X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=42183ca8816cdb03d35cf92264b6609006d4f67b;hb=cee7f3931f46066e9f81a1cac7d29083e49de8d4;hp=87e35c75fa3f02570f56205bad09724f1e3a2240;hpb=81c8008cff0d9a265e0fbe979b17b173e9e4fc0a;p=jalview.git
diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 87e35c7..42183ca 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -35,13 +35,15 @@ import jalview.schemes.FeatureColour;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Map;
-import junit.extensions.PA;
-
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SequenceAnnotationReportTest
{
@@ -62,22 +64,54 @@ public class SequenceAnnotationReportTest
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);
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);
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);
+ assertEquals("123456disulfide bond 1:3
disulfide bond 1:3",
sb.toString());
}
@Test(groups = "Functional")
+ public void testAppendFeatures_longText()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ 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);
+ 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.appendFeaturesLengthLimit(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);
@@ -86,7 +120,7 @@ public class SequenceAnnotationReportTest
Float.NaN, "group");
sf.setStatus("Confirmed");
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null);
assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
}
@@ -100,7 +134,7 @@ public class SequenceAnnotationReportTest
FeatureRendererModel fr = new FeatureRenderer(null);
Map minmax = fr.getMinMax();
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null);
/*
* map has no entry for this feature type - score is not shown:
*/
@@ -110,9 +144,9 @@ 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);
+ //
is appended to a buffer > 6 in length
+ assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3",
sb.toString());
/*
@@ -120,7 +154,7 @@ 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);
assertEquals("METAL 1 3; Fe2-S", sb.toString());
}
@@ -132,7 +166,7 @@ public class SequenceAnnotationReportTest
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);
assertEquals("METAL 1 3; Fe2-S", sb.toString());
}
@@ -152,17 +186,18 @@ 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);
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);
assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
/*
@@ -170,7 +205,7 @@ public class SequenceAnnotationReportTest
*/
fc.setAttributeName("clinical_significance");
sb.setLength(0);
- sar.appendFeature(sb, 1, fr, sf);
+ sar.appendFeature(sb, 1, fr, sf, null);
assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
sb.toString());
}
@@ -187,11 +222,12 @@ 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);
assertEquals(
"METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
@@ -207,13 +243,13 @@ public class SequenceAnnotationReportTest
Float.NaN, "group");
// description is not included if it duplicates type:
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null);
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);
assertEquals("METAL 1 3; Metal", sb.toString());
}
@@ -226,13 +262,13 @@ public class SequenceAnnotationReportTest
"helloworld", 1, 3,
Float.NaN, "group");
- sar.appendFeature(sb, 1, null, sf);
+ sar.appendFeature(sb, 1, null, sf, null);
// !! 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);
// if no tag, html-encodes > and < (only):
assertEquals("METAL 1 3; <br>&kHD>6", sb.toString());
}
@@ -246,14 +282,13 @@ public class SequenceAnnotationReportTest
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());
+ sar.createSequenceAnnotationReport(sb, seq, true, true, null);
+ assertEquals("SeqDesc", sb.toString());
/*
* non-positional feature
@@ -262,7 +297,7 @@ public class SequenceAnnotationReportTest
null));
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, null);
- String expected = "
SeqDesc
Type1 ; Nonpos Score=1.0";
+ String expected = "SeqDesc
Type1 ; Nonpos Score=1.0";
assertEquals(expected, sb.toString());
/*
@@ -270,7 +305,7 @@ public class SequenceAnnotationReportTest
*/
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, false, null);
- assertEquals("
SeqDesc", sb.toString());
+ assertEquals("SeqDesc", sb.toString());
/*
* add non-pos feature with score inside min-max range for feature type
@@ -287,7 +322,7 @@ public class SequenceAnnotationReportTest
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- expected = "
SeqDesc
Metal ; Desc
Type1 ; Nonpos";
+ expected = "SeqDesc
Metal ; Desc
Type1 ; Nonpos";
assertEquals(expected, sb.toString());
/*
@@ -303,8 +338,8 @@ 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);
@@ -312,7 +347,7 @@ public class SequenceAnnotationReportTest
seq.addSequenceFeature(sf2);
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
- expected = "
SeqDesc
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana";
+ expected = "SeqDesc
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana";
assertEquals(expected, sb.toString());
/*
@@ -328,17 +363,28 @@ 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
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";
+ expected = "SeqDesc
UNIPROT P30419
PDB 3iu1";
+ 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
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
@@ -372,8 +418,10 @@ public class SequenceAnnotationReportTest
sar.createSequenceAnnotationReport(sb, seq, true, true, null, true);
String report = sb.toString();
assertTrue(report
- .startsWith("
UNIPROT P30410, P30411, P30412, P30413,...
PDB0 3iu1"));
+ .startsWith(
+ "
UNIPROT P30410, P30411, P30412, P30413,...
PDB0 3iu1"));
assertTrue(report
- .endsWith("
PDB7 3iu1
PDB8,...
(Output Sequence Details to list all database references)"));
+ .endsWith(
+ "
PDB7 3iu1
PDB8,...
(Output Sequence Details to list all database references)"));
}
}