JAL-3251 SequenceToSequenceMapping now SequenceMapping, MappingType++

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

diff --git a/src/jalview/datamodel/SequenceMapping.java b/src/jalview/datamodel/SequenceMapping.java
new file mode 100644 (file)
index 0000000..ade5673
--- /dev/null
+++ b/src/jalview/datamodel/SequenceMapping.java
@@ -0,0 +1,83 @@
+package jalview.datamodel;
+
+/**
+ * Data bean that holds a mapping from one sequence to another
+ */
+public class SequenceMapping
+{
+  SequenceI fromSeq;
+
+  Mapping mapping;
+
+  private MappingType type;
+
+  SequenceMapping(SequenceI from, Mapping map)
+  {
+    this.fromSeq = from;
+    this.mapping = map;
+  }
+
+  /**
+   * Readable representation for debugging only, not guaranteed not to change
+   */
+  @Override
+  public String toString()
+  {
+    return String.format("From %s %s", fromSeq.getName(),
+            mapping.toString());
+  }
+
+  /**
+   * Returns a hashCode derived from the hashcodes of the mappings and fromSeq
+   * 
+   * @see SequenceMapping#hashCode()
+   */
+  @Override
+  public int hashCode()
+  {
+    return (fromSeq == null ? 0 : fromSeq.hashCode() * 31)
+            + mapping.hashCode();
+  }
+
+  /**
+   * Answers true if the objects hold the same mapping between the same two
+   * sequences
+   * 
+   * @see Mapping#equals
+   */
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (!(obj instanceof SequenceMapping))
+    {
+      return false;
+    }
+    SequenceMapping that = (SequenceMapping) obj;
+    if (this.mapping == null)
+    {
+      return that.mapping == null;
+    }
+    // TODO: can simplify by asserting fromSeq is a dataset sequence
+    return (this.fromSeq == that.fromSeq
+            || (this.fromSeq != null && that.fromSeq != null
+                    && this.fromSeq.getDatasetSequence() != null
+                    && this.fromSeq.getDatasetSequence() == that.fromSeq
+                            .getDatasetSequence()))
+            && this.mapping.equals(that.mapping);
+  }
+
+  public SequenceI getFromSeq()
+  {
+    return fromSeq;
+  }
+
+  public Mapping getMapping()
+  {
+    return mapping;
+  }
+
+  public MappingType getType()
+  {
+    return type;
+  }
+}
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