Basic implementation of an adapter for locatable.

src/main/scala/com/fulcrumgenomics/util/LocatableAdapter.scala

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+/*
+ * The MIT License
+ *
+ * Copyright (c) 2020 Fulcrum Genomics LLC
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package com.fulcrumgenomics.util
+
+import com.fulcrumgenomics.FgBioDef._
+
+import htsjdk.samtools.util.{CoordMath, Locatable}
+
+/**
+  * Trait that can be added to any class that defines chrom/start/end to implement Locatable
+  */
+trait LocatableAdapter[A <: LocatableAdapter[A]] extends Locatable with Ordered[A] {
+  def chrom: String
+  def start: Int
+  def end: Int
+  def name: String
+  def negativeStrand: Boolean
+  def positiveStrand: Boolean = !negativeStrand
+
+  // Implementations of Locatable interface methods
+  final override def getContig: String = chrom
+  final override def getStart: Int     = start
+  final override def getEnd: Int       = end
+
+  final def length: Int = getLengthOnReference
+
+  /** Calculates the overlap between two locatables assuming that they do in fact overlap. */
+  def overlap(other: Locatable): Int = CoordMath.getOverlap(start, end, other.getStart, other.getEnd)
+
+  /** Provides a basic comparison that orders on chrom (lexicographically) and then start and end position. */
+  def compare(that: A): Int = {
+    var result = this.chrom.compareTo(that.chrom)
+    if (result == 0) result = this.start - that.start
+    if (result == 0) result = this.end - that.end
+    result
+  }
+}