+/*
+ * 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.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignedCodonFrame;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.io.FileLoader;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.io.FormatAdapter;
+import jalview.io.StructureFile;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
-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;
{
private StructureSelectionManager ssm;
- @BeforeClass(alwaysRun = true)
- public static void setUpBeforeClass() throws Exception
- {
- jalview.bin.Jalview.main(new String[] { "-props",
- "test/jalview/testProps.jvprops" });
- }
-
- @BeforeMethod(alwaysRun = true)
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
ssm = new StructureSelectionManager();
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testRegisterMapping()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
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" })
+ @Test(groups = { "Functional" })
public void testRegisterMappings()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
AlignedCodonFrame acf3 = new AlignedCodonFrame();
- 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));
}
/**
- * Test that a mapping is not deregistered if an alignment holds a reference
- * to it
+ * Verify that RESNUM sequence features are present after creating a PDB
+ * mapping
*/
- @Test(groups ={ "Functional" })
- public void testDeregisterMapping_withAlignmentReference()
+ @Test(groups = { "Functional" })
+ public void testSetMapping_seqFeatures()
{
- Desktop d = Desktop.instance;
- assertNotNull(d);
-
- /*
- * alignment with reference to mappings
- */
- AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nCAGT\n", FormatAdapter.PASTE);
-
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
-
- Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
- mappings.add(acf1);
- mappings.add(acf2);
- af1.getViewport().getAlignment().setCodonFrames(mappings);
-
- /*
- * Add one and remove it.
- */
- ssm.registerMapping(acf1);
- ssm.deregisterMapping(acf1);
- assertEquals(1, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- }
-
- /**
- * Test that a mapping is deregistered if no alignment holds a reference to it
- */
- @Test(groups ={ "Functional" })
- public void testDeregisterMapping_withNoReference()
- {
- Desktop d = Desktop.instance;
- assertNotNull(d);
-
- /*
- * alignment with reference to mappings
- */
- AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nCAGT\n", FormatAdapter.PASTE);
-
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
-
- Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
- mappings.add(acf2);
- af1.getViewport().getAlignment().setCodonFrames(mappings);
-
- /*
- * Add one and remove it.
- */
- ssm.registerMapping(acf1);
- assertEquals(1, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- ssm.deregisterMapping(acf1);
- assertEquals(0, ssm.seqmappings.size());
- }
-
- /**
- * Test that a mapping is not deregistered when a second view is closed but
- * the first still holds a reference to the mapping
- */
- @Test(groups ={ "Functional" })
- public void testDeregisterMapping_onCloseView()
- {
- /*
- * alignment with reference to mappings
- */
- AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nCAGT\n", FormatAdapter.PASTE);
-
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
-
- Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
- mappings.add(acf1);
- mappings.add(acf2);
- af1.getViewport().getAlignment().setCodonFrames(mappings);
- af1.newView_actionPerformed(null);
+ 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());
/*
- * Verify that creating the alignment for the new View has registered the
- * mappings
+ * Verify a RESNUM sequence feature in the PDBfile sequence
*/
- ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
+ SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
+ assertEquals("RESNUM", sf.getType());
+ assertEquals("1gaq", sf.getFeatureGroup());
+ assertEquals("GLU: 19 1gaqA", sf.getDescription());
/*
- * Close the second view. Verify that mappings are not removed as the first
- * view still holds a reference to them.
+ * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
+ * sequence
*/
- af1.closeMenuItem_actionPerformed(false);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
+ 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