--- /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.
+ */
+ 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 ascending.
+ */
+ 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
+ * @return true if equal
+ */
+ 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