X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=bb5d1c4f1a47716ac71ec292a466cdc721917aac;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=87e35c75fa3f02570f56205bad09724f1e3a2240;hpb=81c8008cff0d9a265e0fbe979b17b173e9e4fc0a;p=jalview.git
diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 87e35c7..bb5d1c4 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -23,8 +23,18 @@ package jalview.io;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.api.FeatureColourI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
@@ -32,16 +42,10 @@ import jalview.gui.JvOptionPane;
import jalview.io.gff.GffConstants;
import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.FeatureColour;
+import jalview.util.MapList;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-
-import java.awt.Color;
-import java.util.Map;
-
import junit.extensions.PA;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
public class SequenceAnnotationReportTest
{
@@ -55,52 +59,88 @@ public class SequenceAnnotationReportTest
@Test(groups = "Functional")
public void testAppendFeature_disulfideBond()
{
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
sb.append("123456");
- SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
- 3, 1.2f, "group");
+ 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);
+ sar.appendFeature(sb, 2, null, sf, null, 0);
assertEquals("123456", sb.toString());
- // residuePos == 1 matches start of feature, text appended (but no
)
+ // residuePos == 1 matches start of feature, text appended (but no
)
// feature score is not included
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null, 0);
assertEquals("123456disulfide bond 1:3", sb.toString());
// residuePos == 3 matches end of feature, text appended
- //
is prefixed once sb.length() > 6
- sar.appendFeature(sb, 3, null, sf);
- assertEquals("123456disulfide bond 1:3
disulfide bond 1:3",
+ //
is prefixed once sb.length() > 6
+ sar.appendFeature(sb, 3, null, sf, null, 0);
+ assertEquals("123456disulfide bond 1:3
disulfide bond 1:3",
sb.toString());
}
@Test(groups = "Functional")
+ public void testAppendFeatures_longText()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+ StringBuilder sb = new StringBuilder();
+ String longString = "Abcd".repeat(50);
+ SequenceFeature sf = new SequenceFeature("sequence", longString, 1, 3,
+ "group");
+
+ sar.appendFeature(sb, 1, null, sf, null, 0);
+ assertTrue(sb.length() < 100);
+
+ List sfl = new ArrayList<>();
+ sb.setLength(0);
+ sfl.add(sf);
+ sfl.add(sf);
+ sfl.add(sf);
+ sfl.add(sf);
+ sfl.add(sf);
+ sfl.add(sf);
+ sfl.add(sf);
+ sfl.add(sf);
+ sfl.add(sf);
+ sfl.add(sf);
+ int n = sar.appendFeatures(sb, 1, sfl, new FeatureRenderer(null), 200); // text
+ // should
+ // terminate
+ // before
+ // 200
+ // characters
+ String s = sb.toString();
+ assertTrue(s.length() < 200);
+ assertEquals(n, 7); // should be 7 features left over
+
+ }
+
+ @Test(groups = "Functional")
public void testAppendFeature_status()
{
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
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);
+ sar.appendFeature(sb, 1, null, sf, null, 0);
assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
}
@Test(groups = "Functional")
public void testAppendFeature_withScore()
{
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
"group");
FeatureRendererModel fr = new FeatureRenderer(null);
Map minmax = fr.getMinMax();
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null, 0);
/*
* map has no entry for this feature type - score is not shown:
*/
@@ -110,9 +150,9 @@ 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, fr, sf);
- //
is appended to a buffer > 6 in length
- assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3",
+ sar.appendFeature(sb, 1, fr, sf, null, 0);
+ //
is appended to a buffer > 6 in length
+ assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3",
sb.toString());
/*
@@ -120,19 +160,19 @@ public class SequenceAnnotationReportTest
*/
minmax.put("METAL", new float[][] { { 2f, 2f }, null });
sb.setLength(0);
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null, 0);
assertEquals("METAL 1 3; Fe2-S", sb.toString());
}
@Test(groups = "Functional")
public void testAppendFeature_noScore()
{
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
Float.NaN, "group");
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null, 0);
assertEquals("METAL 1 3; Fe2-S", sb.toString());
}
@@ -142,7 +182,7 @@ public class SequenceAnnotationReportTest
@Test(groups = "Functional")
public void testAppendFeature_colouredByAttribute()
{
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
Float.NaN, "group");
@@ -152,17 +192,18 @@ public class SequenceAnnotationReportTest
* first with no colour by attribute
*/
FeatureRendererModel fr = new FeatureRenderer(null);
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null, 0);
assertEquals("METAL 1 3; Fe2-S", sb.toString());
/*
* then with colour by an attribute the feature lacks
*/
- FeatureColourI fc = new FeatureColour(Color.white, Color.black, 5, 10);
+ 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);
+ sar.appendFeature(sb, 1, fr, sf, null, 0);
assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
/*
@@ -170,7 +211,7 @@ public class SequenceAnnotationReportTest
*/
fc.setAttributeName("clinical_significance");
sb.setLength(0);
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null, 0);
assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
sb.toString());
}
@@ -178,7 +219,7 @@ public class SequenceAnnotationReportTest
@Test(groups = "Functional")
public void testAppendFeature_withScoreStatusAttribute()
{
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
"group");
@@ -187,11 +228,12 @@ public class SequenceAnnotationReportTest
FeatureRendererModel fr = new FeatureRenderer(null);
Map minmax = fr.getMinMax();
- FeatureColourI fc = new FeatureColour(Color.white, Color.blue, 12, 22);
+ 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);
+ sar.appendFeature(sb, 1, fr, sf, null, 0);
assertEquals(
"METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
@@ -201,38 +243,38 @@ public class SequenceAnnotationReportTest
@Test(groups = "Functional")
public void testAppendFeature_DescEqualsType()
{
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
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);
+ sar.appendFeature(sb, 1, null, sf, null, 0);
assertEquals("METAL 1 3", sb.toString());
sb.setLength(0);
sf.setDescription("Metal");
// test is case-sensitive:
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null, 0);
assertEquals("METAL 1 3; Metal", sb.toString());
}
@Test(groups = "Functional")
public void testAppendFeature_stripHtml()
{
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
SequenceFeature sf = new SequenceFeature("METAL",
"helloworld", 1, 3,
Float.NaN, "group");
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null, 0);
// !! strips off
??
assertEquals("METAL 1 3; helloworld", sb.toString());
sb.setLength(0);
sf.setDescription("
&kHD>6");
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null, 0);
// if no tag, html-encodes > and < (only):
assertEquals("METAL 1 3; <br>&kHD>6", sb.toString());
}
@@ -240,29 +282,29 @@ public class SequenceAnnotationReportTest
@Test(groups = "Functional")
public void testCreateSequenceAnnotationReport()
{
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
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());
+ seq.addSequenceFeature(
+ new SequenceFeature("Domain", "Ferredoxin", 5, 10, 1f, null));
+ sar.createSequenceAnnotationReport(sb, seq, true, true, null);
+ assertEquals("SeqDesc\n" + "\n" + "", sb.toString());
/*
* non-positional feature
*/
- seq.addSequenceFeature(new SequenceFeature("Type1", "Nonpos", 0, 0, 1f,
- null));
+ 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";
+ String expected = "SeqDesc\n" + "\n"
+ + "
Type1 ; Nonpos Score=1.0";
assertEquals(expected, sb.toString());
/*
@@ -270,7 +312,7 @@ public class SequenceAnnotationReportTest
*/
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, false, null);
- assertEquals("
SeqDesc", sb.toString());
+ assertEquals("SeqDesc\n\n", sb.toString());
/*
* add non-pos feature with score inside min-max range for feature type
@@ -278,8 +320,8 @@ public class SequenceAnnotationReportTest
* 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));
+ seq.addSequenceFeature(
+ new SequenceFeature("Metal", "Desc", 0, 0, 5f, null));
FeatureRendererModel fr = new FeatureRenderer(null);
Map minmax = fr.getMinMax();
@@ -287,9 +329,10 @@ public class SequenceAnnotationReportTest
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- expected = "
SeqDesc
Metal ; Desc
Type1 ; Nonpos";
+ expected = "SeqDesc\n" + "\n"
+ + "
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
@@ -303,16 +346,17 @@ public class SequenceAnnotationReportTest
assertEquals(expected, sb.toString()); // unchanged!
/*
- * 'clinical_significance' attribute only included when
- * used for feature colouring
+ * 'clinical_significance' attribute is only included in description
+ * when used for feature colouring
*/
- SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0,
- 5f, null);
+ 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";
+ expected = "SeqDesc\n" + "\n"
+ + "
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana";
assertEquals(expected, sb.toString());
/*
@@ -328,17 +372,31 @@ public class SequenceAnnotationReportTest
// with showDbRefs = true, colour Variant features by clinical_significance
sb.setLength(0);
- FeatureColourI fc = new FeatureColour(Color.green, Color.pink, 2, 3);
+ 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";
+ expected = "SeqDesc\n" + "
\n" + "UNIPROT P30419
\n"
+ + "PDB 3iu1\n"
+ + "
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";
+ expected = "SeqDesc\n" + "
\n" + "UNIPROT P30419
\n"
+ + "PDB 3iu1\n" + "";
+ assertEquals(expected, sb.toString());
+
+ /*
+ * long feature description is truncated with ellipsis
+ */
+ sb.setLength(0);
+ sf2.setDescription(
+ "This is a very long description which should be truncated");
+ sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
+ expected = "SeqDesc\n" + "\n"
+ + "
Metal ; Desc
Type1 ; Nonpos
Variant ; This is a very long description which sh...; clinical_significance=benign";
assertEquals(expected, sb.toString());
// see other tests for treatment of status and html
@@ -352,9 +410,9 @@ public class SequenceAnnotationReportTest
@Test(groups = "Functional")
public void testCreateSequenceAnnotationReport_withEllipsis()
{
- SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
-
+
SequenceI seq = new Sequence("s1", "ABC");
int maxSources = (int) PA.getValue(sar, "MAX_SOURCES");
@@ -362,18 +420,80 @@ public class SequenceAnnotationReportTest
{
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)"));
+ assertTrue(report.startsWith("\n" + "
\n" + "UNIPROT P30410,\n"
+ + " P30411,\n" + " P30412,\n" + " P30413,...
\n"
+ + "PDB0 3iu1
\n" + "PDB1 3iu1
"));
+ assertTrue(report.endsWith("PDB5 3iu1
\n" + "PDB6 3iu1
\n"
+ + "PDB7 3iu1
\n" + "PDB8,...
\n"
+ + "(Output Sequence Details to list all database references)\n"
+ + ""));
+ }
+
+ /**
+ * Test adding a linked feature to the tooltip
+ */
+ @Test(groups = "Functional")
+ public void testAppendFeature_virtualFeature()
+ {
+ /*
+ * map CDS to peptide sequence
+ */
+ SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
+ SequenceI peptide = new Sequence("Peptide/8-14", "PLRFQMD");
+ MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
+ 3, 1);
+ Mapping mapping = new Mapping(peptide, map);
+
+ /*
+ * assume variant feature found at CDS position 106 G>C
+ */
+ List features = new ArrayList<>();
+ // vary ttg (Leu) to ttc (Phe)
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
+ Float.NaN, null);
+ features.add(sf);
+ MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
+
+ StringBuilder sb = new StringBuilder();
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
+ sar.appendFeature(sb, 1, null, sf, mf, 0);
+
+ /*
+ * linked feature shown in tooltip in protein coordinates
+ */
+ assertEquals("variant 9; G,C", sb.toString());
+
+ /*
+ * adding "alleles" attribute to variant allows peptide consequence
+ * to be calculated and added to the tooltip
+ */
+ sf.setValue("alleles", "G,C");
+ sb = new StringBuilder();
+ sar.appendFeature(sb, 1, null, sf, mf, 0);
+ assertEquals("variant 9; G,C p.Leu9Phe", sb.toString());
+
+ /*
+ * now a virtual peptide feature on CDS
+ * feature at 11-12 on peptide maps to 110-115 on CDS
+ * here we test for tooltip at 113 (t)
+ */
+ SequenceFeature sf2 = new SequenceFeature("metal", "Fe", 11, 12, 2.3f,
+ "Uniprot");
+ features.clear();
+ features.add(sf2);
+ mapping = new Mapping(peptide, map);
+ mf = new MappedFeatures(mapping, peptide, 113, 't', features);
+ sb = new StringBuilder();
+ sar.appendFeature(sb, 1, null, sf2, mf, 0);
+ assertEquals("metal 110 115; Fe Score=2.3", sb.toString());
}
}