+/*
+ * 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.structure;
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 jalview.io.StructureFile;
+import jalview.util.MapList;
-import java.util.HashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
{
private StructureSelectionManager ssm;
- @BeforeMethod(alwaysRun = true)
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
+ StructureImportSettings.setShowSeqFeatures(true);
ssm = new StructureSelectionManager();
}
- @Test(groups ={ "Functional" })
- public void testAddMapping()
+ @Test(groups = { "Functional" })
+ public void testRegisterMapping()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
- /*
- * One mapping only.
- */
- ssm.addMapping(acf1);
- assertEquals(1, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertEquals(1, ssm.getMappingReferenceCount(acf1));
+ ssm.registerMapping(acf1);
+ assertEquals(1, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
- /*
- * A second mapping.
- */
- ssm.addMapping(acf2);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(1, ssm.getMappingReferenceCount(acf1));
- assertEquals(1, ssm.getMappingReferenceCount(acf2));
+ ssm.registerMapping(acf2);
+ assertEquals(2, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
/*
- * A second reference to the first mapping.
+ * Re-adding the first mapping does nothing
*/
- ssm.addMapping(acf1);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.getMappingReferenceCount(acf1));
- assertEquals(1, ssm.getMappingReferenceCount(acf2));
+ ssm.registerMapping(acf1);
+ assertEquals(2, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
}
- @Test(groups ={ "Functional" })
- public void testAddMappings()
+ @Test(groups = { "Functional" })
+ public void testRegisterMappings()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf3 = new AlignedCodonFrame();
+ acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
- Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
set1.add(acf1);
set1.add(acf2);
- Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> set2 = new ArrayList<AlignedCodonFrame>();
set2.add(acf2);
set2.add(acf3);
/*
- * Adding both sets adds acf2 twice and acf1 and acf3 once each.
- */
- ssm.addMappings(set1);
- ssm.addMappings(set2);
-
- assertEquals(3, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertTrue(ssm.seqmappings.contains(acf3));
- assertEquals(1, ssm.getMappingReferenceCount(acf1));
- assertEquals(2, ssm.getMappingReferenceCount(acf2));
- assertEquals(1, ssm.getMappingReferenceCount(acf3));
- }
-
- @Test(groups ={ "Functional" })
- public void testRemoveMapping()
- {
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
-
- /*
- * Add one and remove it.
- */
- ssm.addMapping(acf1);
- ssm.removeMapping(acf1);
- ssm.removeMapping(acf2);
- assertEquals(0, ssm.seqmappings.size());
- assertEquals(0, ssm.getMappingReferenceCount(acf1));
- assertEquals(0, ssm.getMappingReferenceCount(acf2));
-
- /*
- * 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(1, ssm.getMappingReferenceCount(acf1));
- assertEquals(1, ssm.getMappingReferenceCount(acf2));
-
- /*
- * Remove both once more to clear the set.
+ * Add both sets twice; each mapping should be added once only
*/
- ssm.removeMapping(acf1);
- ssm.removeMapping(acf2);
- assertEquals(0, ssm.seqmappings.size());
- assertEquals(0, ssm.getMappingReferenceCount(acf1));
- assertEquals(0, ssm.getMappingReferenceCount(acf2));
+ ssm.registerMappings(set1);
+ ssm.registerMappings(set1);
+ ssm.registerMappings(set2);
+ ssm.registerMappings(set2);
+
+ assertEquals(3, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
+ assertTrue(ssm.getSequenceMappings().contains(acf3));
}
- @Test(groups ={ "Functional" })
- 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();
-
- /*
- * Initial ref counts are 3/2/1:
- */
- ssm.addMapping(acf1);
- ssm.addMapping(acf1);
- ssm.addMapping(acf1);
- ssm.addMapping(acf2);
- ssm.addMapping(acf2);
- ssm.addMapping(acf3);
-
- Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
- set1.add(acf1);
- set1.add(acf2);
- Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
- set2.add(acf2);
- set2.add(acf3);
+ SequenceI seq = new Sequence(
+ "1GAQ|B",
+ "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
+ StructureSelectionManager sm = new StructureSelectionManager();
+ sm.setProcessSecondaryStructure(true);
+ sm.setAddTempFacAnnot(true);
+ StructureFile 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());
/*
- * Remove one ref each to acf1, acf2, counts are now 2/1/1:
+ * Verify a RESNUM sequence feature in the PDBfile sequence
*/
- ssm.removeMappings(set1);
- assertEquals(3, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertTrue(ssm.seqmappings.contains(acf3));
- assertEquals(2, ssm.getMappingReferenceCount(acf1));
- assertEquals(1, ssm.getMappingReferenceCount(acf2));
- assertEquals(1, ssm.getMappingReferenceCount(acf3));
+ 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(2, ssm.getMappingReferenceCount(acf1));
+ 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());
}
}
git://source.jalview.org / jalview.git / blobdiff