+/*
+ * 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 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;
-import MCview.PDBfile;
-
public class StructureSelectionManagerTest
{
private StructureSelectionManager ssm;
@BeforeMethod(alwaysRun = true)
public void setUp()
{
+ StructureImportSettings.setShowSeqFeatures(true);
ssm = new StructureSelectionManager();
}
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));
ssm.registerMapping(acf1);
- assertEquals(1, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
+ assertEquals(1, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
ssm.registerMapping(acf2);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
+ assertEquals(2, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
/*
* Re-adding the first mapping does nothing
*/
ssm.registerMapping(acf1);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
+ assertEquals(2, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
}
@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);
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.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
+ assertTrue(ssm.getSequenceMappings().contains(acf3));
}
/**
StructureSelectionManager sm = new StructureSelectionManager();
sm.setProcessSecondaryStructure(true);
sm.setAddTempFacAnnot(true);
- PDBfile pmap = sm.setMapping(true, new SequenceI[] { seq },
+ StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
new String[] { null }, "examples/1gaq.txt", FormatAdapter.FILE);
assertTrue(pmap != null);
SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
- assertEquals("GLU: 19 1gaqA", sf.getDescription());
+ assertEquals("GLU:19 1gaqA", sf.getDescription());
/*
* Verify a RESNUM sequence feature in the StructureSelectionManager mapped
sf = map.sequence.getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
- assertEquals("ALA: 1 1gaqB", sf.getDescription());
+ assertEquals("ALA:1 1gaqB", sf.getDescription());
}
}