/*
* 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.renderer.seqfeatures;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.schemes.FeatureColour;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import org.testng.annotations.Test;
public class FeatureRendererTest
{
@Test(groups = "Functional")
public void testFindAllFeatures()
{
String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
AlignViewportI av = af.getViewport();
FeatureRenderer fr = new FeatureRenderer(av);
/*
* with no features
*/
fr.findAllFeatures(true);
assertTrue(fr.getRenderOrder().isEmpty());
assertTrue(fr.getFeatureGroups().isEmpty());
List seqs = av.getAlignment().getSequences();
// add a non-positional feature - should be ignored by FeatureRenderer
SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f,
"Group");
seqs.get(0).addSequenceFeature(sf1);
fr.findAllFeatures(true);
// ? bug - types and groups added for non-positional features
List types = fr.getRenderOrder();
List groups = fr.getFeatureGroups();
assertEquals(types.size(), 0);
assertFalse(types.contains("Type"));
assertEquals(groups.size(), 0);
assertFalse(groups.contains("Group"));
// add some positional features
seqs.get(1).addSequenceFeature(
new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup"));
seqs.get(2).addSequenceFeature(
new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup"));
// bug in findAllFeatures - group not checked for a known feature type
seqs.get(2).addSequenceFeature(
new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN,
"RfamGroup"));
// existing feature type with null group
seqs.get(3).addSequenceFeature(
new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
// new feature type with null group
seqs.get(3).addSequenceFeature(
new SequenceFeature("Scop", "Desc", 5, 9, Float.NaN, null));
// null value for type produces NullPointerException
fr.findAllFeatures(true);
types = fr.getRenderOrder();
groups = fr.getFeatureGroups();
assertEquals(types.size(), 3);
assertFalse(types.contains("Type"));
assertTrue(types.contains("Pfam"));
assertTrue(types.contains("Rfam"));
assertTrue(types.contains("Scop"));
assertEquals(groups.size(), 2);
assertFalse(groups.contains("Group"));
assertTrue(groups.contains("PfamGroup"));
assertTrue(groups.contains("RfamGroup"));
assertFalse(groups.contains(null)); // null group is ignored
/*
* check min-max values
*/
Map minMax = fr.getMinMax();
assertEquals(minMax.size(), 1); // non-positional and NaN not stored
assertEquals(minMax.get("Pfam")[0][0], 1f); // positional min
assertEquals(minMax.get("Pfam")[0][1], 2f); // positional max
// increase max for Pfam, add scores for Rfam
seqs.get(0).addSequenceFeature(
new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup"));
seqs.get(1).addSequenceFeature(
new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup"));
fr.findAllFeatures(true);
// note minMax is not a defensive copy, shouldn't expose this
assertEquals(minMax.size(), 2);
assertEquals(minMax.get("Pfam")[0][0], 1f);
assertEquals(minMax.get("Pfam")[0][1], 8f);
assertEquals(minMax.get("Rfam")[0][0], 6f);
assertEquals(minMax.get("Rfam")[0][1], 6f);
/*
* check render order (last is on top)
*/
List renderOrder = fr.getRenderOrder();
assertEquals(renderOrder, Arrays.asList("Scop", "Rfam", "Pfam"));
/*
* change render order (todo: an easier way)
* nb here last comes first in the data array
*/
Object[][] data = new Object[3][];
FeatureColourI colour = new FeatureColour(Color.RED);
data[0] = new Object[] { "Rfam", colour, true };
data[1] = new Object[] { "Pfam", colour, false };
data[2] = new Object[] { "Scop", colour, false };
fr.setFeaturePriority(data);
assertEquals(fr.getRenderOrder(), Arrays.asList("Scop", "Pfam", "Rfam"));
assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
/*
* add a new feature type: should go on top of render order as visible,
* other feature ordering and visibility should be unchanged
*/
seqs.get(2).addSequenceFeature(
new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
fr.findAllFeatures(true);
assertEquals(fr.getRenderOrder(),
Arrays.asList("Scop", "Pfam", "Rfam", "Metal"));
assertEquals(fr.getDisplayedFeatureTypes(),
Arrays.asList("Rfam", "Metal"));
}
@Test(groups = "Functional")
public void testFindFeaturesAtColumn()
{
String seqData = ">s1/4-29\n-ab--cdefghijklmnopqrstuvwxyz\n";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
AlignViewportI av = af.getViewport();
FeatureRenderer fr = new FeatureRenderer(av);
SequenceI seq = av.getAlignment().getSequenceAt(0);
/*
* with no features
*/
List features = fr.findFeaturesAtColumn(seq, 3);
assertTrue(features.isEmpty());
/*
* add features
*/
SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
"Group"); // non-positional
seq.addSequenceFeature(sf1);
SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 8, 18, 1f,
"Group1");
seq.addSequenceFeature(sf2);
SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
"Group2");
seq.addSequenceFeature(sf3);
SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
null); // null group is always treated as visible
seq.addSequenceFeature(sf4);
/*
* add contact features
*/
SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 7,
15, 1f, "Group1");
seq.addSequenceFeature(sf5);
SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 7,
15, 1f, "Group2");
seq.addSequenceFeature(sf6);
SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 7,
15, 1f, null);
seq.addSequenceFeature(sf7);
// feature spanning B--C
SequenceFeature sf8 = new SequenceFeature("Type1", "Desc", 5, 6, 1f,
"Group");
seq.addSequenceFeature(sf8);
// contact feature B/C
SequenceFeature sf9 = new SequenceFeature("Disulphide Bond", "Desc", 5,
6, 1f, "Group");
seq.addSequenceFeature(sf9);
/*
* let feature renderer discover features (and make visible)
*/
fr.findAllFeatures(true);
features = fr.findFeaturesAtColumn(seq, 15); // all positional
assertEquals(features.size(), 6);
assertTrue(features.contains(sf2));
assertTrue(features.contains(sf3));
assertTrue(features.contains(sf4));
assertTrue(features.contains(sf5));
assertTrue(features.contains(sf6));
assertTrue(features.contains(sf7));
/*
* at a non-contact position
*/
features = fr.findFeaturesAtColumn(seq, 14);
assertEquals(features.size(), 3);
assertTrue(features.contains(sf2));
assertTrue(features.contains(sf3));
assertTrue(features.contains(sf4));
/*
* make "Type2" not displayed
*/
Object[][] data = new Object[4][];
FeatureColourI colour = new FeatureColour(Color.RED);
data[0] = new Object[] { "Type1", colour, true };
data[1] = new Object[] { "Type2", colour, false };
data[2] = new Object[] { "Type3", colour, true };
data[3] = new Object[] { "Disulphide Bond", colour, true };
fr.setFeaturePriority(data);
features = fr.findFeaturesAtColumn(seq, 15);
assertEquals(features.size(), 5); // no sf2
assertTrue(features.contains(sf3));
assertTrue(features.contains(sf4));
assertTrue(features.contains(sf5));
assertTrue(features.contains(sf6));
assertTrue(features.contains(sf7));
/*
* make "Group2" not displayed
*/
fr.setGroupVisibility("Group2", false);
features = fr.findFeaturesAtColumn(seq, 15);
assertEquals(features.size(), 3); // no sf2, sf3, sf6
assertTrue(features.contains(sf4));
assertTrue(features.contains(sf5));
assertTrue(features.contains(sf7));
// features 'at' a gap between b and c
// - returns enclosing feature BC but not contact feature B/C
features = fr.findFeaturesAtColumn(seq, 4);
assertEquals(features.size(), 1);
assertTrue(features.contains(sf8));
features = fr.findFeaturesAtColumn(seq, 5);
assertEquals(features.size(), 1);
assertTrue(features.contains(sf8));
}
@Test(groups = "Functional")
public void testFilterFeaturesForDisplay()
{
String seqData = ">s1\nabcdef\n";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
AlignViewportI av = af.getViewport();
FeatureRenderer fr = new FeatureRenderer(av);
List features = new ArrayList<>();
fr.filterFeaturesForDisplay(features, null); // empty list, does nothing
SequenceI seq = av.getAlignment().getSequenceAt(0);
SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
"group1");
seq.addSequenceFeature(sf1);
SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
"group2");
seq.addSequenceFeature(sf2);
SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
"group3");
seq.addSequenceFeature(sf3);
SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
"group4");
seq.addSequenceFeature(sf4);
SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
"group4");
seq.addSequenceFeature(sf5);
fr.findAllFeatures(true);
features = seq.getSequenceFeatures();
assertEquals(features.size(), 5);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
assertTrue(features.contains(sf3));
assertTrue(features.contains(sf4));
assertTrue(features.contains(sf5));
/*
* filter out duplicate (co-located) features
* note: which gets removed is not guaranteed
*/
fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
assertEquals(features.size(), 3);
assertTrue(features.contains(sf1) || features.contains(sf4));
assertFalse(features.contains(sf1) && features.contains(sf4));
assertTrue(features.contains(sf2) || features.contains(sf3));
assertFalse(features.contains(sf2) && features.contains(sf3));
assertTrue(features.contains(sf5));
/*
* hide group 3 - sf3 is removed, sf2 is retained
*/
fr.setGroupVisibility("group3", false);
features = seq.getSequenceFeatures();
fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
assertEquals(features.size(), 3);
assertTrue(features.contains(sf1) || features.contains(sf4));
assertFalse(features.contains(sf1) && features.contains(sf4));
assertTrue(features.contains(sf2));
assertFalse(features.contains(sf3));
assertTrue(features.contains(sf5));
/*
* hide group 2, show group 3 - sf2 is removed, sf3 is retained
*/
fr.setGroupVisibility("group2", false);
fr.setGroupVisibility("group3", true);
features = seq.getSequenceFeatures();
fr.filterFeaturesForDisplay(features, null);
assertEquals(features.size(), 3);
assertTrue(features.contains(sf1) || features.contains(sf4));
assertFalse(features.contains(sf1) && features.contains(sf4));
assertFalse(features.contains(sf2));
assertTrue(features.contains(sf3));
assertTrue(features.contains(sf5));
/*
* no filtering of co-located features with graduated colour scheme
* filterFeaturesForDisplay does _not_ check colour threshold
* sf2 is removed as its group is hidden
*/
features = seq.getSequenceFeatures();
fr.filterFeaturesForDisplay(features, new FeatureColour(Color.black,
Color.white, 0f, 1f));
assertEquals(features.size(), 4);
assertFalse(features.contains(sf2));
/*
* co-located features with colour by label
* should not get filtered
*/
features = seq.getSequenceFeatures();
FeatureColour fc = new FeatureColour(Color.black);
fc.setColourByLabel(true);
fr.filterFeaturesForDisplay(features, fc);
assertEquals(features.size(), 4);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf3));
assertTrue(features.contains(sf4));
assertTrue(features.contains(sf5));
/*
* no filtering if transparency is applied
*/
fr.setTransparency(0.5f);
features = seq.getSequenceFeatures();
fr.setGroupVisibility("group2", true);
fr.filterFeaturesForDisplay(features, new FeatureColour(Color.RED));
assertEquals(features.size(), 5);
}
}