X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=42183ca8816cdb03d35cf92264b6609006d4f67b;hb=f60b33ad2547914dfcb536db65dd793a7f82e9de;hp=0b5dfdda390449a21a9d72de37336426db090fa9;hpb=e51f922b88b1f316e27cf4c19eef437ff592d74d;p=jalview.git
diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 0b5dfdd..42183ca 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -35,6 +35,8 @@ 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 org.testng.annotations.BeforeClass;
@@ -65,19 +67,51 @@ public class SequenceAnnotationReportTest
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, null);
assertEquals("123456disulfide bond 1:3", sb.toString());
// residuePos == 3 matches end of feature, text appended
- //
is prefixed once sb.length() > 6
+ //
is prefixed once sb.length() > 6
sar.appendFeature(sb, 3, null, sf, null);
- assertEquals("123456disulfide bond 1:3
disulfide bond 1:3",
+ 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);
@@ -111,8 +145,8 @@ public class SequenceAnnotationReportTest
*/
minmax.put("METAL", new float[][] { { 0f, 1f }, null });
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",
+ //
is appended to a buffer > 6 in length
+ assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3",
sb.toString());
/*
@@ -248,14 +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
@@ -264,7 +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());
/*
@@ -272,7 +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
@@ -289,7 +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());
/*
@@ -305,8 +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);
@@ -314,7 +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());
/*
@@ -335,13 +368,23 @@ public class SequenceAnnotationReportTest
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
@@ -375,8 +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)"));
}
}