urlLeafName, structExt);
// BH - switching to File object here so as to hold
- // ._bytes array directly
+ // .秘bytes array directly
File tempFile = new File(tempStructureFileStr);
UrlDownloadClient.download(file, tempFile);
public static byte[] getFileBytes(File f)
{
- return /** @j2sNative f && f._bytes || */
+ // TODO temporary doubling of 秘bytes and _bytes;
+ // just remove _bytes when new transpiler has been installed
+ return /** @j2sNative f && (f.秘bytes || f._bytes) || */
null;
}
}
@SuppressWarnings("unused")
byte[] bytes = getFileAsBytes(urlstring);
+ // TODO temporary doubling of 秘bytes and _bytes;
+ // just remove _bytes when new transpiler has been installed
/**
- * @j2sNative f._bytes = bytes;
+ * @j2sNative f.秘bytes = f._bytes = bytes;
*/
return true;
}
private boolean _highlightAnnotation = false;
private int _titleHeight;
- private Dimension _myBorder = new Dimension(0, 0);
+ private Dimension _border = new Dimension(0, 0);
private boolean _drawBBox = false;
private boolean _drawBorder = false;
public void paintComponent(Graphics g, boolean transparentBackground) {
if (_premierAffichage) {
- // _myBorder = new Dimension(0, 0);
+ // _border = new Dimension(0, 0);
_translation.x = 0;
_translation.y = (int) (-getTitleHeight() / 2.0);
_popup.buildPopupMenu();
* The new border size
*/
public void setBorderSize(Dimension b) {
- _myBorder = b;
+ _border = b;
}
/**
* @return The border size
*/
public Dimension getBorderSize() {
- return _myBorder;
+ return _border;
}
/**
* @return X-coordinate of the translation
*/
public int getLeftOffset() {
- return _myBorder.width
- + ((this.getWidth() - 2 * _myBorder.width) - this.getInnerWidth())
+ return _border.width
+ + ((this.getWidth() - 2 * _border.width) - this.getInnerWidth())
/ 2 + _translation.x;
}
*/
public int getInnerWidth() {
// Largeur du dessin
- return (int) Math.round((this.getWidth() - 2 * _myBorder.width)
+ return (int) Math.round((this.getWidth() - 2 * _border.width)
* _conf._zoom);
}
* @return Y-coordinate of the translation
*/
public int getTopOffset() {
- return _myBorder.height
- + ((this.getHeight() - 2 * _myBorder.height) - this
+ return _border.height
+ + ((this.getHeight() - 2 * _border.height) - this
.getInnerHeight()) / 2 + _translation.y;
}
public int getInnerHeight() {
// Hauteur du dessin
return (int) Math.round((this.getHeight()) * _conf._zoom - 2
- * _myBorder.height - getTitleHeight());
+ * _border.height - getTitleHeight());
}
/**
--- /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
+{
+ /**
+ * 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.compare(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.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<? extends IntervalI> intervals,
+ final boolean forwardStrand)
+ {
+ Collections.sort(intervals,
+ forwardStrand ? FORWARD_STRAND : REVERSE_STRAND);
+ }
+}
--- /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.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);
+
+ /**
+ * Returns a string representation of the data where containment is shown by
+ * indentation on new lines
+ *
+ * @return
+ */
+ String prettyPrint();
+
+ /**
+ * Answers true if the data held satisfy the rules of construction of an
+ * IntervalStore, else false.
+ *
+ * @return
+ */
+ 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();
+
+}
\ No newline at end of file
--- /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.impl;
+
+import java.util.List;
+import java.util.function.Function;
+
+/**
+ * Provides a method to perform binary search of an ordered list for the first
+ * entry that satisfies a supplied condition
+ *
+ * @author gmcarstairs
+ */
+public final class BinarySearcher
+{
+ private BinarySearcher()
+ {
+ }
+
+ /**
+ * Performs a binary search of the list to find the index of the first entry
+ * for which the test returns true. Answers the length of the list if there is
+ * no such entry.
+ * <p>
+ * For correct behaviour, the provided list must be ordered consistent with
+ * the test, that is, any entries returning false must precede any entries
+ * returning true. Note that this means that this method is <em>not</em>
+ * usable to search for equality (to find a specific entry), as all unequal
+ * entries will answer false to the test. To do that, use
+ * <code>Collections.binarySearch</code> instead.
+ *
+ * @param list
+ * @param test
+ * @return
+ * @see java.util.Collections#binarySearch(List, Object)
+ */
+ public static <T> int findFirst(List<? extends T> list,
+ Function<T, Boolean> test)
+ {
+ int start = 0;
+ int end = list.size() - 1;
+ int matched = list.size();
+
+ while (start <= end)
+ {
+ int mid = (start + end) / 2;
+ T entry = list.get(mid);
+ boolean itsTrue = test.apply(entry);
+ if (itsTrue)
+ {
+ matched = mid;
+ end = mid - 1;
+ }
+ else
+ {
+ start = mid + 1;
+ }
+ }
+
+ return matched;
+ }
+}
--- /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.impl;
+
+import java.util.AbstractCollection;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.NoSuchElementException;
+
+import intervalstore.api.IntervalI;
+import intervalstore.api.IntervalStoreI;
+
+/**
+ * A collection class to store interval-associated data, with O(log N)
+ * performance for overlap queries, insertion and deletion (where N is the size
+ * of the store). Accepts duplicate entries but not null values.
+ *
+ * @author gmcarstairs
+ *
+ * @param <T>
+ * any type providing <code>getBegin()</code> and <code>getEnd()</code>
+ */
+public class IntervalStore<T extends IntervalI>
+ extends AbstractCollection<T> implements IntervalStoreI<T>
+{
+ /**
+ * An iterator over the intervals held in this store, with no particular
+ * ordering guaranteed. The iterator does not support the optional
+ * <code>remove</code> operation (throws
+ * <code>UnsupportedOperationException</code> if attempted).
+ *
+ * @author gmcarstairs
+ *
+ * @param <V>
+ */
+ private class IntervalIterator<V extends IntervalI> implements Iterator<V>
+ {
+ /*
+ * iterator over top level non-nested intervals
+ */
+ Iterator<? extends IntervalI> topLevelIterator;
+
+ /*
+ * iterator over NCList (if any)
+ */
+ Iterator<? extends IntervalI> nestedIterator;
+
+ /**
+ * Constructor initialises iterators over the top level list and any nested
+ * NCList
+ *
+ * @param intervalStore
+ */
+ public IntervalIterator(
+ IntervalStore<? extends IntervalI> intervalStore)
+ {
+ topLevelIterator = nonNested.iterator();
+ if (nested != null)
+ {
+ nestedIterator = nested.iterator();
+ }
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return topLevelIterator.hasNext() ? true
+ : (nestedIterator != null && nestedIterator.hasNext());
+ }
+
+ @Override
+ public V next()
+ {
+ if (topLevelIterator.hasNext())
+ {
+ return (V) topLevelIterator.next();
+ }
+ if (nestedIterator != null)
+ {
+ return (V) nestedIterator.next();
+ }
+ throw new NoSuchElementException();
+ }
+
+ }
+
+ private List<T> nonNested;
+
+ private NCList<T> nested;
+
+ /**
+ * Constructor
+ */
+ public IntervalStore()
+ {
+ nonNested = new ArrayList<>();
+ }
+
+ /**
+ * Constructor given a list of intervals. Note that the list may get sorted as
+ * a side-effect of calling this constructor.
+ */
+ public IntervalStore(List<T> intervals)
+ {
+ this();
+
+ /*
+ * partition into subranges whose root intervals
+ * have no mutual containment (if no intervals are nested,
+ * each subrange is of length 1 i.e. a single interval)
+ */
+ List<IntervalI> sublists = new NCListBuilder<T>()
+ .partitionNestedSublists(intervals);
+
+ /*
+ * add all 'subrange root intervals' (and any co-located intervals)
+ * to our top level list of 'non-nested' intervals;
+ * put aside any left over for our NCList
+ */
+ List<T> nested = new ArrayList<>();
+
+ for (IntervalI subrange : sublists)
+ {
+ int listIndex = subrange.getBegin();
+ IntervalI root = intervals.get(listIndex);
+ while (listIndex <= subrange.getEnd())
+ {
+ T t = intervals.get(listIndex);
+ if (root.equalsInterval(t))
+ {
+ nonNested.add(t);
+ }
+ else
+ {
+ nested.add(t);
+ }
+ listIndex++;
+ }
+ }
+
+ if (!nested.isEmpty())
+ {
+ this.nested = new NCList<>(nested);
+ }
+ }
+
+ /**
+ * Adds one interval to the store.
+ *
+ * @param interval
+ */
+ @Override
+ public boolean add(T interval)
+ {
+ if (interval == null)
+ {
+ return false;
+ }
+ if (!addNonNestedInterval(interval))
+ {
+ /*
+ * detected a nested interval - put it in the NCList structure
+ */
+ addNestedInterval(interval);
+ }
+ return true;
+ }
+
+ @Override
+ public boolean contains(Object entry)
+ {
+ if (listContains(nonNested, entry))
+ {
+ return true;
+ }
+
+ return nested == null ? false : nested.contains(entry);
+ }
+
+ protected boolean addNonNestedInterval(T entry)
+ {
+ synchronized (nonNested)
+ {
+ /*
+ * find the first stored interval which doesn't precede the new one
+ */
+ int insertPosition = BinarySearcher.findFirst(nonNested,
+ val -> val.getBegin() >= entry.getBegin());
+ /*
+ * fail if we detect interval enclosure
+ * - of the new interval by the one before or after it
+ * - of the next interval by the new one
+ */
+ if (insertPosition > 0)
+ {
+ if (nonNested.get(insertPosition - 1).properlyContainsInterval(entry))
+ {
+ return false;
+ }
+ }
+ if (insertPosition < nonNested.size())
+ {
+ T following = nonNested.get(insertPosition);
+ if (entry.properlyContainsInterval(following)
+ || following.properlyContainsInterval(entry))
+ {
+ return false;
+ }
+ }
+
+ /*
+ * checks passed - add the interval
+ */
+ nonNested.add(insertPosition, entry);
+
+ return true;
+ }
+ }
+
+ @Override
+ public List<T> findOverlaps(long from, long to)
+ {
+ List<T> result = new ArrayList<>();
+
+ findNonNestedOverlaps(from, to, result);
+
+ if (nested != null)
+ {
+ result.addAll(nested.findOverlaps(from, to));
+ }
+
+ return result;
+ }
+
+ @Override
+ public String prettyPrint()
+ {
+ String pp = nonNested.toString();
+ if (nested != null)
+ {
+ pp += System.lineSeparator() + nested.prettyPrint();
+ }
+ return pp;
+ }
+
+ @Override
+ public boolean isValid()
+ {
+ for (int i = 0; i < nonNested.size() - 1; i++)
+ {
+ IntervalI i1 = nonNested.get(i);
+ IntervalI i2 = nonNested.get(i + 1);
+
+ if (i2.getBegin() < i1.getBegin())
+ {
+ System.err.println("nonNested wrong start order : " + i1.toString()
+ + ", " + i2.toString());
+ return false;
+ }
+ if (i1.properlyContainsInterval(i2)
+ || i2.properlyContainsInterval(i1))
+ {
+ System.err.println("nonNested invalid containment!: "
+ + i1.toString()
+ + ", " + i2.toString());
+ return false;
+ }
+ }
+ return nested == null ? true : nested.isValid();
+ }
+
+ @Override
+ public int size()
+ {
+ int i = nonNested.size();
+ if (nested != null)
+ {
+ i += nested.size();
+ }
+ return i;
+ }
+
+ @Override
+ public synchronized boolean remove(Object o)
+ {
+ if (o == null)
+ {
+ return false;
+ }
+ try
+ {
+ @SuppressWarnings("unchecked")
+ T entry = (T) o;
+
+ /*
+ * try the non-nested positional intervals first
+ */
+ boolean removed = removeNonNested(entry);
+
+ /*
+ * if not found, try nested intervals
+ */
+ if (!removed && nested != null)
+ {
+ removed = nested.remove(entry);
+ }
+
+ return removed;
+ } catch (ClassCastException e)
+ {
+ return false;
+ }
+ }
+
+ /**
+ * Removes the given entry from the list of non-nested entries, returning true
+ * if found and removed, or false if not found. Specifically, removes the
+ * first item in the list for which <code>item.equals(entry)</code>.
+ *
+ * @param entry
+ * @return
+ */
+ protected boolean removeNonNested(T entry)
+ {
+ /*
+ * find the first interval that might match, i.e. whose
+ * start position is not less than the target range start
+ * (NB inequality test ensures the first match if any is found)
+ */
+ int startIndex = BinarySearcher.findFirst(nonNested,
+ val -> val.getBegin() >= entry.getBegin());
+
+ /*
+ * traverse intervals to look for a match
+ */
+ int from = entry.getBegin();
+ int i = startIndex;
+ int size = nonNested.size();
+ while (i < size)
+ {
+ T sf = nonNested.get(i);
+ if (sf.getBegin() > from)
+ {
+ break;
+ }
+ if (sf.equals(entry))
+ {
+ nonNested.remove(i);
+ return true;
+ }
+ i++;
+ }
+ return false;
+ }
+
+ @Override
+ public int getDepth()
+ {
+ if (size() == 0)
+ {
+ return 0;
+ }
+ return (nonNested.isEmpty() ? 0 : 1)
+ + (nested == null ? 0 : nested.getDepth());
+ }
+
+ /**
+ * Adds one interval to the NCList that can manage nested intervals (creating
+ * the NCList if necessary)
+ */
+ protected synchronized void addNestedInterval(T interval)
+ {
+ if (nested == null)
+ {
+ nested = new NCList<>();
+ }
+ nested.add(interval);
+ }
+
+ /**
+ * Answers true if the list contains the interval, else false. This method is
+ * optimised for the condition that the list is sorted on interval start
+ * position ascending, and will give unreliable results if this does not hold.
+ *
+ * @param intervals
+ * @param entry
+ * @return
+ */
+ protected boolean listContains(List<T> intervals, Object entry)
+ {
+ if (intervals == null || entry == null || !(entry instanceof IntervalI))
+ {
+ return false;
+ }
+
+ IntervalI interval = (IntervalI) entry;
+
+ /*
+ * locate the first entry in the list which does not precede the interval
+ */
+ int pos = BinarySearcher.findFirst(intervals,
+ val -> val.getBegin() >= interval.getBegin());
+ int len = intervals.size();
+ while (pos < len)
+ {
+ T sf = intervals.get(pos);
+ if (sf.getBegin() > interval.getBegin())
+ {
+ return false; // no match found
+ }
+ if (sf.equals(interval))
+ {
+ return true;
+ }
+ pos++;
+ }
+ return false;
+ }
+
+ /**
+ * Answers an iterator over the intervals in the store, with no particular
+ * ordering guaranteed. The iterator does not support the optional
+ * <code>remove</code> operation (throws
+ * <code>UnsupportedOperationException</code> if attempted).
+ */
+ @Override
+ public Iterator<T> iterator()
+ {
+ return new IntervalIterator<>(this);
+ }
+
+ @Override
+ public void clear()
+ {
+ this.nonNested.clear();
+ this.nested = new NCList<>();
+ }
+
+ /**
+ * Adds non-nested intervals to the result list that lie within the target
+ * range
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ protected void findNonNestedOverlaps(long from, long to,
+ List<T> result)
+ {
+ /*
+ * find the first interval whose end position is
+ * after the target range start
+ */
+ int startIndex = BinarySearcher.findFirst(nonNested,
+ val -> val.getEnd() >= from);
+
+ final int startIndex1 = startIndex;
+ int i = startIndex1;
+ while (i < nonNested.size())
+ {
+ T sf = nonNested.get(i);
+ if (sf.getBegin() > to)
+ {
+ break;
+ }
+ if (sf.getBegin() <= to && sf.getEnd() >= from)
+ {
+ result.add(sf);
+ }
+ i++;
+ }
+ }
+
+ @Override
+ public String toString()
+ {
+ String s = nonNested.toString();
+ if (nested != null)
+ {
+ s = s + System.lineSeparator() + nested.toString();
+ }
+ return s;
+ }
+}
--- /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.impl;
+
+import java.util.AbstractCollection;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.NoSuchElementException;
+
+import intervalstore.api.IntervalI;
+
+/**
+ * An adapted implementation of NCList as described in the paper
+ *
+ * <pre>
+ * Nested Containment List (NCList): a new algorithm for accelerating
+ * interval query of genome alignment and interval databases
+ * - Alexander V. Alekseyenko, Christopher J. Lee
+ * https://doi.org/10.1093/bioinformatics/btl647
+ * </pre>
+ */
+public class NCList<T extends IntervalI> extends AbstractCollection<T>
+{
+ /**
+ * A depth-first iterator over the elements stored in the NCList
+ */
+ private class NCListIterator implements Iterator<T>
+ {
+ int subrangeIndex;
+
+ Iterator<T> nodeIterator;
+
+ /**
+ * Constructor bootstraps a pointer to an iterator over the first subrange
+ * (if any)
+ */
+ NCListIterator()
+ {
+ subrangeIndex = nextSubrange(-1);
+ }
+
+ /**
+ * Moves the subrange iterator to the next subrange, and answers its index
+ * in the list of subranges. If there are no more, sets the iterator to null
+ * and answers -1.
+ *
+ * @return
+ */
+ private int nextSubrange(int after)
+ {
+ int nextIndex = after + 1;
+ if (nextIndex < subranges.size())
+ {
+ nodeIterator = subranges.get(nextIndex).iterator();
+ return nextIndex;
+ }
+ nodeIterator = null;
+ return -1;
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return nodeIterator != null && nodeIterator.hasNext();
+ }
+
+ /**
+ * Answers the next element returned by the current NCNode's iterator, and
+ * advances the iterator (to the next NCNode if necessary)
+ */
+ @Override
+ public T next()
+ {
+ if (nodeIterator == null || !nodeIterator.hasNext())
+ {
+ throw new NoSuchElementException();
+ }
+ T result = nodeIterator.next();
+
+ if (!nodeIterator.hasNext())
+ {
+ subrangeIndex = nextSubrange(subrangeIndex);
+ }
+ return result;
+ }
+
+ }
+
+ /*
+ * the number of interval instances represented
+ */
+ private int size;
+
+ /*
+ * a list, in start position order, of sublists of ranges ordered so
+ * that each contains (or is the same as) the one that follows it
+ */
+ private List<NCNode<T>> subranges;
+
+ /**
+ * Constructor given a list of things that are each located on a contiguous
+ * interval. Note that the constructor may reorder the list.
+ * <p>
+ * We assume here that for each range, start <= end. Behaviour for reverse
+ * ordered ranges is undefined.
+ *
+ * @param ranges
+ */
+ public NCList(List<T> ranges)
+ {
+ this();
+ build(ranges);
+ }
+
+ /**
+ * Sorts and groups ranges into sublists where each sublist represents an
+ * interval and its contained subintervals
+ *
+ * @param ranges
+ */
+ protected void build(List<T> ranges)
+ {
+ /*
+ * sort and partition into subranges
+ * which have no mutual containment
+ */
+ List<IntervalI> sublists = partitionNestedSublists(ranges);
+
+ /*
+ * convert each subrange to an NCNode consisting of a range and
+ * (possibly) its contained NCList
+ */
+ for (IntervalI sublist : sublists)
+ {
+ subranges.add(new NCNode<>(
+ ranges.subList(sublist.getBegin(), sublist.getEnd() + 1)));
+ }
+
+ size = ranges.size();
+ }
+
+ /**
+ * Default constructor
+ */
+ public NCList()
+ {
+ subranges = new ArrayList<>();
+ }
+
+ /**
+ * Sorts and traverses the ranges to identify sublists, whose start intervals
+ * are overlapping or disjoint but not mutually contained. Answers a list of
+ * start-end indices of the sorted list of ranges.
+ *
+ * @param ranges
+ * @return
+ */
+ protected List<IntervalI> partitionNestedSublists(List<T> ranges)
+ {
+ List<IntervalI> sublists = new ArrayList<>();
+
+ if (ranges.isEmpty())
+ {
+ return sublists;
+ }
+
+ /*
+ * sort by start ascending, length descending, so that
+ * contained intervals follow their containing interval
+ */
+ Collections.sort(ranges, new NCListBuilder<>().getComparator());
+
+ int listStartIndex = 0;
+
+ IntervalI lastParent = ranges.get(0);
+ boolean first = true;
+
+ for (int i = 0; i < ranges.size(); i++)
+ {
+ IntervalI nextInterval = ranges.get(i);
+ if (!first && !lastParent.properlyContainsInterval(nextInterval))
+ {
+ /*
+ * this interval is not properly contained in the parent;
+ * close off the last sublist
+ */
+ sublists.add(new Range(listStartIndex, i - 1));
+ listStartIndex = i;
+ lastParent = nextInterval;
+ }
+ first = false;
+ }
+
+ sublists.add(new Range(listStartIndex, ranges.size() - 1));
+ return sublists;
+ }
+
+ /**
+ * Adds one entry to the stored set
+ *
+ * @param entry
+ */
+ @Override
+ public synchronized boolean add(final T entry)
+ {
+ final NCNode<T> newNode = new NCNode<>(entry);
+ addNode(newNode);
+ return true;
+ }
+
+ /**
+ * Adds one NCNode to this NCList
+ * <p>
+ * This method does not update the <code>size</code> (interval count) of this
+ * NCList, as it may be used to rearrange nodes without changing their count.
+ * Callers should increment the count if needed.
+ *
+ * @param newNode
+ */
+ protected void addNode(final NCNode<T> newNode)
+ {
+ final long start = newNode.getBegin();
+ final long end = newNode.getEnd();
+ size += newNode.size();
+
+ /*
+ * cases:
+ * 1) precedes all subranges - add as NCNode on front of list
+ * 2) follows all subranges - add as NCNode on end of list
+ * 3) matches a subrange - add as a sibling in the list
+ * 4) properly enclosed by a subrange - add recursively to subrange
+ * 5) properly encloses one or more subranges - push them inside it
+ * 6) spans two subranges - insert between them
+ */
+
+ /*
+ * find the first subrange whose end does not precede entry's start
+ */
+ int candidateIndex = findFirstOverlap(start);
+
+ /*
+ * search for maximal span of subranges i-k that the new entry
+ * encloses; or a subrange that encloses the new entry
+ */
+ boolean enclosing = false;
+ int firstEnclosed = 0;
+ int lastEnclosed = 0;
+
+ for (int j = candidateIndex; j < subranges.size(); j++)
+ {
+ NCNode<T> subrange = subranges.get(j);
+
+ if (subrange.equalsInterval(newNode))
+ {
+ /*
+ * matching interval - insert adjacent
+ */
+ subranges.add(j, newNode);
+ return;
+ }
+
+ if (end < subrange.getBegin() && !enclosing)
+ {
+ /*
+ * new entry lies between subranges j-1 j
+ */
+ subranges.add(j, newNode);
+ return;
+ }
+
+ if (subrange.properlyContainsInterval(newNode))
+ {
+ /*
+ * push new entry inside this subrange as it encloses it
+ */
+ subrange.addNode(newNode);
+ return;
+ }
+
+ if (start <= subrange.getBegin())
+ {
+ if (end >= subrange.getEnd())
+ {
+ /*
+ * new entry encloses this subrange (and possibly preceding ones);
+ * continue to find the maximal list it encloses
+ */
+ if (!enclosing)
+ {
+ firstEnclosed = j;
+ }
+ lastEnclosed = j;
+ enclosing = true;
+ continue;
+ }
+ else
+ {
+ /*
+ * entry spans from before this subrange to inside it
+ */
+ if (enclosing)
+ {
+ /*
+ * entry encloses one or more preceding subranges
+ */
+ push(newNode, firstEnclosed, lastEnclosed);
+ }
+ else
+ {
+ /*
+ * entry overlaps two subranges but doesn't enclose either
+ * so just add it
+ */
+ subranges.add(j, newNode);
+ }
+ return;
+ }
+ }
+ }
+
+ /*
+ * drops through to here if new range encloses all others
+ * or overlaps the last one
+ */
+ if (enclosing)
+ {
+ push(newNode, firstEnclosed, lastEnclosed);
+ }
+ else
+ {
+ subranges.add(newNode);
+ }
+ }
+
+ @Override
+ public boolean contains(Object entry)
+ {
+ if (!(entry instanceof IntervalI))
+ {
+ return false;
+ }
+ IntervalI interval = (IntervalI) entry;
+
+ /*
+ * find the first sublist that might overlap, i.e.
+ * the first whose end position is >= from
+ */
+ int candidateIndex = findFirstOverlap(interval.getBegin());
+
+ int to = interval.getEnd();
+
+ for (int i = candidateIndex; i < subranges.size(); i++)
+ {
+ NCNode<T> candidate = subranges.get(i);
+ if (candidate.getBegin() > to)
+ {
+ /*
+ * we are past the end of our target range
+ */
+ break;
+ }
+ if (candidate.contains(interval))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Update the tree so that the new node encloses current subranges i to j
+ * (inclusive). That is, replace subranges i-j (inclusive) with a new subrange
+ * that contains them.
+ *
+ * @param node
+ * @param i
+ * @param j
+ * @throws IllegalArgumentException
+ * if any of the subranges is not contained by the node's start-end
+ * range
+ */
+ protected synchronized void push(NCNode<T> node, final int i,
+ final int j)
+ {
+ for (int k = i; k <= j; k++)
+ {
+ NCNode<T> n = subranges.get(k);
+ if (!node.containsInterval(n)) {
+ throw new IllegalArgumentException("Can't push " + n.toString()
+ + " inside " + node.toString());
+ }
+ node.addNode(n);
+ }
+
+ for (int k = j; k >= i; k--)
+ {
+ subranges.remove(k);
+ }
+ subranges.add(i, node);
+ }
+
+ /**
+ * Answers a list of contained intervals that overlap the given range
+ *
+ * @param from
+ * @param to
+ * @return
+ */
+ public List<T> findOverlaps(long from, long to)
+ {
+ List<T> result = new ArrayList<>();
+
+ findOverlaps(from, to, result);
+
+ return result;
+ }
+
+ /**
+ * Recursively searches the NCList adding any items that overlap the from-to
+ * range to the result list
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ protected void findOverlaps(long from, long to, List<T> result)
+ {
+ /*
+ * find the first sublist that might overlap, i.e.
+ * the first whose end position is >= from
+ */
+ int candidateIndex = findFirstOverlap(from);
+
+ for (int i = candidateIndex; i < subranges.size(); i++)
+ {
+ NCNode<T> candidate = subranges.get(i);
+ if (candidate.getBegin() > to)
+ {
+ /*
+ * we are past the end of our target range
+ */
+ break;
+ }
+ candidate.findOverlaps(from, to, result);
+ }
+
+ }
+
+ /**
+ * Search subranges for the first one whose end position is not before the
+ * target range's start position, i.e. the first one that may overlap the
+ * target range. Returns the index in the list of the first such range found,
+ * or the length of the list if none found.
+ *
+ * @param from
+ * @return
+ */
+ protected int findFirstOverlap(final long from)
+ {
+ return BinarySearcher.findFirst(subranges,
+ val -> val.getEnd() >= from);
+ }
+
+ /**
+ * Formats the tree as a bracketed list e.g.
+ *
+ * <pre>
+ * [1-100 [10-30 [10-20]], 15-30 [20-20]]
+ * </pre>
+ */
+ @Override
+ public String toString()
+ {
+ return subranges.toString();
+ }
+
+ /**
+ * Answers the NCList as an indented list
+ *
+ * @return
+ */
+ public String prettyPrint()
+ {
+ StringBuilder sb = new StringBuilder(512);
+ int offset = 0;
+ int indent = 2;
+ prettyPrint(sb, offset, indent);
+ sb.append(System.lineSeparator());
+ return sb.toString();
+ }
+
+ /**
+ * @param sb
+ * @param offset
+ * @param indent
+ */
+ void prettyPrint(StringBuilder sb, int offset, int indent)
+ {
+ boolean first = true;
+ for (NCNode<T> subrange : subranges)
+ {
+ if (!first)
+ {
+ sb.append(System.lineSeparator());
+ }
+ first = false;
+ subrange.prettyPrint(sb, offset, indent);
+ }
+ }
+
+ /**
+ * Answers true if the store's structure is valid (nesting containment rules
+ * are obeyed), else false. For use in testing and debugging.
+ *
+ * @return
+ */
+ public boolean isValid()
+ {
+ int count = 0;
+ for (NCNode<T> subrange : subranges)
+ {
+ count += subrange.size();
+ }
+ if (count != size)
+ {
+ return false;
+ }
+ return isValid(Integer.MIN_VALUE, Integer.MAX_VALUE);
+ }
+
+ /**
+ * Answers true if the data held satisfy the rules of construction of an
+ * NCList bounded within the given start-end range, else false.
+ * <p>
+ * Each subrange must lie within start-end (inclusive). Subranges must be
+ * ordered by start position ascending, and within that by end position
+ * descending.
+ * <p>
+ *
+ * @param start
+ * @param end
+ * @return
+ */
+ boolean isValid(final int start, final int end)
+ {
+ NCNode<T> lastRange = null;
+
+ for (NCNode<T> subrange : subranges)
+ {
+ if (subrange.getBegin() < start)
+ {
+ System.err.println("error in NCList: range " + subrange.toString()
+ + " starts before " + end);
+ return false;
+ }
+ if (subrange.getEnd() > end)
+ {
+ System.err.println("error in NCList: range " + subrange.toString()
+ + " ends after " + end);
+ return false;
+ }
+
+ if (lastRange != null)
+ {
+ if (subrange.getBegin() < lastRange.getBegin())
+ {
+ System.err.println("error in NCList: range " + subrange.toString()
+ + " starts before " + lastRange.toString());
+ return false;
+ }
+ if (subrange.properlyContainsInterval(lastRange))
+ {
+ System.err.println("error in NCList: range " + subrange.toString()
+ + " encloses preceding: " + lastRange.toString());
+ return false;
+ }
+ if (lastRange.properlyContainsInterval(subrange))
+ {
+ System.err.println("error in NCList: range " + subrange.toString()
+ + " enclosed by preceding: " + lastRange.toString());
+ return false;
+ }
+ }
+ lastRange = subrange;
+
+ if (!subrange.isValid())
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Answers the number of intervals stored
+ *
+ * @return
+ */
+ @Override
+ public int size()
+ {
+ return size;
+ }
+
+ /**
+ * Answers a list of all entries stored, in no guaranteed order. This method
+ * is not synchronized, so is not thread-safe.
+ */
+ public List<T> getEntries()
+ {
+ List<T> result = new ArrayList<>();
+ getEntries(result);
+ return result;
+ }
+
+ /**
+ * Adds all contained entries to the given list
+ *
+ * @param result
+ */
+ void getEntries(List<T> result)
+ {
+ for (NCNode<T> subrange : subranges)
+ {
+ subrange.getEntries(result);
+ }
+ }
+
+ /**
+ * Removes the first interval <code>I</code>found that is equal to T
+ * (<code>I.equals(T)</code>). Answers true if an interval is removed, false
+ * if no match is found. This method is synchronized so thread-safe.
+ *
+ * @param entry
+ * @return
+ */
+ public synchronized boolean remove(T entry)
+ {
+ if (entry == null)
+ {
+ return false;
+ }
+ int i = findFirstOverlap(entry.getBegin());
+
+ for (; i < subranges.size(); i++)
+ {
+ NCNode<T> subrange = subranges.get(i);
+ if (subrange.getBegin() > entry.getBegin())
+ {
+ /*
+ * not found
+ */
+ return false;
+ }
+ NCList<T> subRegions = subrange.getSubRegions();
+
+ if (subrange.getRegion().equals(entry))
+ {
+ /*
+ * if the subrange is rooted on this entry, remove it,
+ * and remove and promote its subregions (if any)
+ */
+ subranges.remove(i);
+ size -= subrange.size();
+ if (subRegions != null)
+ {
+ for (NCNode<T> r : subRegions.subranges)
+ {
+ addNode(r);
+ }
+ }
+ return true;
+ }
+ else
+ {
+ if (subrange.remove(entry))
+ {
+ size--;
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Answers the depth of interval nesting of this object, where 1 means there
+ * are no nested sub-intervals
+ *
+ * @return
+ */
+ public int getDepth()
+ {
+ int subDepth = 0;
+ for (NCNode<T> subrange : subranges)
+ {
+ subDepth = Math.max(subDepth, subrange.getDepth());
+ }
+
+ return subDepth;
+ }
+
+ /**
+ * Answers an iterator over the contained intervals, with no particular order
+ * guaranteed. The iterator does not support the optional <code>remove</code>
+ * operation (throws <code>UnsupportedOperationException</code> if attempted).
+ */
+ @Override
+ public Iterator<T> iterator()
+ {
+ return new NCListIterator();
+ }
+
+ @Override
+ public synchronized void clear()
+ {
+ subranges.clear();
+ size = 0;
+ }
+}
--- /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.impl;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import intervalstore.api.IntervalI;
+
+/**
+ * A comparator that orders ranges by either start position ascending. If
+ * position matches, ordering is by length descending. This provides the
+ * canonical ordering of intervals into subranges in order to build a nested
+ * containment list.
+ *
+ * @author gmcarstairs
+ */
+public class NCListBuilder<T extends IntervalI>
+{
+ class NCListComparator<V extends IntervalI> implements Comparator<V>
+ {
+ /**
+ * Compares two intervals in a way that will sort a list by start position
+ * ascending, then by length descending. Answers
+ * <ul>
+ * <li>a negative value if o1.begin < o2.begin</li>
+ * <li>else a positive value if o1.begin > o2.begin</li>
+ * <li>else a negative value if o1.end > o2.end</li>
+ * <li>else a positive value of o1.end < o2.end</li>
+ * <li>else zero</li
+ * </ul>
+ */
+ @Override
+ public int compare(V o1, V o2)
+ {
+ int order = Integer.compare(o1.getBegin(), o2.getBegin());
+ if (order == 0)
+ {
+ /*
+ * if tied on start position, longer length sorts to left
+ * i.e. the negation of normal ordering by length
+ */
+ order = Integer.compare(o2.getEnd(), o1.getEnd());
+ }
+ return order;
+ }
+ }
+
+ private Comparator<T> comparator = new NCListComparator<>();
+
+ /**
+ * Default constructor
+ */
+ public NCListBuilder()
+ {
+ }
+
+ /**
+ * Answers a comparator which sorts items of type T by start position
+ * ascending, and within that by end position (length) descending)
+ *
+ * @return
+ */
+ Comparator<T> getComparator()
+ {
+ return comparator;
+ }
+
+ /**
+ * Sorts and traverses the ranges to identify sublists, whose start intervals
+ * are overlapping or disjoint but not mutually contained. Answers a list of
+ * start-end indices of the sorted list of ranges.
+ *
+ * @param ranges
+ * @return
+ */
+ List<IntervalI> partitionNestedSublists(List<T> ranges)
+ {
+ List<IntervalI> sublists = new ArrayList<>();
+
+ /*
+ * sort by start ascending, length descending, so that
+ * contained intervals follow their containing interval
+ */
+ Collections.sort(ranges, comparator);
+
+ int listStartIndex = 0;
+
+ IntervalI lastParent = ranges.get(0);
+ boolean first = true;
+
+ for (int i = 0; i < ranges.size(); i++)
+ {
+ IntervalI nextInterval = ranges.get(i);
+ if (!first && !lastParent.properlyContainsInterval(nextInterval))
+ {
+ /*
+ * this interval is not properly contained in the parent;
+ * close off the last sublist
+ */
+ sublists.add(new Range(listStartIndex, i - 1));
+ listStartIndex = i;
+ lastParent = nextInterval;
+ }
+ first = false;
+ }
+
+ sublists.add(new Range(listStartIndex, ranges.size() - 1));
+ return sublists;
+ }
+}
--- /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.impl;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.NoSuchElementException;
+
+import intervalstore.api.IntervalI;
+
+/**
+ * Each node of the NCList tree consists of a range, and (optionally) the NCList
+ * of ranges it encloses
+ *
+ * @param <T>
+ */
+class NCNode<T extends IntervalI> implements IntervalI
+{
+ /**
+ * A depth-first iterator over the intervals stored in the NCNode. The
+ * optional <code>remove</code> operation is not supported.
+ *
+ * @author gmcarstairs
+ *
+ */
+ private class NCNodeIterator implements Iterator<T>
+ {
+ boolean first = true;
+ Iterator<T> subregionIterator;
+
+ @Override
+ public boolean hasNext()
+ {
+ return first
+ || (subregionIterator != null && subregionIterator.hasNext());
+ }
+
+ /**
+ * Answers the next interval - initially the top level interval for this
+ * node, thereafter the intervals returned by the NCList's iterator
+ */
+ @Override
+ public T next()
+ {
+ if (first)
+ {
+ subregionIterator = subregions == null ? null
+ : subregions.iterator();
+ first = false;
+ return region;
+ }
+ if (subregionIterator == null || !subregionIterator.hasNext())
+ {
+ throw new NoSuchElementException();
+ }
+ return subregionIterator.next();
+ }
+ }
+
+ private T region;
+
+ /*
+ * null, or an object holding contained subregions of this nodes region
+ */
+ private NCList<T> subregions;
+
+ /**
+ * Constructor given a list of ranges. The list not be empty, and should be
+ * ordered so that the first range contains all the others. If not, behaviour
+ * will likely be invalid.
+ *
+ * @param ranges
+ * @throws IllegalArgumentException
+ * if the list is empty
+ */
+ NCNode(List<T> ranges)
+ {
+ if (ranges.isEmpty())
+ {
+ throw new IllegalArgumentException("List may not be empty");
+ }
+ region = ranges.get(0);
+
+ if (ranges.size() > 1)
+ {
+ subregions = new NCList<>(ranges.subList(1, ranges.size()));
+ }
+ }
+
+ /**
+ * Constructor given a single range
+ *
+ * @param range
+ */
+ NCNode(T range)
+ {
+ region = range;
+ }
+
+ @Override
+ public int getBegin()
+ {
+ return region.getBegin();
+ }
+
+ @Override
+ public int getEnd()
+ {
+ return region.getEnd();
+ }
+
+ /**
+ * Formats the node as a bracketed list e.g.
+ *
+ * <pre>
+ * [1-100 [10-30 [10-20]], 15-30 [20-20]]
+ * </pre>
+ *
+ * where the format for each interval is as given by <code>T.toString()</code>
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder(10 * size());
+ sb.append(region.toString());
+ if (subregions != null)
+ {
+ sb.append(" ").append(subregions.toString());
+ }
+ return sb.toString();
+ }
+
+ void prettyPrint(StringBuilder sb, int offset, int indent)
+ {
+ for (int i = 0; i < offset; i++)
+ {
+ sb.append(" ");
+ }
+ sb.append(region.toString());
+ if (subregions != null)
+ {
+ sb.append(System.lineSeparator());
+ subregions.prettyPrint(sb, offset + 2, indent);
+ }
+ }
+
+ /**
+ * Add any ranges that overlap the from-to range to the result list
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ void findOverlaps(long from, long to, List<T> result)
+ {
+ if (region.getBegin() <= to && region.getEnd() >= from)
+ {
+ result.add(region);
+ if (subregions != null)
+ {
+ subregions.findOverlaps(from, to, result);
+ }
+ }
+ }
+
+ /**
+ * Add one node to this node's subregions.
+ *
+ * @param entry
+ * @throws IllegalArgumentException
+ * if the added node is not contained by the node's start-end range
+ */
+ synchronized void addNode(NCNode<T> entry)
+ {
+ if (!region.containsInterval(entry))
+ {
+ throw new IllegalArgumentException(
+ String.format("adding improper subrange %d-%d to range %d-%d",
+ entry.getBegin(), entry.getEnd(), region.getBegin(),
+ region.getEnd()));
+ }
+ if (subregions == null)
+ {
+ subregions = new NCList<>();
+ }
+
+ subregions.addNode(entry);
+ }
+
+ /**
+ * Answers true if the data held satisfy the rules of construction of an
+ * NCList, else false
+ *
+ * @return
+ */
+ boolean isValid()
+ {
+ /*
+ * we don't handle reverse ranges
+ */
+ if (region != null && region.getBegin() > region.getEnd())
+ {
+ return false;
+ }
+ if (subregions == null)
+ {
+ return true;
+ }
+ if (subregions.isEmpty())
+ {
+ /*
+ * we expect empty subregions to be nulled
+ */
+ return false;
+ }
+ return subregions.isValid(getBegin(), getEnd());
+ }
+
+ /**
+ * Adds all contained entries to the given list
+ *
+ * @param entries
+ */
+ void getEntries(List<T> entries)
+ {
+ entries.add(region);
+ if (subregions != null)
+ {
+ subregions.getEntries(entries);
+ }
+ }
+
+ /**
+ * Answers true if this object contains the given entry (by object equals
+ * test), else false
+ *
+ * @param entry
+ * @return
+ */
+ boolean contains(IntervalI entry)
+ {
+ if (entry == null)
+ {
+ return false;
+ }
+ if (entry.equals(region))
+ {
+ return true;
+ }
+ return subregions == null ? false : subregions.contains(entry);
+ }
+
+ /**
+ * Answers the 'root' region modelled by this object
+ *
+ * @return
+ */
+ T getRegion()
+ {
+ return region;
+ }
+
+ /**
+ * Answers the (possibly null) contained regions within this object
+ *
+ * @return
+ */
+ NCList<T> getSubRegions()
+ {
+ return subregions;
+ }
+
+ /**
+ * Answers the (deep) size of this node i.e. the number of intervals it models
+ *
+ * @return
+ */
+ int size()
+ {
+ return subregions == null ? 1 : 1 + subregions.size();
+ }
+
+ /**
+ * Answers the depth of NCNode / NCList nesting in the data tree
+ *
+ * @return
+ */
+ int getDepth()
+ {
+ return subregions == null ? 1 : 1 + subregions.getDepth();
+ }
+
+ /**
+ * Answers an iterator over the intervals stored in this node. The iterator
+ * does not support the optional <code>remove</code> operation (throws
+ * <code>UnsupportedOperationException</code> if attempted).
+ *
+ * @return
+ */
+ public Iterator<T> iterator()
+ {
+ return new NCNodeIterator();
+ }
+
+ /**
+ * Removes the first interval found equal to the given entry. Answers true if
+ * a matching interval is found and removed, else false.
+ *
+ * @param entry
+ * @return
+ */
+ boolean remove(T entry)
+ {
+ if (region.equals(entry))
+ {
+ /*
+ * this case must be handled by NCList, to allow any
+ * children of a deleted interval to be promoted
+ */
+ throw new IllegalArgumentException("NCNode can't remove self");
+ }
+ if (subregions == null)
+ {
+ return false;
+ }
+ if (subregions.remove(entry))
+ {
+ if (subregions.isEmpty())
+ {
+ subregions = null;
+ }
+ return true;
+ }
+ return false;
+ }
+}
--- /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.impl;
+
+import intervalstore.api.IntervalI;
+
+/**
+ * An immutable data bean that models a start-end range
+ */
+public class Range implements IntervalI
+{
+ public final int start;
+
+ public final int end;
+
+ @Override
+ public int getBegin()
+ {
+ return start;
+ }
+
+ @Override
+ public int getEnd()
+ {
+ return end;
+ }
+
+ public Range(int i, int j)
+ {
+ start = i;
+ end = j;
+ }
+
+ @Override
+ public String toString()
+ {
+ return String.valueOf(start) + "-" + String.valueOf(end);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return start * 31 + end;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj instanceof Range)
+ {
+ Range r = (Range) obj;
+ return (start == r.start && end == r.end);
+ }
+ return false;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff