X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;fp=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=270de2d8fbe47eb2dd5a1fdab06f5d74304b84c9;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=bb5d1c4f1a47716ac71ec292a466cdc721917aac;hpb=04c8f7bff663aa469127e9eed4164e02933782f1;p=jalview.git
diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index bb5d1c4..270de2d 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -62,22 +62,22 @@ public class SequenceAnnotationReportTest
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, 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, null, 0);
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, 0);
- assertEquals("123456disulfide bond 1:3
disulfide bond 1:3",
+ assertEquals("123456disulfide bond 1:3
disulfide bond 1:3",
sb.toString());
}
@@ -105,12 +105,8 @@ public class SequenceAnnotationReportTest
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
+ 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
@@ -151,8 +147,8 @@ public class SequenceAnnotationReportTest
*/
minmax.put("METAL", new float[][] { { 0f, 1f }, null });
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",
+ //
is appended to a buffer > 6 in length
+ assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3",
sb.toString());
/*
@@ -332,7 +328,7 @@ public class SequenceAnnotationReportTest
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
@@ -412,7 +408,7 @@ public class SequenceAnnotationReportTest
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
-
+
SequenceI seq = new Sequence("s1", "ABC");
int maxSources = (int) PA.getValue(sar, "MAX_SOURCES");
@@ -420,13 +416,13 @@ 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("\n" + "
\n" + "UNIPROT P30410,\n"