Java tutorial
/* dsh-bio-range Guava ranges for genomics. Copyright (c) 2013-2019 held jointly by the individual authors. 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.fsf.org/licensing/licenses/lgpl.html > http://www.opensource.org/licenses/lgpl-license.php */ package org.dishevelled.bio.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. * * <pre> * import static org.dishevelled.bio.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()) { * // ... * } * </pre> * * @author Michael Heuer */ public final class RangeGeometries { /** * Private no-arg constructor. */ private RangeGeometries() { // empty } /** * Create and return a new point geometry from the specified singleton value. * * @param <N> value type * @param value singleton value, must not be null * @return a new point geometry from the specified singleton value */ public static <N extends Number & Comparable<? super N>> 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 <code>[lower..upper]</code>. * * @param <N> value type * @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 <N extends Number & Comparable<? super N>> 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 <code>[lower..upper)</code>. * * @param <N> value type * @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 <N extends Number & Comparable<? super N>> 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 <code>(lower..upper]</code> * * @param <N> value type * @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 <N extends Number & Comparable<? super N>> 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 <code>(lower..upper)</code>. * * @param <N> value type * @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 <N extends Number & Comparable<? super N>> 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 <N> value type * @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 <N extends Number & Comparable<? super N>> Rectangle range(final Range<N> 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 subtract 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); } }