
* rtree = rtree.add("bar", closedOpen(14, 28));
* rtree = rtree.add("baz", open(18, 36));
*
* for (String result : rtree.search(singleton(20)).toBlocking().toIterable()) {
* // ...
* }
*
*/
public final class RangeGeometries {
/**
* Private no-arg constructor.
*/
private RangeGeometries() {
// empty
}
/**
* Create and return a new point geometry from the specified singleton value.
*
* @param value singleton value, must not be null
* @return a new point geometry from the specified singleton value
*/
public static > Point singleton(final N value) {
checkNotNull(value);
return Geometries.point(value.doubleValue(), 0.5d);
}
/**
* Create and return a new rectangle geometry from the specified closed range [lower..upper].
*
* @param lower lower endpoint, must not be null
* @param upper upper endpoint, must not be null
* @return a new rectangle geometry from the specified closed range
*/
public static > Rectangle closed(final N lower, final N upper) {
checkNotNull(lower);
checkNotNull(upper);
return range(Range.closed(lower, upper));
}
/**
* Create and return a new rectangle geometry from the specified closed open range [lower..upper).
*
* @param lower lower endpoint, must not be null
* @param upper upper endpoint, must not be null
* @return a new rectangle geometry from the specified closed range
*/
public static > Rectangle closedOpen(final N lower, final N upper) {
checkNotNull(lower);
checkNotNull(upper);
return range(Range.closedOpen(lower, upper));
}
/**
* Create and return a new rectangle geometry from the specified open closed range (lower..upper]
*
* @param lower lower endpoint, must not be null
* @param upper upper endpoint, must not be null
* @return a new rectangle geometry from the specified closed range
*/
public static > Rectangle openClosed(final N lower, final N upper) {
checkNotNull(lower);
checkNotNull(upper);
return range(Range.openClosed(lower, upper));
}
/**
* Create and return a new rectangle geometry from the specified open range (lower..upper).
*
* @param lower lower endpoint, must not be null
* @param upper upper endpoint, must not be null
* @return a new rectangle geometry from the specified closed range
*/
public static > Rectangle open(final N lower, final N upper) {
checkNotNull(lower);
checkNotNull(upper);
return range(Range.open(lower, upper));
}
/**
* Create and return a new rectangle geometry from the specified range.
*
* @param range range, must not be null, must not be empty, and must have lower and upper bounds
* @return a new rectangle geometry from the specified range
*/
public static > Rectangle range(final Range range) {
checkNotNull(range);
if (range.isEmpty()) {
throw new IllegalArgumentException("range must not be empty");
}
if (!range.hasLowerBound() || !range.hasUpperBound()) {
throw new IllegalArgumentException("range must have lower and upper bounds");
}
Number lowerEndpoint = range.lowerEndpoint();
BoundType lowerBoundType = range.lowerBoundType();
Number upperEndpoint = range.upperEndpoint();
BoundType upperBoundType = range.upperBoundType();
/*
Since we are representing genomic coordinate systems, the expectation is
that endpoints are instance of Integer, Long, or BigInteger; thus for open
lower and upper bounds we can safely add or substract 1.0 respectively.
Then by convention a rectangle with y1 0.0 and height of 1.0 is used.
closed(10, 20) --> (10.0, 0.0, 20.0, 1.0)
closedOpen(10, 20) --> (10.0, 0.0, 19.0, 1.0)
openClosed(10, 20) --> (11.0, 0.0, 20.0, 1.0)
open(10, 20) --> (11.0, 0.0, 19.0, 1.0);
closed(10, 11) --> (10.0, 0.0, 11.0, 1.0)
closedOpen(10, 11) --> (10.0, 0.0, 10.0, 1.0)
openClosed(10, 11) --> (11.0, 0.0, 11.0, 1.0)
open(10, 11) --> empty, throw exception
closed(10, 10) --> (10.0, 0.0, 10.0, 1.0)
closedOpen(10, 10) --> empty, throw exception
openClosed(10, 10) --> empty, throw exception
open(10, 10) --> empty, throw exception
*/
double x1 = lowerBoundType == BoundType.OPEN ? lowerEndpoint.doubleValue() + 1.0d : lowerEndpoint.doubleValue();
double y1 = 0.0d;
double x2 = upperBoundType == BoundType.OPEN ? upperEndpoint.doubleValue() - 1.0d : upperEndpoint.doubleValue();
double y2 = 1.0d;
return Geometries.rectangle(x1, y1, x2, y2);
}
}