/*
* 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.structures.models;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import java.awt.Color;
import java.io.IOException;
import java.util.Arrays;
import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import jalview.api.AlignmentViewPanel;
import jalview.api.SequenceRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.ChimeraCommands;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpec;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import junit.extensions.PA;
/**
* Unit tests for non-abstract methods of abstract base class
*
* @author gmcarstairs
*
*/
public class AAStructureBindingModelTest
{
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
/*
* Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
*/
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"
// artificial jump in residue numbering to prove it is correctly
// mapped:
+ "ATOM 31 CA LYS A 102 33.323 11.587 43.115 1.00 41.69 C \n"
+ "ATOM 1857 CA GLU B 374 9.193 -16.005 95.870 1.00 54.22 C \n"
+ "ATOM 1866 CA ILE B 375 7.101 -14.921 92.847 1.00 46.82 C \n"
+ "ATOM 1874 CA VAL B 376 10.251 -13.625 91.155 1.00 47.80 C \n"
+ "ATOM 1881 CA LYS B 377 11.767 -17.068 91.763 1.00 50.21 C \n"
+ "ATOM 1890 CA PHE B 378 8.665 -18.948 90.632 1.00 44.85 C \n";
private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
+ "ATOM 2 CA MET B 1 15.366 -11.648 24.854 1.00 32.05 C \n"
+ "ATOM 10 CA LYS B 2 16.846 -9.215 22.340 1.00 25.68 C \n"
+ "ATOM 19 CA LYS B 3 15.412 -6.335 20.343 1.00 19.42 C \n"
+ "ATOM 28 CA LEU B 4 15.629 -5.719 16.616 1.00 15.49 C \n"
+ "ATOM 36 CA GLN B 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 7 29.427 3.330 -6.578 1.00 32.50 C \n"
+ "ATOM 8 CA PRO A 8 29.975 3.340 -2.797 1.00 17.62 C \n"
+ "ATOM 16 CA ALYS A 9 26.958 3.024 -0.410 0.50 8.78 C \n"
+ "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n"
+ "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n";
/**
* Multichain PDB with identical sequences imported - Binding should correctly
* recover chain mappings for each derived sequence
*/
private static final String PDB_4_MC = "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"
+ "ATOM 1030 CA MET B 1 18.869 -7.572 3.432 1.00 31.52 C \n"
+ "ATOM 1038 CA LYS B 2 19.182 -10.025 6.313 1.00 26.41 C \n"
+ "ATOM 1047 CA LYS B 3 17.107 -12.963 7.534 1.00 19.71 C \n"
+ "ATOM 1056 CA LEU B 4 16.142 -13.579 11.164 1.00 14.81 C \n"
+ "ATOM 1064 CA GLN B 5 14.648 -17.005 11.785 1.00 13.38 C \n";
// TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains
@Test(groups = { "Functional" })
public void testImportPDBPreservesChainMappings() throws IOException
{
AlignmentI importedAl = new jalview.io.FormatAdapter().readFile(
PDB_4_MC, DataSourceType.PASTE, FileFormats.getInstance()
.forName(jalview.io.FileFormat.PDB.toString()));
// ideally, we would match on the actual data for the 'File' handle for
// pasted files,
// see JAL-623 - pasting is still not correctly handled...
PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB, "Paste");
AAStructureBindingModel binder = new AAStructureBindingModel(
new StructureSelectionManager(), new PDBEntry[]
{ importedPDB },
new SequenceI[][]
{ importedAl.getSequencesArray() }, null)
{
@Override
public void updateColours(Object source)
{
}
@Override
public void releaseReferences(Object svl)
{
}
@Override
public String[] getStructureFiles()
{
return null;
}
@Override
public void highlightAtoms(List atoms)
{
}
@Override
public SequenceRenderer getSequenceRenderer(
AlignmentViewPanel alignment)
{
return null;
}
@Override
protected List executeCommand(StructureCommandI command,
boolean getReply)
{
return null;
}
@Override
protected String getModelIdForFile(String chainId)
{
return "";
}
@Override
protected ViewerType getViewerType()
{
return null;
}
};
String[][] chains = binder.getChains();
assertFalse(chains == null || chains[0] == null,
"No chains discovered by binding");
assertEquals(chains[0].length, 2);
assertEquals(chains[0][0], "A");
assertEquals(chains[0][1], "B");
}
AAStructureBindingModel testee;
AlignmentI al = null;
/**
* Set up test conditions with three aligned sequences,
*/
@BeforeMethod(alwaysRun = true)
public void setUp()
{
SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
al.setDataset(null);
/*
* give pdb files the name generated by Jalview for PASTE source
*/
PDBEntry[] pdbFiles = new PDBEntry[3];
pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
SequenceI[][] seqs = new SequenceI[3][];
seqs[0] = new SequenceI[] { seq1a, seq1b };
seqs[1] = new SequenceI[] { seq2 };
seqs[2] = new SequenceI[] { seq3 };
StructureSelectionManager ssm = new StructureSelectionManager();
ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
DataSourceType.PASTE, null);
testee = newBindingModel(pdbFiles, seqs, ssm, null);
}
/**
* A helper method to construct the test target object
*
* @param pdbFiles
* @param seqs
* @param ssm
* @param alignPanel
*/
protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles,
SequenceI[][] seqs, StructureSelectionManager ssm,
AlignmentViewPanel avp)
{
AAStructureBindingModel model = new AAStructureBindingModel(ssm,
pdbFiles, seqs, null)
{
@Override
public String[] getStructureFiles()
{
String[] files = new String[getPdbCount()];
for (int i = 0; i < this.getPdbCount(); i++)
{
files[i] = getPdbEntry(i).getFile();
}
return files;
}
@Override
public void updateColours(Object source)
{
}
@Override
public void releaseReferences(Object svl)
{
}
@Override
public void highlightAtoms(List atoms)
{
}
@Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
{
return avp == null ? null
: new jalview.gui.SequenceRenderer(avp.getAlignViewport());
}
@Override
protected List executeCommand(StructureCommandI command,
boolean getReply)
{
return null;
}
/*
* for this test, let structure model ids be 0, 1, ...
* corresponding to first, second etc pdbfile
*/
@Override
protected String getModelIdForFile(String pdbfile)
{
for (int i = 0; i < this.getPdbCount(); i++)
{
if (pdbfile.equals(this.getPdbEntry(i).getFile()))
{
return String.valueOf(i);
}
}
return "";
}
@Override
protected ViewerType getViewerType()
{
return null;
}
};
PA.setValue(model, "commandGenerator", new ChimeraCommands());
return model;
}
/**
* Verify that the method determines that columns 2, 5 and 6 of the alignment
* are alignable in structure
*/
@Test(groups = { "Functional" })
public void testFindSuperposableResidues()
{
/*
* create a data bean to hold data per structure file
*/
AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee
.getStructureFiles().length];
for (int i = 0; i < structs.length; i++)
{
structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
"0");
}
/*
* initialise BitSet of 'superposable columns' to true (would be false for
* hidden columns)
*/
BitSet matched = new BitSet();
for (int i = 0; i < al.getWidth(); i++)
{
matched.set(i);
}
int refStructure = testee.findSuperposableResidues(al, matched,
structs);
assertEquals(refStructure, 0);
/*
* only ungapped, structure-mapped columns are superposable
*/
assertFalse(matched.get(0)); // gap in first sequence
assertTrue(matched.get(1));
assertFalse(matched.get(2)); // gap in third sequence
assertFalse(matched.get(3)); // gap in fourth sequence
assertTrue(matched.get(4));
assertTrue(matched.get(5)); // gap in second sequence
assertEquals(structs[0].pdbId, "1YCS");
assertEquals(structs[1].pdbId, "3A6S");
assertEquals(structs[2].pdbId, "1OOT");
assertEquals(structs[0].chain, "A"); // ? struct has chains A _and_ B
assertEquals(structs[1].chain, "B");
assertEquals(structs[2].chain, "A");
// the 0's for unsuperposable positions propagate down the columns:
assertEquals(Arrays.toString(structs[0].pdbResNo),
"[0, 97, 98, 99, 100, 102]");
assertEquals(Arrays.toString(structs[1].pdbResNo),
"[0, 2, 0, 3, 4, 5]");
assertEquals(Arrays.toString(structs[2].pdbResNo),
"[0, 8, 0, 0, 10, 12]");
}
@Test(groups = { "Functional" })
public void testFindSuperposableResidues_hiddenColumn()
{
AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al
.getHeight()];
for (int i = 0; i < structs.length; i++)
{
structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
"0");
}
/*
* initialise BitSet of 'superposable columns' to true (would be false for
* hidden columns)
*/
BitSet matched = new BitSet();
for (int i = 0; i < al.getWidth(); i++)
{
matched.set(i);
}
// treat column 5 of the alignment as hidden
matched.clear(4);
int refStructure = testee.findSuperposableResidues(al, matched,
structs);
assertEquals(refStructure, 0);
// only ungapped, structure-mapped columns are not superposable
assertFalse(matched.get(0));
assertTrue(matched.get(1));
assertFalse(matched.get(2));
assertFalse(matched.get(3));
assertFalse(matched.get(4)); // superposable, but hidden, column
assertTrue(matched.get(5));
}
@Test(groups = { "Functional" })
public void testBuildColoursMap()
{
/*
* load these sequences, coloured by Strand propensity,
* with columns 2-4 hidden
*/
String fasta = ">seq1\nMHRSQSSSGG\n>seq2\nMVRSNGGSSS";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
DataSourceType.PASTE);
AlignmentI al = af.getViewport().getAlignment();
af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
ColumnSelection cs = new ColumnSelection();
cs.addElement(2);
cs.addElement(3);
cs.addElement(4);
af.getViewport().setColumnSelection(cs);
af.hideSelColumns_actionPerformed(null);
SequenceI seq1 = al.getSequenceAt(0);
SequenceI seq2 = al.getSequenceAt(1);
SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
PDBEntry[] pdbFiles = new PDBEntry[2];
pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
StructureSelectionManager ssm = new StructureSelectionManager();
/*
* map residues 1-10 to residues 21-30 (atoms 105-150) in structures
*/
HashMap map = new HashMap<>();
for (int pos = 1; pos <= seq1.getLength(); pos++)
{
map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
}
StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
"A", map, null);
ssm.addStructureMapping(sm1);
StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
"B", map, null);
ssm.addStructureMapping(sm2);
AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm,
af.alignPanel);
/*
* method under test builds a map of structures residues by colour
* verify the map holds what it should
*/
Map