X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FNCNode.java;fp=src%2Fjalview%2Fdatamodel%2Ffeatures%2FNCNode.java;h=0000000000000000000000000000000000000000;hb=74393b51f368cb9f58589472d432a433d9c4386d;hp=b9917501717f0379283545fc67fe84ebe32a8bd8;hpb=7a0d503181fe41452120a8a02ca63476392aa08c;p=jalview.git

diff --git a/src/jalview/datamodel/features/NCNode.java b/src/jalview/datamodel/features/NCNode.java
deleted file mode 100644
index b991750..0000000
--- a/src/jalview/datamodel/features/NCNode.java
+++ /dev/null
@@ -1,275 +0,0 @@
-/*
- * 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;
-  }
-}