X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;fp=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=f5515718539f9c7b2455d4e0a474a87187f9c069;hb=99d5f1d805e530f23a53dad4484d44ecd0fbfdf3;hp=0000000000000000000000000000000000000000;hpb=e6134bccddc2c7faad28fad1a4e77ccd0ceb3d84;p=jalview.git
diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
new file mode 100644
index 0000000..f551571
--- /dev/null
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -0,0 +1,166 @@
+package jalview.io;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import jalview.datamodel.SequenceFeature;
+
+import java.util.Hashtable;
+import java.util.Map;
+
+import org.testng.annotations.Test;
+
+public class SequenceAnnotationReportTest
+{
+ @Test(groups = "Functional")
+ public void testAppendFeature_disulfideBond()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ StringBuffer sb = new StringBuffer();
+ sb.append("123456");
+ 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);
+ assertEquals("123456", sb.toString());
+
+ // residuePos == 1 matches start of feature, text appended (but no
)
+ // feature score is not included
+ sar.appendFeature(sb, 1, null, sf);
+ 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",
+ sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_status()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ StringBuffer sb = new StringBuffer();
+ SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
+ Float.NaN, "group");
+ sf.setStatus("Confirmed");
+
+ sar.appendFeature(sb, 1, null, sf);
+ assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_withScore()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ StringBuffer sb = new StringBuffer();
+ SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
+ "group");
+
+ Map
is appended to a buffer > 6 in length
+ assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3",
+ sb.toString());
+
+ /*
+ * map has min == max for this feature type - score is not shown:
+ */
+ minmax.put("METAL", new float[][] { { 2f, 2f }, null });
+ sb.setLength(0);
+ sar.appendFeature(sb, 1, minmax, sf);
+ assertEquals("METAL 1 3; Fe2-S", sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_noScore()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ StringBuffer sb = new StringBuffer();
+ SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
+ Float.NaN, "group");
+
+ sar.appendFeature(sb, 1, null, sf);
+ assertEquals("METAL 1 3; Fe2-S", sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_clinicalSignificance()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ StringBuffer sb = new StringBuffer();
+ 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());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_withScoreStatusClinicalSignificance()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+ StringBuffer sb = new StringBuffer();
+ SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
+ "group");
+ sf.setStatus("Confirmed");
+ sf.setValue("clinical_significance", "Benign");
+ Map