+++ /dev/null
-/*
- * 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.io;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.api.FeatureColourI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.io.gff.GffConstants;
-import jalview.renderer.seqfeatures.FeatureRenderer;
-import jalview.schemes.FeatureColour;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-
-import java.awt.Color;
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-import junit.extensions.PA;
-
-public class SequenceAnnotationReportTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = "Functional")
- public void testAppendFeature_disulfideBond()
- {
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuilder sb = new StringBuilder();
- sb.append("123456");
- SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
- 3, 1.2f, "group");
-
- // residuePos == 2 does not match start or end of feature, nothing done:
- sar.appendFeature(sb, 2, null, sf);
- assertEquals("123456", sb.toString());
-
- // residuePos == 1 matches start of feature, text appended (but no <br>)
- // feature score is not included
- sar.appendFeature(sb, 1, null, sf);
- assertEquals("123456disulfide bond 1:3", sb.toString());
-
- // residuePos == 3 matches end of feature, text appended
- // <br> is prefixed once sb.length() > 6
- sar.appendFeature(sb, 3, null, sf);
- assertEquals("123456disulfide bond 1:3<br>disulfide bond 1:3",
- sb.toString());
- }
-
- @Test(groups = "Functional")
- public void testAppendFeature_status()
- {
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuilder sb = new StringBuilder();
- SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
- Float.NaN, "group");
- sf.setStatus("Confirmed");
-
- sar.appendFeature(sb, 1, null, sf);
- assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
- }
-
- @Test(groups = "Functional")
- public void testAppendFeature_withScore()
- {
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuilder sb = new StringBuilder();
- SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
- "group");
-
- FeatureRendererModel fr = new FeatureRenderer(null);
- Map<String, float[][]> minmax = fr.getMinMax();
- sar.appendFeature(sb, 1, fr, sf);
- /*
- * map has no entry for this feature type - score is not shown:
- */
- assertEquals("METAL 1 3; Fe2-S", sb.toString());
-
- /*
- * map has entry for this feature type - score is shown:
- */
- minmax.put("METAL", new float[][] { { 0f, 1f }, null });
- sar.appendFeature(sb, 1, fr, sf);
- // <br> is appended to a buffer > 6 in length
- assertEquals("METAL 1 3; Fe2-S<br>METAL 1 3; Fe2-S Score=1.3",
- sb.toString());
-
- /*
- * map has min == max for this feature type - score is not shown:
- */
- minmax.put("METAL", new float[][] { { 2f, 2f }, null });
- sb.setLength(0);
- sar.appendFeature(sb, 1, fr, sf);
- assertEquals("METAL 1 3; Fe2-S", sb.toString());
- }
-
- @Test(groups = "Functional")
- public void testAppendFeature_noScore()
- {
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuilder sb = new StringBuilder();
- SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
- Float.NaN, "group");
-
- sar.appendFeature(sb, 1, null, sf);
- assertEquals("METAL 1 3; Fe2-S", sb.toString());
- }
-
- /**
- * A specific attribute value is included if it is used to colour the feature
- */
- @Test(groups = "Functional")
- public void testAppendFeature_colouredByAttribute()
- {
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuilder sb = new StringBuilder();
- SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
- Float.NaN, "group");
- sf.setValue("clinical_significance", "Benign");
-
- /*
- * first with no colour by attribute
- */
- FeatureRendererModel fr = new FeatureRenderer(null);
- sar.appendFeature(sb, 1, fr, sf);
- assertEquals("METAL 1 3; Fe2-S", sb.toString());
-
- /*
- * then with colour by an attribute the feature lacks
- */
- FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
- null, 5, 10);
- fc.setAttributeName("Pfam");
- fr.setColour("METAL", fc);
- sb.setLength(0);
- sar.appendFeature(sb, 1, fr, sf);
- assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
-
- /*
- * then with colour by an attribute the feature has
- */
- fc.setAttributeName("clinical_significance");
- sb.setLength(0);
- sar.appendFeature(sb, 1, fr, sf);
- assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
- sb.toString());
- }
-
- @Test(groups = "Functional")
- public void testAppendFeature_withScoreStatusAttribute()
- {
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuilder sb = new StringBuilder();
- SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
- "group");
- sf.setStatus("Confirmed");
- sf.setValue("clinical_significance", "Benign");
-
- FeatureRendererModel fr = new FeatureRenderer(null);
- Map<String, float[][]> minmax = fr.getMinMax();
- FeatureColourI fc = new FeatureColour(null, Color.white, Color.blue,
- null, 12, 22);
- fc.setAttributeName("clinical_significance");
- fr.setColour("METAL", fc);
- minmax.put("METAL", new float[][] { { 0f, 1f }, null });
- sar.appendFeature(sb, 1, fr, sf);
-
- assertEquals(
- "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
- sb.toString());
- }
-
- @Test(groups = "Functional")
- public void testAppendFeature_DescEqualsType()
- {
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuilder sb = new StringBuilder();
- SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3,
- Float.NaN, "group");
-
- // description is not included if it duplicates type:
- sar.appendFeature(sb, 1, null, sf);
- assertEquals("METAL 1 3", sb.toString());
-
- sb.setLength(0);
- sf.setDescription("Metal");
- // test is case-sensitive:
- sar.appendFeature(sb, 1, null, sf);
- assertEquals("METAL 1 3; Metal", sb.toString());
- }
-
- @Test(groups = "Functional")
- public void testAppendFeature_stripHtml()
- {
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuilder sb = new StringBuilder();
- SequenceFeature sf = new SequenceFeature("METAL",
- "<html><body>hello<em>world</em></body></html>", 1, 3,
- Float.NaN, "group");
-
- sar.appendFeature(sb, 1, null, sf);
- // !! strips off </body> but not <body> ??
- assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString());
-
- sb.setLength(0);
- sf.setDescription("<br>&kHD>6");
- sar.appendFeature(sb, 1, null, sf);
- // if no <html> tag, html-encodes > and < (only):
- assertEquals("METAL 1 3; <br>&kHD>6", sb.toString());
- }
-
- @Test(groups = "Functional")
- public void testCreateSequenceAnnotationReport()
- {
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuilder sb = new StringBuilder();
-
- SequenceI seq = new Sequence("s1", "MAKLKRFQSSTLL");
- seq.setDescription("SeqDesc");
-
- sar.createSequenceAnnotationReport(sb, seq, true, true, null);
-
- /*
- * positional features are ignored
- */
- seq.addSequenceFeature(new SequenceFeature("Domain", "Ferredoxin", 5,
- 10, 1f, null));
- assertEquals("<i><br>SeqDesc</i>", sb.toString());
-
- /*
- * non-positional feature
- */
- seq.addSequenceFeature(new SequenceFeature("Type1", "Nonpos", 0, 0, 1f,
- null));
- sb.setLength(0);
- sar.createSequenceAnnotationReport(sb, seq, true, true, null);
- String expected = "<i><br>SeqDesc<br>Type1 ; Nonpos Score=1.0</i>";
- assertEquals(expected, sb.toString());
-
- /*
- * non-positional features not wanted
- */
- sb.setLength(0);
- sar.createSequenceAnnotationReport(sb, seq, true, false, null);
- assertEquals("<i><br>SeqDesc</i>", sb.toString());
-
- /*
- * add non-pos feature with score inside min-max range for feature type
- * minmax holds { [positionalMin, positionalMax], [nonPosMin, nonPosMax] }
- * score is only appended for positional features so ignored here!
- * minMax are not recorded for non-positional features
- */
- seq.addSequenceFeature(new SequenceFeature("Metal", "Desc", 0, 0, 5f,
- null));
-
- FeatureRendererModel fr = new FeatureRenderer(null);
- Map<String, float[][]> minmax = fr.getMinMax();
- minmax.put("Metal", new float[][] { null, new float[] { 2f, 5f } });
-
- sb.setLength(0);
- sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos</i>";
- assertEquals(expected, sb.toString());
-
- /*
- * 'linkonly' features are ignored; this is obsolete, as linkonly
- * is only set by DasSequenceFetcher, and DAS is history
- */
- SequenceFeature sf = new SequenceFeature("Metal", "Desc", 0, 0, 5f,
- null);
- sf.setValue("linkonly", Boolean.TRUE);
- seq.addSequenceFeature(sf);
- sb.setLength(0);
- sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- assertEquals(expected, sb.toString()); // unchanged!
-
- /*
- * 'clinical_significance' attribute only included when
- * used for feature colouring
- */
- SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0,
- 5f, null);
- sf2.setValue(GffConstants.CLINICAL_SIGNIFICANCE, "benign");
- seq.addSequenceFeature(sf2);
- sb.setLength(0);
- sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos<br>Variant ; Havana</i>";
- assertEquals(expected, sb.toString());
-
- /*
- * add dbrefs
- */
- seq.addDBRef(new DBRefEntry("PDB", "0", "3iu1"));
- seq.addDBRef(new DBRefEntry("Uniprot", "1", "P30419"));
-
- // with showDbRefs = false
- sb.setLength(0);
- sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
- assertEquals(expected, sb.toString()); // unchanged
-
- // with showDbRefs = true, colour Variant features by clinical_significance
- sb.setLength(0);
- FeatureColourI fc = new FeatureColour(null, Color.green, Color.pink,
- null, 2, 3);
- fc.setAttributeName("clinical_significance");
- fr.setColour("Variant", fc);
- sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1<br>Metal ; Desc<br>"
- + "Type1 ; Nonpos<br>Variant ; Havana; clinical_significance=benign</i>";
- assertEquals(expected, sb.toString());
- // with showNonPositionalFeatures = false
- sb.setLength(0);
- sar.createSequenceAnnotationReport(sb, seq, true, false, fr);
- expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1</i>";
- assertEquals(expected, sb.toString());
-
- // see other tests for treatment of status and html
- }
-
- /**
- * Test that exercises an abbreviated sequence details report, with ellipsis
- * where there are more than 40 different sources, or more than 4 dbrefs for a
- * single source
- */
- @Test(groups = "Functional")
- public void testCreateSequenceAnnotationReport_withEllipsis()
- {
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuilder sb = new StringBuilder();
-
- SequenceI seq = new Sequence("s1", "ABC");
-
- int maxSources = (int) PA.getValue(sar, "MAX_SOURCES");
- for (int i = 0; i <= maxSources; i++)
- {
- seq.addDBRef(new DBRefEntry("PDB" + i, "0", "3iu1"));
- }
-
- int maxRefs = (int) PA.getValue(sar, "MAX_REFS_PER_SOURCE");
- for (int i = 0; i <= maxRefs; i++)
- {
- seq.addDBRef(new DBRefEntry("Uniprot", "0", "P3041" + i));
- }
-
- sar.createSequenceAnnotationReport(sb, seq, true, true, null, true);
- String report = sb.toString();
- assertTrue(report
- .startsWith("<i><br>UNIPROT P30410, P30411, P30412, P30413,...<br>PDB0 3iu1"));
- assertTrue(report
- .endsWith("<br>PDB7 3iu1<br>PDB8,...<br>(Output Sequence Details to list all database references)</i>"));
- }
-}
git://source.jalview.org / jalview.git / blobdiff