/*
* 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.Assert.assertEquals;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcher;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FileLoader;
import jalview.io.IdentifyFile;
import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureColourTest;
import jalview.util.matcher.Condition;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
public class FeatureSettingsTest
{
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
/*
* use read-only test properties file
*/
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Jalview.main(new String[] { "--nonews" });
}
@AfterMethod(alwaysRun = true)
public void tearDown()
{
if (Desktop.instance != null)
Desktop.instance.closeAll_actionPerformed(null);
}
/**
* Test a roundtrip of save and reload of feature colours and filters as XML
*
* @throws IOException
*/
@Test(groups = "Functional")
public void testSaveLoad() throws IOException
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
/*
* add some features to the sequence
*/
int score = 1;
addFeatures(seq1, "type1", score++);
addFeatures(seq1, "type2", score++);
addFeatures(seq1, "type3", score++);
addFeatures(seq1, "type4", score++);
addFeatures(seq1, "type5", score++);
/*
* set colour schemes for features
*/
FeatureRendererModel fr = af.getFeatureRenderer();
// type1: red
fr.setColour("type1", new FeatureColour(Color.red));
// type2: by label
FeatureColourI byLabel = new FeatureColour();
byLabel.setColourByLabel(true);
fr.setColour("type2", byLabel);
// type3: by score above threshold
FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
Color.BLUE, null, 1, 10);
byScore.setAboveThreshold(true);
byScore.setThreshold(2f);
fr.setColour("type3", byScore);
// type4: by attribute AF
FeatureColourI byAF = new FeatureColour();
byAF.setColourByLabel(true);
byAF.setAttributeName("AF");
fr.setColour("type4", byAF);
// type5: by attribute CSQ:PolyPhen below threshold
FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
Color.BLUE, null, 1, 10);
byPolyPhen.setBelowThreshold(true);
byPolyPhen.setThreshold(3f);
byPolyPhen.setAttributeName("CSQ", "PolyPhen");
fr.setColour("type5", byPolyPhen);
/*
* set filters for feature types
*/
// filter type1 features by (label contains "x")
FeatureMatcherSetI filterByX = new FeatureMatcherSet();
filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
fr.setFeatureFilter("type1", filterByX);
// filter type2 features by (score <= 2.4 and score > 1.1)
FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
fr.setFeatureFilter("type2", filterByScore);
// filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
filterByXY
.and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
"PolyPhen"));
fr.setFeatureFilter("type3", filterByXY);
/*
* save colours and filters to an XML file
*/
File coloursFile = File.createTempFile("testSaveLoad", ".fc");
coloursFile.deleteOnExit();
FeatureSettings fs = new FeatureSettings(af);
fs.save(coloursFile);
/*
* change feature colours and filters
*/
FeatureColourI pink = new FeatureColour(Color.pink);
fr.setColour("type1", pink);
fr.setColour("type2", pink);
fr.setColour("type3", pink);
fr.setColour("type4", pink);
fr.setColour("type5", pink);
FeatureMatcherSetI filter2 = new FeatureMatcherSet();
filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));
fr.setFeatureFilter("type1", filter2);
fr.setFeatureFilter("type2", filter2);
fr.setFeatureFilter("type3", filter2);
fr.setFeatureFilter("type4", filter2);
fr.setFeatureFilter("type5", filter2);
/*
* reload colours and filters from file and verify they are restored
*/
fs.load(coloursFile);
FeatureColourI fc = fr.getFeatureStyle("type1");
assertTrue(fc.isSimpleColour());
assertEquals(fc.getColour(), Color.red);
fc = fr.getFeatureStyle("type2");
assertTrue(fc.isColourByLabel());
fc = fr.getFeatureStyle("type3");
assertTrue(fc.isGraduatedColour());
assertNull(fc.getAttributeName());
assertTrue(fc.isAboveThreshold());
assertEquals(fc.getThreshold(), 2f);
fc = fr.getFeatureStyle("type4");
assertTrue(fc.isColourByLabel());
assertTrue(fc.isColourByAttribute());
assertEquals(fc.getAttributeName(), new String[] { "AF" });
fc = fr.getFeatureStyle("type5");
assertTrue(fc.isGraduatedColour());
assertTrue(fc.isColourByAttribute());
assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
assertTrue(fc.isBelowThreshold());
assertEquals(fc.getThreshold(), 3f);
assertEquals(fr.getFeatureFilter("type1").toStableString(),
"Label Contains x");
assertEquals(fr.getFeatureFilter("type2").toStableString(),
"(Score LE 2.4) AND (Score GT 1.1)");
assertEquals(fr.getFeatureFilter("type3").toStableString(),
"(AF Contains X) OR (CSQ:PolyPhen NE 0)");
}
/**
* Adds two features of the given type to the given sequence, also setting the
* score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
*
* @param seq
* @param featureType
* @param score
*/
private void addFeatures(SequenceI seq, String featureType, int score)
{
addFeature(seq, featureType, score++);
addFeature(seq, featureType, score);
}
private void addFeature(SequenceI seq, String featureType, int score)
{
SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
score, "grp");
sf.setValue("AF", score);
sf.setValue("CSQ", new HashMap()
{
{
put("PolyPhen", Integer.toString(score));
}
});
seq.addSequenceFeature(sf);
}
/**
* @see FeatureColourTest#testGetDescription()
* @throws IOException
*/
@Test(groups = "Functional")
public void testGetColorTooltip() throws IOException
{
assertNull(FeatureSettings.getColorTooltip(null, false));
/*
* simple colour
*/
FeatureColourI fc = new FeatureColour(Color.black);
String simpleTooltip = "Click to edit, right-click for menu";
assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);
assertNull(FeatureSettings.getColorTooltip(fc, false));
/*
* graduated colour tooltip includes description of colour
*/
fc.setColourByLabel(true);
assertEquals(FeatureSettings.getColorTooltip(fc, false),
"By Label");
assertEquals(FeatureSettings.getColorTooltip(fc, true),
"By Label
" + simpleTooltip + "");
/*
* graduated colour with threshold is html-encoded
*/
fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
fc.setBelowThreshold(true);
fc.setThreshold(4f);
assertEquals(FeatureSettings.getColorTooltip(fc, false),
"By Score (< 4.0)");
assertEquals(FeatureSettings.getColorTooltip(fc, true),
"By Score (< 4.0)
" + simpleTooltip
+ "");
fc.setAboveThreshold(true);
assertEquals(FeatureSettings.getColorTooltip(fc, false),
"By Score (> 4.0)");
assertEquals(FeatureSettings.getColorTooltip(fc, true),
"By Score (> 4.0)
" + simpleTooltip
+ "");
}
String fsfile = "",
fsfile2 = "\n";
@Test(groups = "Functional")
public void testIdentifyFeatureSettingsFile() throws Exception
{
FileFormatI type = new IdentifyFile().identify(fsfile,
DataSourceType.PASTE);
assertTrue(FileFormat.FeatureSettings == type,
"Feature settings file was identified as " + type);
type = new IdentifyFile().identify(fsfile2, DataSourceType.PASTE);
assertTrue(FileFormat.FeatureSettings == type,
"Feature settings file with newline was identified as " + type);
}
}