Merge branch 'documentation/JAL-3111_release_211' into bug/JAL-2830_editManglesDatase...

[jalview.git] / src / jalview / datamodel / GeneLocus.java

diff --git a/src/jalview/datamodel/GeneLocus.java b/src/jalview/datamodel/GeneLocus.java
new file mode 100644 (file)
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+++ b/src/jalview/datamodel/GeneLocus.java
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+package jalview.datamodel;
+
+import jalview.util.MapList;
+
+/**
+ * A specialisation of DBRefEntry used to hold the chromosomal coordinates for a
+ * (typically gene) sequence
+ * <ul>
+ * <li>field <code>source</code> is used to hold a species id e.g. human</li>
+ * <li>field <code>version</code> is used to hold assembly id e.g GRCh38</li>
+ * <li>field <code>accession</code> is used to hold the chromosome id</li>
+ * <li>field <code>map</code> is used to hold the mapping from sequence to
+ * chromosome coordinates</li>
+ * </ul>
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class GeneLocus extends DBRefEntry implements GeneLociI
+{
+  /**
+   * Constructor adapts species, assembly, chromosome to DBRefEntry source,
+   * version, accession, respectively, and saves the mapping of sequence to
+   * chromosomal coordinates
+   * 
+   * @param speciesId
+   * @param assemblyId
+   * @param chromosomeId
+   * @param mapping
+   */
+  public GeneLocus(String speciesId, String assemblyId, String chromosomeId,
+          Mapping mapping)
+  {
+    super(speciesId, assemblyId, chromosomeId, mapping);
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param speciesId
+   * @param assemblyId
+   * @param chromosomeId
+   */
+  public GeneLocus(String speciesId, String assemblyId, String chromosomeId)
+  {
+    this(speciesId, assemblyId, chromosomeId, null);
+  }
+
+  @Override
+  public boolean equals(Object o)
+  {
+    return o instanceof GeneLocus && super.equals(o);
+  }
+
+  @Override
+  public MapList getMapping()
+  {
+    return map == null ? null : map.getMap();
+  }
+
+  /**
+   * Answers the species identifier e.g. "human", stored as field <code>source</code> of
+   * DBRefEntry
+   */
+  @Override
+  public String getSpeciesId()
+  {
+    return getSource();
+  }
+
+  /**
+   * Answers the genome assembly id e.g. "GRCh38", stored as field
+   * <code>version</code> of DBRefEntry
+   */
+  @Override
+  public String getAssemblyId()
+  {
+    return getVersion();
+  }
+
+  /**
+   * Answers the chromosome identifier e.g. "X", stored as field
+   * <code>accession</code> of DBRefEntry
+   */
+  @Override
+  public String getChromosomeId()
+  {
+    return getAccessionId();
+  }
+
+}