From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 13 Apr 2016 20:27:10 +0000 (+0100)
Subject: JAL-2046 test to demonstrate feature duplication bug
X-Git-Tag: Release_2_10_0~249^2~30
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=53ff9242cb709fe1e8470c5e88ecf8a8ae783b19;p=jalview.git

JAL-2046 test to demonstrate feature duplication bug
---

diff --git a/test/jalview/analysis/SeqsetUtilsTest.java b/test/jalview/analysis/SeqsetUtilsTest.java
new file mode 100644
index 0000000..b4d079a
--- /dev/null
+++ b/test/jalview/analysis/SeqsetUtilsTest.java
@@ -0,0 +1,76 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+/**
+ * @author jprocter
+ *
+ */
+public class SeqsetUtilsTest
+{
+  /**
+   * test for JAL-2046 bug - duplication of sequence features on reconstructed
+   * alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testSeqFeatureAddition()
+  {
+    SequenceI[] sqset = new SequenceI[] {
+        new Sequence("Aseq1", "AREALSEQ"),
+        new Sequence("Aseq2", "AREALSEQ") };
+
+    AlignmentI al = new Alignment(sqset);
+    al.setDataset(null);
+    AlignmentI ds = al.getDataset();
+    SequenceFeature sf1 = new SequenceFeature("f1", "foo", "bleh", 2, 3,
+            "far"), sf2 = new SequenceFeature("f2", "foo", "bleh", 2, 3,
+            "far");
+    ds.getSequenceAt(0).addSequenceFeature(sf1);
+    Hashtable unq = SeqsetUtils.uniquify(sqset, true);
+    SequenceI[] sqset2 = new SequenceI[] {
+        new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
+        new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
+    Assert.assertTrue(sqset[0].getSequenceFeatures()[0] == sf1);
+    Assert.assertEquals(sqset2[0].getSequenceFeatures(), null);
+    ds.getSequenceAt(0).addSequenceFeature(sf2);
+    Assert.assertEquals(sqset[0].getSequenceFeatures().length, 2);
+    SeqsetUtils.deuniquify(unq, sqset2);
+    // explicitly test that original sequence features still exist because they
+    // are on the shared dataset sequence
+    Assert.assertEquals(sqset[0].getSequenceFeatures().length, 2);
+    Assert.assertEquals(sqset2[0].getSequenceFeatures().length, 2);
+    Assert.assertTrue(sqset[0].getSequenceFeatures()[0] == sqset2[0]
+            .getSequenceFeatures()[0]);
+    Assert.assertTrue(sqset[0].getSequenceFeatures()[1] == sqset2[0]
+            .getSequenceFeatures()[1]);
+  }
+}