X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2Fgff%2FExonerateHelperTest.java;h=825af240aee3dc8d241447e0a86ee06e8945a6c2;hb=refs%2Fheads%2Fbug%2FJAL-3076ensemblGeneId;hp=ce52ee51a4dfb4be002cfed972b8a5351d944444;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git
diff --git a/test/jalview/io/gff/ExonerateHelperTest.java b/test/jalview/io/gff/ExonerateHelperTest.java
index ce52ee5..825af24 100644
--- a/test/jalview/io/gff/ExonerateHelperTest.java
+++ b/test/jalview/io/gff/ExonerateHelperTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -15,8 +35,9 @@ import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
import java.io.IOException;
import java.util.ArrayList;
@@ -24,10 +45,19 @@ import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ExonerateHelperTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testGetMappingType()
{
@@ -238,19 +268,20 @@ public class ExonerateHelperTest
{
FileLoader loader = new FileLoader(false);
AlignFrame af = loader.LoadFileWaitTillLoaded(
- "examples/testdata/exonerateseqs.fa", FormatAdapter.FILE);
-
+ "examples/testdata/exonerateseqs.fa",
+ DataSourceType.FILE);
+
af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",
- FormatAdapter.FILE, null, null);
-
+ DataSourceType.FILE, null, null);
+
/*
* verify one mapping to a dummy sequence, one to a real one
*/
- List mappings = af.getViewport().getAlignment()
- .getDataset().getCodonFrames();
+ List mappings = af
+ .getViewport().getAlignment().getDataset().getCodonFrames();
assertEquals(2, mappings.size());
Iterator iter = mappings.iterator();
-
+
// first mapping is to dummy sequence
AlignedCodonFrame mapping = iter.next();
Mapping[] mapList = mapping.getProtMappings();
@@ -261,7 +292,7 @@ public class ExonerateHelperTest
// 143 in protein should map to codon [11270, 11269, 11268] in dna
int[] mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-
+
// second mapping is to a sequence in the alignment
mapping = iter.next();
mapList = mapping.getProtMappings();
@@ -270,23 +301,23 @@ public class ExonerateHelperTest
.findName("DDB_G0280897");
assertSame(proteinSeq.getDatasetSequence(), mapList[0].getTo());
assertEquals(1, mapping.getdnaToProt().length);
-
+
// 143 in protein should map to codon [11270, 11269, 11268] in dna
mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-
+
// 182 in protein should map to codon [11153, 11152, 11151] in dna
mappedRegion = mapList[0].getMap().locateInFrom(182, 182);
assertArrayEquals(new int[] { 11153, 11151 }, mappedRegion);
-
+
// and the reverse mapping:
mappedRegion = mapList[0].getMap().locateInTo(11151, 11153);
assertArrayEquals(new int[] { 182, 182 }, mappedRegion);
-
+
// 11150 in dna should _not_ map to protein
mappedRegion = mapList[0].getMap().locateInTo(11150, 11150);
assertNull(mappedRegion);
-
+
// similarly 183 in protein should _not_ map to dna
mappedRegion = mapList[0].getMap().locateInFrom(183, 183);
assertNull(mappedRegion);