/*
* 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.analysis.scoremodels;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.math.MatrixI;
import java.util.Arrays;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class FeatureDistanceModelTest
{
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n";
int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 };
int[] sf2 = new int[] { -1, -1, 74, 75, -1, -1, 76, 77 };
int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 };
/**
*
* Load test alignment and add features to sequences:
* FER1_MESCR FER1_SPIOL FER3_RAPSA FER1_MAIZE
* sf1 X X X
* sf2 X X
* sf3 X
*
*
* @return
*/
public AlignFrame getTestAlignmentFrame()
{
AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
alntestFile, DataSourceType.PASTE);
AlignmentI al = alf.getViewport().getAlignment();
Assert.assertEquals(al.getHeight(), 4);
Assert.assertEquals(al.getWidth(), 5);
for (int i = 0; i < 4; i++)
{
SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
if (sf1[i * 2] > 0)
{
ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", sf1[i * 2],
sf1[i * 2 + 1], "sf1"));
}
if (sf2[i * 2] > 0)
{
ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", sf2[i * 2],
sf2[i * 2 + 1], "sf2"));
}
if (sf3[i * 2] > 0)
{
ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", sf3[i * 2],
sf3[i * 2 + 1], "sf3"));
}
}
alf.setShowSeqFeatures(true);
alf.getFeatureRenderer().setVisible("sf1");
alf.getFeatureRenderer().setVisible("sf2");
alf.getFeatureRenderer().setVisible("sf3");
alf.getFeatureRenderer().findAllFeatures(true);
Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
.size(), 3, "Number of feature types");
assertTrue(alf.getCurrentView().areFeaturesDisplayed());
return alf;
}
@Test(groups = { "Functional" })
public void testFeatureScoreModel() throws Exception
{
AlignFrame alf = getTestAlignmentFrame();
ScoreModelI sm = new FeatureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
MatrixI dm = sm.findDistances(
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
"FER1_MESCR (0) should be identical with RAPSA (2)");
assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
"FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
}
@Test(groups = { "Functional" })
public void testFeatureScoreModel_hiddenFirstColumn() throws Exception
{
AlignFrame alf = getTestAlignmentFrame();
// hiding first two columns shouldn't affect the tree
alf.getViewport().hideColumns(0, 1);
ScoreModelI sm = new FeatureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
MatrixI dm = sm.findDistances(
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
"FER1_MESCR (0) should be identical with RAPSA (2)");
assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
"FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
}
@Test(groups = { "Functional" })
public void testFeatureScoreModel_HiddenColumns() throws Exception
{
AlignFrame alf = getTestAlignmentFrame();
// hide columns and check tree changes
alf.getViewport().hideColumns(3, 4);
alf.getViewport().hideColumns(0, 1);
// getName() can become static in Java 8
ScoreModelI sm = new FeatureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
MatrixI dm = sm.findDistances(
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(
dm.getValue(0, 2),
0d,
"After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
assertEquals(
dm.getValue(0, 1),
0d,
"After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
for (int s = 0; s < 3; s++)
{
assertTrue(dm.getValue(s, 3) > 0d, "After hiding last two columns "
+ alf.getViewport().getAlignment().getSequenceAt(s).getName()
+ "(" + s + ") should still be distinct from FER1_MAIZE (3)");
}
}
/**
* Check findFeatureAt doesn't return contact features except at contact
* points TODO:move to under the FeatureRendererModel test suite
*/
@Test(groups = { "Functional" })
public void testFindFeatureAt_PointFeature() throws Exception
{
String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n"
+ "c CCCCCCGGGGGGCCCCCC\n";
AlignFrame af = new jalview.io.FileLoader(false)
.LoadFileWaitTillLoaded(alignment, DataSourceType.PASTE);
SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0);
SequenceFeature sf = null;
sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, "");
aseq.addSequenceFeature(sf);
assertTrue(sf.isContactFeature());
af.refreshFeatureUI(true);
af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
.size(), 1, "Should be just one feature type displayed");
// step through and check for pointwise feature presence/absence
Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1)
.size(), 0);
// step through and check for pointwise feature presence/absence
Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2)
.size(), 1);
// step through and check for pointwise feature presence/absence
Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3)
.size(), 0);
// step through and check for pointwise feature presence/absence
Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4)
.size(), 0);
// step through and check for pointwise feature presence/absence
Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5)
.size(), 1);
// step through and check for pointwise feature presence/absence
Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6)
.size(), 0);
}
@Test(groups = { "Functional" })
public void testFindDistances() throws Exception
{
String seqs = ">s1\nABCDE\n>seq2\nABCDE\n";
AlignFrame alf = new FileLoader().LoadFileWaitTillLoaded(seqs,
DataSourceType.PASTE);
SequenceI s1 = alf.getViewport().getAlignment().getSequenceAt(0);
SequenceI s2 = alf.getViewport().getAlignment().getSequenceAt(1);
/*
* set domain and variant features thus:
* ----5
* s1 ddd..
* s1 .vvv.
* s1 ..vvv
* s2 .ddd.
* s2 vv..v
* The number of unshared feature types per column is
* 20120 (two features of the same type doesn't affect score)
* giving an average (pairwise distance) of 5/5 or 1.0
*/
s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 3, 0f,
null));
s1.addSequenceFeature(new SequenceFeature("variant", null, 2, 4, 0f,
null));
s1.addSequenceFeature(new SequenceFeature("variant", null, 3, 5, 0f,
null));
s2.addSequenceFeature(new SequenceFeature("domain", null, 2, 4, 0f,
null));
s2.addSequenceFeature(new SequenceFeature("variant", null, 1, 2, 0f,
null));
s2.addSequenceFeature(new SequenceFeature("variant", null, 5, 5, 0f,
null));
alf.setShowSeqFeatures(true);
alf.getFeatureRenderer().findAllFeatures(true);
ScoreModelI sm = new FeatureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
AlignmentView alignmentView = alf.getViewport()
.getAlignmentView(true);
MatrixI distances = sm.findDistances(alignmentView,
SimilarityParams.Jalview);
assertEquals(distances.width(), 2);
assertEquals(distances.height(), 2);
assertEquals(distances.getValue(0, 0), 0d);
assertEquals(distances.getValue(1, 1), 0d);
assertEquals(distances.getValue(0, 1), 1d,
"expected identical pairs. (check normalisation for similarity score)");
assertEquals(distances.getValue(1, 0), 1d);
}
/**
* Verify computed distances with varying parameter options
*/
@Test(groups = "Functional")
public void testFindDistances_withParams()
{
AlignFrame af = setupAlignmentView();
AlignViewport viewport = af.getViewport();
AlignmentView view = viewport.getAlignmentView(false);
ScoreModelI sm = new FeatureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
af.alignPanel);
/*
* feature distance model always normalises by region width
* gap-gap is always included (but scores zero)
* the only variable parameter is 'includeGaps'
*/
/*
* include gaps
* score = 3 + 3 + 0 + 2 + 3 + 2 = 13/6
*/
SimilarityParamsI params = new SimilarityParams(true, true, true, true);
MatrixI distances = sm.findDistances(view, params);
assertEquals(distances.getValue(0, 0), 0d);
assertEquals(distances.getValue(1, 1), 0d);
assertEquals(distances.getValue(0, 1), 13d / 6); // should be 13d/6
assertEquals(distances.getValue(1, 0), 13d / 6);
/*
* exclude gaps
* score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6
*/
params = new SimilarityParams(true, true, false, true);
distances = sm.findDistances(view, params);
assertEquals(distances.getValue(0, 1), 6d / 6);// should be 6d/6
}
/**
*
* Set up
* column 1 2 3 4 5 6
* seq s1 F R - K - S
* seq s2 F S - - L
* s1 chain c c c c
* s1 domain d d d d
* s2 chain c c c
* s2 metal m m m
* s2 Pfam P P P
* scores: 3 3 0 2 3 2
*
*
* @return
*/
protected AlignFrame setupAlignmentView()
{
/*
* for now, using space for gap to match callers of
* AlignmentView.getSequenceStrings()
* may change this to '-' (with corresponding change to matrices)
*/
SequenceI s1 = new Sequence("s1", "FR K S");
SequenceI s2 = new Sequence("s2", "FS L");
s1.addSequenceFeature(new SequenceFeature("chain", null, 1, 4, 0f, null));
s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 4, 0f,
null));
s2.addSequenceFeature(new SequenceFeature("chain", null, 1, 3, 0f, null));
s2.addSequenceFeature(new SequenceFeature("metal", null, 1, 3, 0f, null));
s2.addSequenceFeature(new SequenceFeature("Pfam", null, 1, 3, 0f, null));
AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
AlignFrame af = new AlignFrame(al, 300, 300);
af.setShowSeqFeatures(true);
af.getFeatureRenderer().findAllFeatures(true);
return af;
}
}