JAL-3253-applet JAL-3397

[jalview.git] / src / intervalstore / nonc / IntervalStore0Impl.java

diff --git a/src/intervalstore/nonc/IntervalStore0Impl.java b/src/intervalstore/nonc/IntervalStore0Impl.java
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+/*
+BSD 3-Clause License
+
+Copyright (c) 2018, Mungo Carstairs
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+package intervalstore.nonc;
+
+import jalview.datamodel.SequenceFeature;
+
+import intervalstore.api.IntervalI;
+
+/**
+ * extend intervalstore.nonc.IntervalStore to account for the fact that
+ * SequenceFeature.equalsInterval only checks ranges
+ */
+@SuppressWarnings("rawtypes")
+public class IntervalStore0Impl<T extends IntervalI> extends IntervalStore0
+{
+
+
+  /**
+   * Constructor
+   */
+  public IntervalStore0Impl()
+  {
+    super();
+  }
+
+  /**
+   * CAUTION! This presumes that equalsInterval does check descriptions. Note
+   * that bartongroup.IntervalStoreJ does NOT do this and
+   * jalview.datamodel.features.SequenceFeature does not, either. But
+   * nonc.SimpleFeature in test DOES, because it overrides equalsInterval.
+   * 
+   * The reason we do it this way is to avoid an unnecessary and costly test for
+   * obj instanceof IntervalI.
+   * 
+   * Added by Mungo to use equals, but that requires use of instance checking,
+   * which is not significant in Java (apparently), but is a bigger deal in
+   * JavaScript. So here we have to hack
+   * bobhanson.IntervalStoreJ.nonc.InervalStore to bypass equals.
+   * 
+   * @param i1
+   * @param i2
+   * @return
+   */
+  @Override
+  boolean sameInterval(IntervalI i1, IntervalI i2)
+  {
+    // avoiding equals() for JavaScript performance
+    return ((SequenceFeature) i1).equals((SequenceFeature) i2, false);
+  }
+
+}