+/*
+ * 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.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.io.gff.GffConstants;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.Map;
+import junit.extensions.PA;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
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);
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
sb.append("123456");
SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
3, 1.2f, "group");
public void testAppendFeature_status()
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
Float.NaN, "group");
sf.setStatus("Confirmed");
public void testAppendFeature_withScore()
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
"group");
public void testAppendFeature_noScore()
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
Float.NaN, "group");
public void testAppendFeature_clinicalSignificance()
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
Float.NaN, "group");
sf.setValue("clinical_significance", "Benign");
public void testAppendFeature_withScoreStatusClinicalSignificance()
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
"group");
sf.setStatus("Confirmed");
public void testAppendFeature_DescEqualsType()
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3,
Float.NaN, "group");
public void testAppendFeature_stripHtml()
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL",
"<html><body>hello<em>world</em></body></html>", 1, 3,
Float.NaN, "group");
// 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</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));
+ Map<String, float[][]> minmax = new HashMap<String, float[][]>();
+ minmax.put("Metal", new float[][] { null, new float[] { 2f, 5f } });
+ sb.setLength(0);
+ sar.createSequenceAnnotationReport(sb, seq, true, true, minmax);
+ 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, minmax);
+ assertEquals(expected, sb.toString()); // unchanged!
+
+ /*
+ * 'clinical_significance' currently being specially included
+ */
+ 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, minmax);
+ expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos<br>Variant ; Havana; benign</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, minmax);
+ assertEquals(expected, sb.toString()); // unchanged
+ // with showDbRefs = true
+ sb.setLength(0);
+ sar.createSequenceAnnotationReport(sb, seq, true, true, minmax);
+ expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1<br>Metal ; Desc<br>Type1 ; Nonpos<br>Variant ; Havana; benign</i>";
+ assertEquals(expected, sb.toString());
+ // with showNonPositionalFeatures = false
+ sb.setLength(0);
+ sar.createSequenceAnnotationReport(sb, seq, true, false, minmax);
+ 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