Sketch Locatable interface

Author: magicDGS

core/src/main/java/org/htsjdk/core/api/Locatable.java

@@ -0,0 +1,140 @@
+package org.htsjdk.core.api;
+
+/**
+ * Represents the location of a sequence with respect to another sequence (reference).
+ *
+ * <p>
+ * This interface represents a location or "mapping" with respect to a reference sequence. Examples
+ * of this abstraction are features located on the genome or alignment between two sequences (query
+ * with respect to a reference).
+ * </p>
+ *
+ * @implSpec note that 0-length intervals are allowed for intervals with undefined end.
+ */
+public interface Locatable {
+
+    /**
+     * Represents the reference name for unplaced locations.
+     *
+     * @see #getRefName()
+     */
+    public static final String UNPLACED_REF_NAME = "*";
+
+    /**
+     * Gets the reference name where this location is placed.
+     *
+     * <p>
+     * {@link Locatable} should either be placed on a reference sequence or being unplaced
+     * ({@link #UNPLACED_REF_NAME}).
+     * </p>
+     *
+     * @return name of the reference for the location; {@link #UNPLACED_REF_NAME} if unplaced.
+     * Never {@code null}
+     */
+    String getRefName();
+
+    /**
+     * Gets the start position on the reference (1-based).
+     *
+     * <p>
+     * {@link Locatable} should have a non-negative location on the reference sequence; if unplaced
+     * ({@code getReferenceName() == UNPLACED_REF_NAME}), position is undefined.
+     * </p>
+     *
+     * @return 1-based start position on the reference; undefined if {@link #getRefName()}
+     * returns {@link #UNPLACED_REF_NAME}.
+     */
+    long getStart();
+
+    /**
+     * Gets the end position on the reference (1-based fully-closed).
+     *
+     * @return 1-based fully-closed if present; {@code getStart() - 1} otherwise.
+     *
+     * @implSpec if present, end position should be downstream te start position ({@code getStart()
+     * > getEnd()}); otherwise, {@code getEnd() == getStart() - 1 }.
+     * @see #getStart()
+     */
+    long getEnd();
+
+    /**
+     * Gets the number of bases of reference covered by this location.
+     *
+     * <p>
+     * Returns the number of bases on te reference from the start to the end (independently of the
+     * alignment, if any). 0-lenght intervals represents the special case of undetermined eng.
+     * </p>
+     *
+     * @return number of bases of reference; 0 for undefined end.
+     *
+     * @implNote default implementation uses {@code getEnd() - getStart() + 1} to compute
+     * the length on the reference.
+     * @implSpec return value should be the same as the default implementation, but subclasses could
+     * override to more efficient implementations.
+     * @see #getStart()
+     * @see #getEnd()
+     */
+    default long getLengthOnReference() {
+        return getEnd() - getStart() + 1;
+    }
+
+    /**
+     * Determines whether this location overlaps with other.
+     *
+     * @param other location to test.
+     *
+     * @return {@code true} if this location overlaps other; {@code false} otherwise.
+     *
+     * @implNote default implementation returns {@code withinDistanceOf(other, 0)}.
+     * @implSpec should return {@code false} if {@code referenceMatch(other) == false}.
+     * @see #withinDistanceOf(Locatable, int)
+     */
+    // TODO: default implementation?
+    default boolean overlaps(Locatable other) {
+        return withinDistanceOf(other, 0);
+    }
+
+    /**
+     * Determines whether this location is within a {@code distance} of other (overlap with margin).
+     *
+     * @param other    location to test.
+     * @param distance number of bases between the intervals to use as padding for test the
+     *                 overlap.
+     *
+     * @return {@code true} if this location overlaps other with the provided margin; {@code false}
+     * otherwise.
+     *
+     * @implSpec should return {@code false} if {@code referenceMatch(other) == false}.
+     */
+    // TODO: default implementation?
+    boolean withinDistanceOf(Locatable other, int distance);
+
+    /**
+     * Determines whether this location contains entirely other.
+     *
+     * <p>
+     * A location contains the entire location represented by other when it contains all positions
+     * spanned by the other (or more).
+     * </p>
+     *
+     * @param other location to test.
+     *
+     * @return {@code true} if this location contains the other; {@code false} otherwise.
+     *
+     * @implSpec should return {@code false} if {@code referenceMatch(other) == false}.
+     */
+    // TODO: default implementation?
+    boolean contains(Locatable other);
+
+    /**
+     * Determines if this location is on the same reference as other.
+     *
+     * @return {@code true} if both locations are in the same reference; {@code false} otherwise.
+     *
+     * @implNote default implementation compares {@link #getRefName()} values.
+     * @implSpec should return the same value as {@code this.getRefName().equals(other.getRefName())}.
+     * @see #getRefName()
+     */
+    // TODO: default implementation?
+    boolean referenceMatch(Locatable other);
+}