JAL-2446 FeatureStore with NCList - work in progress

[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..d4c7b0c
--- /dev/null
+++ b/src/jalview/datamodel/features/NCNode.java
@@ -0,0 +1,124 @@
+package jalview.datamodel.features;
+
+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>
+{
+  /*
+   * deep size (number of ranges included)
+   */
+  private int size;
+
+  private V region;
+
+  private NCList<V> subregions;
+
+  /**
+   * Constructor
+   * 
+   * @param ranges
+   */
+  NCNode(List<V> ranges)
+  {
+    build(ranges);
+  }
+
+  /**
+   * Constructo
+   * 
+   * @param range
+   */
+  NCNode(V range)
+  {
+    List<V> ranges = new ArrayList<V>();
+    ranges.add(range);
+    build(ranges);
+  }
+
+  /**
+   * @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()));
+    }
+  }
+
+  int getStart()
+  {
+    return region.getBegin();
+  }
+
+  int getEnd()
+  {
+    return region.getEnd();
+  }
+
+  @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();
+  }
+
+  /**
+   * Add any ranges that overlap the from-to range to the result list
+   * 
+   * @param from
+   * @param to
+   * @param result
+   */
+  void addOverlaps(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
+   */
+  public 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);
+    }
+  }
+}