import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+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.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import MCview.PDBfile;
-
public class StructureSelectionManagerTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
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 },
- new String[] { null }, "examples/1gaq.txt", FormatAdapter.FILE);
+ StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
+ new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals(3, pmap.getSeqs().size());
/*
* Verify a RESNUM sequence feature in the PDBfile sequence
*/
- SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
+ SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures().get(0);
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
assertEquals("GLU: 19 1gaqA", sf.getDescription());
* sequence
*/
StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
- sf = map.sequence.getSequenceFeatures()[0];
+ sf = map.sequence.getSequenceFeatures().get(0);
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
assertEquals("ALA: 1 1gaqB", sf.getDescription());