+++ /dev/null
-/*
-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
-{
-
- /**
- * Compare intervals by start position ascending and end position descending.
- *
- * BIGENDIAN sorts 10-100 ahead of 10-80 (original IntervalStoreJ method
- *
- */
- static Comparator<? super IntervalI> COMPARATOR_BIGENDIAN = new Comparator<IntervalI>()
- {
- @Override
- public int compare(IntervalI o1, IntervalI o2)
- {
- int ret = Integer.signum(o1.getBegin() - o2.getBegin());
- return (ret == 0 ? Integer.signum(o2.getEnd() - o1.getEnd()) : ret);
- }
- };
-
- /**
- * Compare intervals by start position ascending and end position descending.
- *
- * LITTLEENDIAN sorts 10-100 after 10-80
- *
- */
- static Comparator<? super IntervalI> COMPARATOR_LITTLEENDIAN = new Comparator<IntervalI>()
- {
- @Override
- public int compare(IntervalI o1, IntervalI o2)
- {
- int ret = Integer.signum(o1.getBegin() - o2.getBegin());
- return (ret == 0 ? Integer.signum(o1.getEnd() - o2.getEnd()) : ret);
- }
- };
-
- /**
- * a comparator for sorting intervals by start position ascending
- */
- static Comparator<? super IntervalI> FORWARD_STRAND = new Comparator<IntervalI>()
- {
- @Override
- public int compare(IntervalI o1, IntervalI o2)
- {
- return Integer.signum(o1.getBegin() - o2.getBegin());
- }
- };
-
- /**
- * a comparator for sorting intervals by end position descending
- */
- static Comparator<? super IntervalI> REVERSE_STRAND = new Comparator<IntervalI>()
- {
- @Override
- public int compare(IntervalI o1, IntervalI o2)
- {
- return Integer.signum(o2.getEnd() - o1.getEnd());
- }
- };
-
- static int NOT_CONTAINED = Integer.MIN_VALUE;
- static int CONTAINMENT_UNKNOWN = 0;
-
- int getBegin();
- int getEnd();
-
- /**
- * Answers true if this interval contains (or matches) the given interval
- * based solely on start and end.
- *
- * @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());
- }
-
- /**
- * Slower than equalsInterval; also includes type.
- *
- * Ensure that subclasses override equals(Object). For example:
- *
- * public boolean equals(Object o) { return o != null && o instanceof XXX &&
- * equalsInterval((XXX) i); }
- *
- *
- * equalsInterval also must be overridden.
- *
- * public boolean equalsInterval(IntervalI i) {return ((SimpleFeature)i).start
- * == start && ((SimpleFeature)i).end == end && ((SimpleFeature)i).description
- * == this.description; }
- *
- *
- * @param o
- * @return true if equal, including a type check
- */
- @Override
- abstract boolean equals(Object o);
-
-
-
- /**
- * Check that two intervals are equal, in terms of end points, descriptions,
- * or any other distinguishing features.
- *
- * Used in IntervalStore in searches, since it is faster than equals(), as at
- * that point we know that we have the correct type.
- *
- * @param i
- * may be null
- * @return true if equal; null value must return false, not throw
- * NullPointerException
- */
- abstract boolean equalsInterval(IntervalI i);
-
- 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<? extends IntervalI> intervals,
- final boolean forwardStrand)
- {
- Collections.sort(intervals,
- forwardStrand ? FORWARD_STRAND : REVERSE_STRAND);
- }
-
-
-}
git://source.jalview.org / jalview.git / blobdiff