/* BSD 3-Clause License Copyright (c) 2018, Mungo Carstairs All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ package intervalstore.api; import java.util.Collections; import java.util.Comparator; import java.util.List; public interface IntervalI { /** * a comparator for sorting intervals by start position ascending */ static Comparator FORWARD_STRAND = new Comparator() { @Override public int compare(IntervalI o1, IntervalI o2) { return Integer.compare(o1.getBegin(), o2.getBegin()); } }; /** * a comparator for sorting intervals by end position descending */ static Comparator REVERSE_STRAND = new Comparator() { @Override public int compare(IntervalI o1, IntervalI o2) { return Integer.compare(o2.getEnd(), o1.getEnd()); } }; int getBegin(); int getEnd(); /** * Answers true if this interval contains (or matches) the given interval * * @param i * @return */ default boolean containsInterval(IntervalI i) { return i != null && i.getBegin() >= getBegin() && i.getEnd() <= getEnd(); } /** * Answers true if this interval properly contains the given interval, that * is, it contains it and is larger than it * * @param i * @return */ default boolean properlyContainsInterval(IntervalI i) { return containsInterval(i) && (i.getBegin() > getBegin() || i.getEnd() < getEnd()); } default boolean equalsInterval(IntervalI i) { return i != null && i.getBegin() == getBegin() && i.getEnd() == getEnd(); } default boolean overlapsInterval(IntervalI i) { if (i == null) { return false; } if (i.getBegin() < getBegin()) { return i.getEnd() >= getBegin(); } if (i.getEnd() > getEnd()) { return i.getBegin() <= getEnd(); } return true; // i internal to this } /** * Sorts the list by start position ascending (if forwardString==true), or by * end position descending * * @param intervals * @param forwardStrand */ static void sortIntervals(List intervals, final boolean forwardStrand) { Collections.sort(intervals, forwardStrand ? FORWARD_STRAND : REVERSE_STRAND); } IntervalI getContainedBy(); void setContainedBy(IntervalI containedBy); }