/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
* Copyright (C) 2015 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.structures.models;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
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.AppletFormatAdapter;
import jalview.structure.AtomSpec;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel.SuperposeData;
import java.util.Arrays;
import java.util.List;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
/**
* Unit tests for non-abstract methods of abstract base class
*
* @author gmcarstairs
*
*/
public class AAStructureBindingModelTest
{
private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n"
+ "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n"
+ "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n"
+ "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n"
+ "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n"
+ "ATOM 31 CA LYS A 101 33.323 11.587 43.115 1.00 41.69 C \n";
private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
+ "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n"
+ "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n"
+ "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n"
+ "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n"
+ "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n";
private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n"
+ "ATOM 2 CA SER A 1 29.427 3.330 -6.578 1.00 32.50 C \n"
+ "ATOM 8 CA PRO A 2 29.975 3.340 -2.797 1.00 17.62 C \n"
+ "ATOM 16 CA ALYS A 3 26.958 3.024 -0.410 0.50 8.78 C \n"
+ "ATOM 33 CA ALA A 4 26.790 4.320 3.172 1.00 11.98 C \n"
+ "ATOM 39 CA AVAL A 5 24.424 3.853 6.106 0.50 13.83 C \n";
AAStructureBindingModel testee;
AlignmentI al = null;
/**
* Set up test conditions with three aligned sequences,
*/
@BeforeMethod(alwaysRun = true)
public void setUp()
{
SequenceI seq1 = new Sequence("1YCS", "-VPSQK");
SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
al.setDataset(null);
PDBEntry[] pdbFiles = new PDBEntry[3];
pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "1YCS.pdb");
pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "3A6S.pdb");
pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "1OOT.pdb");
String[][] chains = new String[3][];
SequenceI[][] seqs = new SequenceI[3][];
seqs[0] = new SequenceI[] { seq1 };
seqs[1] = new SequenceI[] { seq2 };
seqs[2] = new SequenceI[] { seq3 };
StructureSelectionManager ssm = new StructureSelectionManager();
ssm.setMapping(new SequenceI[] { seq1 }, null, PDB_1,
AppletFormatAdapter.PASTE);
ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
AppletFormatAdapter.PASTE);
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
AppletFormatAdapter.PASTE);
testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null)
{
@Override
public String[] getPdbFile()
{
/*
* fudge 'filenames' to match those generated when PDBFile parses PASTE
* data
*/
return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
}
@Override
public void updateColours(Object source)
{
}
@Override
public void releaseReferences(Object svl)
{
}
@Override
public void highlightAtoms(List atoms)
{
}
};
}
/**
* Verify that the method determines that columns 2, 5 and 6 of the alignment
* are alignable in structure
*/
@Test(groups = { "Functional" })
public void testFindSuperposableResidues()
{
SuperposeData[] structs = new SuperposeData[al.getHeight()];
for (int i = 0; i < structs.length; i++)
{
structs[i] = testee.new SuperposeData(al.getWidth());
}
/*
* initialise array of 'superposable columns' to true (would be false for
* hidden columns)
*/
boolean[] matched = new boolean[al.getWidth()];
Arrays.fill(matched, true);
int refStructure = testee
.findSuperposableResidues(al, matched, structs);
assertEquals(0, refStructure);
/*
* only ungapped, structure-mapped columns are superposable
*/
assertFalse(matched[0]); // gap in first sequence
assertTrue(matched[1]);
assertFalse(matched[2]); // gap in second sequence
assertFalse(matched[3]); // gap in third sequence
assertTrue(matched[4]);
assertTrue(matched[5]);
}
@Test(groups = { "Functional" })
public void testFindSuperposableResidues_hiddenColumn()
{
SuperposeData[] structs = new SuperposeData[al.getHeight()];
for (int i = 0; i < structs.length; i++)
{
structs[i] = testee.new SuperposeData(al.getWidth());
}
/*
* initialise array of 'superposable columns' to true (would be false for
* hidden columns)
*/
boolean[] matched = new boolean[al.getWidth()];
Arrays.fill(matched, true);
// treat column 5 of the alignment as hidden
matched[4] = false;
int refStructure = testee
.findSuperposableResidues(al, matched, structs);
assertEquals(0, refStructure);
// only ungapped, structure-mapped columns are not superposable
assertFalse(matched[0]);
assertTrue(matched[1]);
assertFalse(matched[2]);
assertFalse(matched[3]);
assertFalse(matched[4]); // superposable, but hidden, column
assertTrue(matched[5]);
}
}