Merge branch 'develop' into trial_merge/JAL-1950

[jalview.git] / src / jalview / datamodel / features / NCNode.java

diff --git a/src/jalview/datamodel/features/NCNode.java b/src/jalview/datamodel/features/NCNode.java
new file mode 100644 (file)
index 0000000..007f3b1
--- /dev/null
+++ b/src/jalview/datamodel/features/NCNode.java
@@ -0,0 +1,255 @@
+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;
+  }
+}