X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=cf3c7e5ed4027d0fb977666aea2453536139cfc7;hb=refs%2Fheads%2Ftask%2FJAL-3243_PDB_free_text_error;hp=07ae0ab442f7ef4702a3789bccda926ac023e4c8;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git
diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 07ae0ab..cf3c7e5 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -1,21 +1,62 @@
+/*
+ * 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.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.util.Hashtable;
+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);
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
sb.append("123456");
SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
3, 1.2f, "group");
@@ -40,7 +81,7 @@ public class SequenceAnnotationReportTest
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");
@@ -53,12 +94,13 @@ public class SequenceAnnotationReportTest
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");
- Map minmax = new Hashtable();
- sar.appendFeature(sb, 1, minmax, sf);
+ FeatureRendererModel fr = new FeatureRenderer(null);
+ Map minmax = fr.getMinMax();
+ sar.appendFeature(sb, 1, fr, sf);
/*
* map has no entry for this feature type - score is not shown:
*/
@@ -68,7 +110,7 @@ public class SequenceAnnotationReportTest
* map has entry for this feature type - score is shown:
*/
minmax.put("METAL", new float[][] { { 0f, 1f }, null });
- sar.appendFeature(sb, 1, minmax, sf);
+ sar.appendFeature(sb, 1, fr, sf);
//
is appended to a buffer > 6 in length
assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3",
sb.toString());
@@ -78,7 +120,7 @@ public class SequenceAnnotationReportTest
*/
minmax.put("METAL", new float[][] { { 2f, 2f }, null });
sb.setLength(0);
- sar.appendFeature(sb, 1, minmax, sf);
+ sar.appendFeature(sb, 1, fr, sf);
assertEquals("METAL 1 3; Fe2-S", sb.toString());
}
@@ -86,7 +128,7 @@ public class SequenceAnnotationReportTest
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");
@@ -94,33 +136,67 @@ public class SequenceAnnotationReportTest
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_clinicalSignificance()
+ public void testAppendFeature_colouredByAttribute()
{
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");
- sar.appendFeature(sb, 1, null, sf);
- assertEquals("METAL 1 3; Fe2-S; Benign", sb.toString());
+ /*
+ * 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_withScoreStatusClinicalSignificance()
+ public void testAppendFeature_withScoreStatusAttribute()
{
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");
sf.setValue("clinical_significance", "Benign");
- Map minmax = new Hashtable();
+
+ FeatureRendererModel fr = new FeatureRenderer(null);
+ Map 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, minmax, sf);
+ sar.appendFeature(sb, 1, fr, sf);
- assertEquals("METAL 1 3; Fe2-S Score=1.3; (Confirmed); Benign",
+ assertEquals(
+ "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
sb.toString());
}
@@ -128,7 +204,7 @@ public class SequenceAnnotationReportTest
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");
@@ -147,7 +223,7 @@ public class SequenceAnnotationReportTest
public void testAppendFeature_stripHtml()
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL",
"helloworld", 1, 3,
Float.NaN, "group");
@@ -162,4 +238,145 @@ public class SequenceAnnotationReportTest
// if no 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("
SeqDesc", 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 = "
SeqDesc
Type1 ; Nonpos Score=1.0";
+ assertEquals(expected, sb.toString());
+
+ /*
+ * non-positional features not wanted
+ */
+ sb.setLength(0);
+ sar.createSequenceAnnotationReport(sb, seq, true, false, null);
+ assertEquals("
SeqDesc", 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 minmax = fr.getMinMax();
+ minmax.put("Metal", new float[][] { null, new float[] { 2f, 5f } });
+
+ sb.setLength(0);
+ sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
+ expected = "
SeqDesc
Metal ; Desc
Type1 ; Nonpos";
+ 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 = "
SeqDesc
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana";
+ 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 = "
SeqDesc
UNIPROT P30419
PDB 3iu1
Metal ; Desc
"
+ + "Type1 ; Nonpos
Variant ; Havana; clinical_significance=benign";
+ assertEquals(expected, sb.toString());
+ // with showNonPositionalFeatures = false
+ sb.setLength(0);
+ sar.createSequenceAnnotationReport(sb, seq, true, false, fr);
+ expected = "
SeqDesc
UNIPROT P30419
PDB 3iu1";
+ 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("
UNIPROT P30410, P30411, P30412, P30413,...
PDB0 3iu1"));
+ assertTrue(report
+ .endsWith("
PDB7 3iu1
PDB8,...
(Output Sequence Details to list all database references)"));
+ }
}