+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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.assertNotNull;
import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.Test;
+
+import jalview.analysis.GeneticCodes;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
+import jalview.bin.Jalview;
+import jalview.datamodel.MappedFeatures;
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.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.schemes.FeatureColour;
import jalview.util.matcher.Condition;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.Test;
-
public class FeatureRendererTest
{
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ }
@Test(groups = "Functional")
public void testFindAllFeatures()
* give "Type3" features a graduated colour scheme
* - first with no threshold
*/
- FeatureColourI gc = new FeatureColour(Color.yellow, Color.red, null, 0f,
- 10f);
+ FeatureColourI gc = new FeatureColour(Color.green, Color.yellow,
+ Color.red, null, 0f, 10f);
fr.getFeatureColours().put("Type3", gc);
features = fr.findFeaturesAtColumn(seq, 8);
assertTrue(features.contains(sf4));
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(sf1);
+ seq.addSequenceFeature(sf2);
+ seq.addSequenceFeature(sf3);
+ seq.addSequenceFeature(sf4);
seq.addSequenceFeature(sf5);
fr.findAllFeatures(true);
assertTrue(features.contains(sf5));
/*
- * hide groups 2 and 3 makes no difference to this method
+ * features in hidden groups are removed
*/
fr.setGroupVisibility("group2", false);
fr.setGroupVisibility("group3", false);
features = seq.getSequenceFeatures();
fr.filterFeaturesForDisplay(features);
- assertEquals(features.size(), 3);
+ assertEquals(features.size(), 2);
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));
+ assertFalse(features.contains(sf2));
+ assertFalse(features.contains(sf3));
assertTrue(features.contains(sf5));
/*
* graduated colour by score, no threshold, no score
*
*/
- FeatureColourI gc = new FeatureColour(Color.yellow, Color.red,
- Color.green, 1f, 11f);
+ FeatureColourI gc = new FeatureColour(Color.red, Color.yellow,
+ Color.red, Color.green, 1f, 11f);
fr.getFeatureColours().put("Cath", gc);
assertEquals(fr.getColour(sf1), Color.green);
* threshold is min-max; now score 6 is 1/6 of the way from 5 to 11
* or from yellow(255, 255, 0) to red(255, 0, 0)
*/
- gc = new FeatureColour(Color.yellow, Color.red, Color.green, 5f, 11f);
+ gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
+ 5f, 11f);
fr.getFeatureColours().put("Cath", gc);
- gc.setAutoScaled(false); // this does little other than save a checkbox setting!
+ gc.setAutoScaled(false); // this does little other than save a checkbox
+ // setting!
assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
/*
* colour by feature attribute value
* first with no value held
*/
- gc = new FeatureColour(Color.yellow, Color.red, Color.green, 1f, 11f);
+ gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
+ 1f, 11f);
fr.getFeatureColours().put("Cath", gc);
gc.setAttributeName("AF");
assertEquals(fr.getColour(sf2), Color.green);
csqData.put("Feature", "ENST01234");
assertEquals(fr.getColour(sf2), expected);
}
+
+ @Test(groups = "Functional")
+ public void testIsVisible()
+ {
+ String seqData = ">s1\nMLQGIFPRS\n";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+ DataSourceType.PASTE);
+ AlignViewportI av = af.getViewport();
+ FeatureRenderer fr = new FeatureRenderer(av);
+ SequenceI seq = av.getAlignment().getSequenceAt(0);
+ SequenceFeature sf = new SequenceFeature("METAL", "Desc", 10, 10, 1f,
+ "Group");
+ sf.setValue("AC", "11");
+ sf.setValue("CLIN_SIG", "Likely Pathogenic");
+ seq.addSequenceFeature(sf);
+
+ assertFalse(fr.isVisible(null));
+
+ /*
+ * initial state FeatureRenderer hasn't 'found' feature
+ * and so its feature type has not yet been set visible
+ */
+ assertFalse(fr.getDisplayedFeatureCols().containsKey("METAL"));
+ assertFalse(fr.isVisible(sf));
+
+ fr.findAllFeatures(true);
+ assertTrue(fr.isVisible(sf));
+
+ /*
+ * feature group not visible
+ */
+ fr.setGroupVisibility("Group", false);
+ assertFalse(fr.isVisible(sf));
+ fr.setGroupVisibility("Group", true);
+ assertTrue(fr.isVisible(sf));
+
+ /*
+ * feature score outwith colour threshold (score > 2)
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
+ Color.white, 0, 10);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(2f);
+ fr.setColour("METAL", fc);
+ assertFalse(fr.isVisible(sf)); // score 1 is not above threshold 2
+ fc.setBelowThreshold(true);
+ assertTrue(fr.isVisible(sf)); // score 1 is below threshold 2
+
+ /*
+ * colour with threshold on attribute AC (value is 11)
+ */
+ fc.setAttributeName("AC");
+ assertFalse(fr.isVisible(sf)); // value 11 is not below threshold 2
+ fc.setAboveThreshold(true);
+ assertTrue(fr.isVisible(sf)); // value 11 is above threshold 2
+
+ fc.setAttributeName("AF"); // attribute AF is absent in sf
+ assertTrue(fr.isVisible(sf)); // feature is not excluded by threshold
+
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "pathogenic",
+ "CLIN_SIG"));
+ fr.setFeatureFilter("METAL", filter);
+ assertTrue(fr.isVisible(sf)); // feature matches filter
+ filter.and(FeatureMatcher.byScore(Condition.LE, "0.4"));
+ assertFalse(fr.isVisible(sf)); // feature doesn't match filter
+ }
+
+ @Test(groups = "Functional")
+ public void testFindComplementFeaturesAtResidue()
+ {
+ Jalview.main(
+ new String[]
+ { "-nonews", "-props", "test/jalview/testProps.jvprops" });
+
+ // codons for MCWHSE
+ String cdsSeq = ">cds\nATGtgtTGGcacTCAgaa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(cdsSeq,
+ DataSourceType.PASTE);
+ af.showTranslation_actionPerformed(
+ GeneticCodes.getInstance().getStandardCodeTable());
+ af.closeMenuItem_actionPerformed(true);
+
+ /*
+ * find the complement frames (ugly)
+ */
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ assertEquals(frames.length, 2);
+ AlignViewport av1 = frames[0].getViewport();
+ AlignViewport av2 = frames[1].getViewport();
+ AlignViewport cds = av1.getAlignment().isNucleotide() ? av1 : av2;
+ AlignViewport peptide = cds == av1 ? av2 : av1;
+ assertNotNull(cds);
+ assertNotNull(peptide);
+
+ /*
+ * add features to CDS at first codon, positions 2-3
+ */
+ SequenceI seq1 = cds.getAlignment().getSequenceAt(0);
+ SequenceFeature sf1 = new SequenceFeature("sequence_variant", "G,GT", 2,
+ 2, "ensembl");
+ seq1.addSequenceFeature(sf1);
+ SequenceFeature sf2 = new SequenceFeature("sequence_variant", "C, CA",
+ 3, 3, "ensembl");
+ seq1.addSequenceFeature(sf2);
+
+ /*
+ * 'find' mapped features from the peptide position
+ * - first with CDS features _not_ shown on peptide alignment
+ */
+ SequenceI seq2 = peptide.getAlignment().getSequenceAt(0);
+ FeatureRenderer frC = new FeatureRenderer(cds);
+ frC.featuresAdded();
+ MappedFeatures mf = frC.findComplementFeaturesAtResidue(seq2, 1);
+ assertNotNull(mf);
+ assertEquals(mf.features.size(), 2);
+ assertSame(mf.features.get(0), sf1);
+ assertSame(mf.features.get(1), sf2);
+
+ /*
+ * add exon feature and verify it is only returned once for a
+ * peptide position, even though it is on all 3 codon positions
+ */
+ SequenceFeature sf3 = new SequenceFeature("exon", "exon1", 4, 12,
+ "ensembl");
+ seq1.addSequenceFeature(sf3);
+ frC.featuresAdded();
+ mf = frC.findComplementFeaturesAtResidue(seq2, 3);
+ assertNotNull(mf);
+ assertEquals(mf.features.size(), 1);
+ assertSame(mf.features.get(0), sf3);
+ }
}
git://source.jalview.org / jalview.git / blobdiff