/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.structure.StructureSelectionManager;
import java.util.ArrayList;
import java.util.List;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class AlignViewportTest
{
AlignmentI al;
AlignViewport testee;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
jalview.bin.Jalview.main(new String[] { "-props",
"test/jalview/testProps.jvprops" });
}
@BeforeMethod(alwaysRun = true)
public void setUp()
{
SequenceI seq1 = new Sequence("Seq1", "ABC");
SequenceI seq2 = new Sequence("Seq2", "ABC");
SequenceI seq3 = new Sequence("Seq3", "ABC");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
al = new Alignment(seqs);
al.setDataset(null);
testee = new AlignViewport(al);
}
@Test(groups = { "Functional" })
public void testCollateForPdb()
{
/*
* Set up sequence pdb ids
*/
PDBEntry pdb1 = new PDBEntry("1ABC", "A", Type.PDB, "1ABC.pdb");
PDBEntry pdb2 = new PDBEntry("2ABC", "A", Type.PDB, "2ABC.pdb");
PDBEntry pdb3 = new PDBEntry("3ABC", "A", Type.PDB, "3ABC.pdb");
/*
* seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC
*/
al.getSequenceAt(0).getDatasetSequence()
.addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
al.getSequenceAt(2).getDatasetSequence()
.addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
al.getSequenceAt(1).getDatasetSequence()
.addPDBId(new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
/*
* Add a second chain PDB xref to Seq2 - should not result in a duplicate in
* the results
*/
al.getSequenceAt(1).getDatasetSequence()
.addPDBId(new PDBEntry("2ABC", "D", Type.PDB, "2ABC.pdb"));
/*
* Seq3 refers to 3abc - this does not match 3ABC (as the code stands)
*/
al.getSequenceAt(2).getDatasetSequence()
.addPDBId(new PDBEntry("3abc", "D", Type.PDB, "3ABC.pdb"));
/*
* run method under test
*/
SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2,
pdb3 });
// seq1 and seq3 refer to PDBEntry[0]
assertEquals(2, seqs[0].length);
assertSame(al.getSequenceAt(0), seqs[0][0]);
assertSame(al.getSequenceAt(2), seqs[0][1]);
// seq2 refers to PDBEntry[1]
assertEquals(1, seqs[1].length);
assertSame(al.getSequenceAt(1), seqs[1][0]);
// no sequence refers to PDBEntry[2]
assertEquals(0, seqs[2].length);
}
/**
* 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();
List mappings = new ArrayList();
mappings.add(acf1);
mappings.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings);
af1.newView_actionPerformed(null);
/*
* Verify that creating the alignment for the new View has registered the
* mappings
*/
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
assertEquals(2, ssm.getSequenceMappings().size());
assertTrue(ssm.getSequenceMappings().contains(acf1));
assertTrue(ssm.getSequenceMappings().contains(acf2));
/*
* Close the second view. Verify that mappings are not removed as the first
* view still holds a reference to them.
*/
af1.closeMenuItem_actionPerformed(false);
assertEquals(2, ssm.getSequenceMappings().size());
assertTrue(ssm.getSequenceMappings().contains(acf1));
assertTrue(ssm.getSequenceMappings().contains(acf2));
}
/**
* 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);
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
">Seq1\nRSVQ\n", FormatAdapter.PASTE);
AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
">Seq2\nDGEL\n", FormatAdapter.PASTE);
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
AlignedCodonFrame acf3 = new AlignedCodonFrame();
List mappings1 = new ArrayList();
mappings1.add(acf1);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
List mappings2 = new ArrayList();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
/*
* AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
*/
List ssmMappings = ssm.getSequenceMappings();
assertEquals(0, ssmMappings.size());
ssm.registerMapping(acf1);
assertEquals(1, ssmMappings.size());
ssm.registerMapping(acf2);
assertEquals(2, ssmMappings.size());
ssm.registerMapping(acf3);
assertEquals(3, ssmMappings.size());
/*
* Closing AlignFrame2 should remove its mappings from
* StructureSelectionManager, since AlignFrame1 has no reference to them
*/
af2.closeMenuItem_actionPerformed(true);
assertEquals(1, ssmMappings.size());
assertTrue(ssmMappings.contains(acf1));
}
/**
* Test that a mapping is not deregistered if another alignment holds a
* reference to it
*/
@Test(groups = { "Functional" })
public void testDeregisterMapping_withReference()
{
Desktop d = Desktop.instance;
assertNotNull(d);
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
">Seq1\nRSVQ\n", FormatAdapter.PASTE);
AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
">Seq2\nDGEL\n", FormatAdapter.PASTE);
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
AlignedCodonFrame acf3 = new AlignedCodonFrame();
List mappings1 = new ArrayList();
mappings1.add(acf1);
mappings1.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
List mappings2 = new ArrayList();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
/*
* AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
*/
List ssmMappings = ssm.getSequenceMappings();
assertEquals(0, ssmMappings.size());
ssm.registerMapping(acf1);
assertEquals(1, ssmMappings.size());
ssm.registerMapping(acf2);
assertEquals(2, ssmMappings.size());
ssm.registerMapping(acf3);
assertEquals(3, ssmMappings.size());
/*
* Closing AlignFrame2 should remove mapping acf3 from
* StructureSelectionManager, but not acf2, since AlignFrame1 still has a
* reference to it
*/
af2.closeMenuItem_actionPerformed(true);
assertEquals(2, ssmMappings.size());
assertTrue(ssmMappings.contains(acf1));
assertTrue(ssmMappings.contains(acf2));
assertFalse(ssmMappings.contains(acf3));
}
}