JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[jalview.git] / src / intervalstore / api / IntervalStoreI.java

diff --git a/src/intervalstore/api/IntervalStoreI.java b/src/intervalstore/api/IntervalStoreI.java
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+/*
+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.Collection;
+import java.util.List;
+
+import intervalstore.impl.NCList;
+
+public interface IntervalStoreI<T extends IntervalI> extends Collection<T>
+{
+
+  /**
+   * Returns a (possibly empty) list of items whose extent overlaps the given
+   * range
+   * 
+   * @param from
+   *          start of overlap range (inclusive)
+   * @param to
+   *          end of overlap range (inclusive)
+   * @return
+   */
+  List<T> findOverlaps(long from, long to);
+
+  /**
+   * Ensures that the IntervalStore is ready for findOverlap.
+   * 
+   * @return true iff the data held satisfy the rules of construction of an
+   *         IntervalStore.
+   * 
+   */
+  boolean isValid();
+
+  /**
+   * Answers the level of nesting of intervals in the store, as
+   * <ul>
+   * <li>0 if the store is empty</li>
+   * <li>1 if all intervals are 'top level' (non nested)</li>
+   * <li>else 1 plus the depth of the enclosed NCList</li>
+   * </ul>
+   * 
+   * @return
+   * @see NCList#getDepth()
+   */
+  int getDepth();
+
+  /**
+   * Return the number of top-level (not-contained) intervals.
+   * 
+   * @return
+   */
+  int getWidth();
+
+  List<T> findOverlaps(long start, long end, List<T> result);
+
+  String prettyPrint();
+
+  /**
+   * Resort and rebuild links.
+   * 
+   * @return
+   */
+  boolean revalidate();
+
+  IntervalI get(int i);
+
+}
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