Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings

[jalview.git] / test / jalview / io / gff / InterProScanHelperTest.java

diff --git a/test/jalview/io/gff/InterProScanHelperTest.java b/test/jalview/io/gff/InterProScanHelperTest.java
index d118f67..dde83a3 100644 (file)
--- a/test/jalview/io/gff/InterProScanHelperTest.java
+++ b/test/jalview/io/gff/InterProScanHelperTest.java
@@ -1,6 +1,27 @@
+/*
+ * 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.io.gff;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
@@ -10,18 +31,28 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class InterProScanHelperTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * Test processing one InterProScan GFF line
    * 
@@ -47,6 +78,16 @@ public class InterProScanHelperTest
     assertEquals(1, newseqs.size());
     assertTrue(newseqs.get(0) instanceof SequenceDummy);
     assertEquals("match$17_5_30", newseqs.get(0).getName());
+
+    assertNotNull(newseqs.get(0).getSequenceFeatures());
+    assertEquals(1, newseqs.get(0).getSequenceFeatures().size());
+    SequenceFeature sf = newseqs.get(0).getSequenceFeatures().get(0);
+    assertEquals(1, sf.getBegin());
+    assertEquals(26, sf.getEnd());
+    assertEquals("Pfam", sf.getType());
+    assertEquals("4Fe-4S dicluster domain", sf.getDescription());
+    assertEquals("InterProScan", sf.getFeatureGroup());
+
     assertEquals(1, align.getCodonFrames().size());
     AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();