X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructure%2FStructureSelectionManagerTest.java;h=6d66f7cc94881c20717308df8a931dba942605fb;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=487ef2c046b20d62470a6df41f7f6376c97261cf;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git
diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index 487ef2c..6d66f7c 100644
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -1,65 +1,78 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.structure;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
import java.util.HashSet;
import java.util.Set;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
public class StructureSelectionManagerTest
{
private StructureSelectionManager ssm;
- @Before
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
ssm = new StructureSelectionManager();
}
- @Test
- public void testAddMapping()
+ @Test(groups = { "Functional" })
+ public void testRegisterMapping()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
- /*
- * One mapping only.
- */
- ssm.addMapping(acf1);
+ ssm.registerMapping(acf1);
assertEquals(1, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
- assertEquals(1, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
- /*
- * A second mapping.
- */
- ssm.addMapping(acf2);
+ ssm.registerMapping(acf2);
assertEquals(2, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
/*
- * A second reference to the first mapping.
+ * Re-adding the first mapping does nothing
*/
- ssm.addMapping(acf1);
+ ssm.registerMapping(acf1);
assertEquals(2, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.seqMappingRefCounts.size());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
}
- @Test
- public void testAddMappings()
+ @Test(groups = { "Functional" })
+ public void testRegisterMappings()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
@@ -73,103 +86,57 @@ public class StructureSelectionManagerTest
set2.add(acf3);
/*
- * Adding both sets adds acf2 twice and acf1 and acf3 once each.
+ * Add both sets twice; each mapping should be added once only
*/
- ssm.addMappings(set1);
- ssm.addMappings(set2);
+ ssm.registerMappings(set1);
+ ssm.registerMappings(set1);
+ ssm.registerMappings(set2);
+ ssm.registerMappings(set2);
assertEquals(3, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
assertTrue(ssm.seqmappings.contains(acf3));
- assertEquals(3, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf2).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
- }
-
- @Test
- public void testRemoveMapping()
- {
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
- ssm.addMapping(acf1);
-
- /*
- * Add one and remove it.
- */
- ssm.removeMapping(acf1);
- ssm.removeMapping(acf2);
- assertEquals(0, ssm.seqmappings.size());
- assertEquals(0, ssm.seqMappingRefCounts.size());
-
- /*
- * Add one twice and remove it once.
- */
- ssm.addMapping(acf1);
- ssm.addMapping(acf2);
- ssm.addMapping(acf1);
- ssm.removeMapping(acf1);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
-
- /*
- * Remove both once more to clear the set.
- */
- ssm.removeMapping(acf1);
- ssm.removeMapping(acf2);
- assertEquals(0, ssm.seqmappings.size());
- assertEquals(0, ssm.seqMappingRefCounts.size());
}
- @Test
- public void testRemoveMappings()
+ /**
+ * Verify that RESNUM sequence features are present after creating a PDB
+ * mapping
+ */
+ @Test(groups = { "Functional" })
+ public void testSetMapping_seqFeatures()
{
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
- AlignedCodonFrame acf3 = new AlignedCodonFrame();
+ SequenceI seq = new Sequence(
+ "1GAQ|B",
+ "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
+ StructureSelectionManager sm = new StructureSelectionManager();
+ sm.setProcessSecondaryStructure(true);
+ sm.setAddTempFacAnnot(true);
+ PDBfile pmap = sm.setMapping(true, new SequenceI[] { seq },
+ new String[] { null }, "examples/1gaq.txt", FormatAdapter.FILE);
+ assertTrue(pmap != null);
+
+ assertEquals(3, pmap.getSeqs().size());
+ assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName());
+ assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName());
+ assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName());
/*
- * Initial ref counts are 3/2/1:
+ * Verify a RESNUM sequence feature in the PDBfile sequence
*/
- ssm.addMapping(acf1);
- ssm.addMapping(acf1);
- ssm.addMapping(acf1);
- ssm.addMapping(acf2);
- ssm.addMapping(acf2);
- ssm.addMapping(acf3);
-
- Set set1 = new HashSet();
- set1.add(acf1);
- set1.add(acf2);
- Set set2 = new HashSet();
- set2.add(acf2);
- set2.add(acf3);
-
- /*
- * Remove one ref each to acf1, acf2, counts are now 2/1/1:
- */
- ssm.removeMappings(set1);
- assertEquals(3, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertTrue(ssm.seqmappings.contains(acf3));
- assertEquals(3, ssm.seqMappingRefCounts.size());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
+ SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
+ assertEquals("RESNUM", sf.getType());
+ assertEquals("1gaq", sf.getFeatureGroup());
+ assertEquals("GLU: 19 1gaqA", sf.getDescription());
/*
- * Remove one ref each to acf2, acf3 - they are removed
+ * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
+ * sequence
*/
- ssm.removeMappings(set2);
- assertEquals(1, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertEquals(1, ssm.seqMappingRefCounts.size());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
+ StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
+ sf = map.sequence.getSequenceFeatures()[0];
+ assertEquals("RESNUM", sf.getType());
+ assertEquals("1gaq", sf.getFeatureGroup());
+ assertEquals("ALA: 1 1gaqB", sf.getDescription());
}
}