X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2Fgff%2FInterProScanHelperTest.java;h=dde83a35848123f2a24eab9dac65909025ffcf54;hb=refs%2Fheads%2Ftask%2FJAL-3243_PDB_free_text_error;hp=2ef4c99396e15ba50b71483386e602fe14550fb1;hpb=8f920d337154e092f5f9056ffde3cdf2735eca43;p=jalview.git
diff --git a/test/jalview/io/gff/InterProScanHelperTest.java b/test/jalview/io/gff/InterProScanHelperTest.java
index 2ef4c99..dde83a3 100644
--- 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 .
+ * 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
*
@@ -38,7 +69,7 @@ public class InterProScanHelperTest
seq.createDatasetSequence();
AlignmentI align = new Alignment(new SequenceI[] {});
Map> set = Gff3Helper.parseNameValuePairs(gff[8]);
-
+
/*
* this should create a mapping from Prot1/5-30 to virtual sequence
* match$17_5_30 (added to newseqs) positions 1-26
@@ -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();