+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.features;
-
-import jalview.datamodel.ContiguousI;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Each node of the NCList tree consists of a range, and (optionally) the NCList
- * of ranges it encloses
- *
- * @param <V>
- */
-class NCNode<V extends ContiguousI> implements ContiguousI
-{
- /*
- * deep size (number of ranges included)
- */
- private int size;
-
- private V region;
-
- /*
- * null, or an object holding contained subregions of this nodes region
- */
- private NCList<V> subregions;
-
- /**
- * Constructor given a list of ranges
- *
- * @param ranges
- */
- NCNode(List<V> ranges)
- {
- build(ranges);
- }
-
- /**
- * Constructor given a single range
- *
- * @param range
- */
- NCNode(V range)
- {
- List<V> ranges = new ArrayList<>();
- ranges.add(range);
- build(ranges);
- }
-
- NCNode(V entry, NCList<V> newNCList)
- {
- region = entry;
- subregions = newNCList;
- size = 1 + newNCList.size();
- }
-
- /**
- * @param ranges
- */
- protected void build(List<V> ranges)
- {
- size = ranges.size();
-
- if (!ranges.isEmpty())
- {
- region = ranges.get(0);
- }
- if (ranges.size() > 1)
- {
- subregions = new NCList<V>(ranges.subList(1, ranges.size()));
- }
- }
-
- @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>
- */
- @Override
- public String toString() {
- StringBuilder sb = new StringBuilder(10 * size);
- sb.append(region.getBegin()).append("-").append(region.getEnd());
- 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.getBegin()).append("-").append(region.getEnd());
- 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<V> result)
- {
- if (region.getBegin() <= to && region.getEnd() >= from)
- {
- result.add(region);
- }
- if (subregions != null)
- {
- subregions.findOverlaps(from, to, result);
- }
- }
-
- /**
- * Add one range to this subrange
- *
- * @param entry
- */
- synchronized void add(V entry)
- {
- if (entry.getBegin() < region.getBegin() || entry.getEnd() > region.getEnd()) {
- 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<V>(entry);
- }
- else
- {
- subregions.add(entry);
- }
- size++;
- }
-
- /**
- * 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;
- }
- return subregions.isValid(getBegin(), getEnd());
- }
-
- /**
- * Adds all contained entries to the given list
- *
- * @param entries
- */
- void getEntries(List<V> 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(V 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
- */
- V getRegion()
- {
- return region;
- }
-
- /**
- * Answers the (possibly null) contained regions within this object
- *
- * @return
- */
- NCList<V> getSubRegions()
- {
- return subregions;
- }
-
- /**
- * Nulls the subregion reference if it is empty (after a delete entry
- * operation)
- */
- void deleteSubRegionsIfEmpty()
- {
- if (subregions != null && subregions.size() == 0)
- {
- subregions = null;
- }
- }
-
- /**
- * Answers the (deep) size of this node i.e. the number of ranges it models
- *
- * @return
- */
- int size()
- {
- return size;
- }
-}
git://source.jalview.org / jalview.git / blobdiff