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JAL-1737 updated JUnit so it creates positional annotations
[jalview.git]
/
test
/
jalview
/
analysis
/
AlignmentAnnotationUtilsTest.java
diff --git
a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java
b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java
index
19a5163
..
c34bb68
100644
(file)
--- a/
test/jalview/analysis/AlignmentAnnotationUtilsTest.java
+++ b/
test/jalview/analysis/AlignmentAnnotationUtilsTest.java
@@
-3,10
+3,6
@@
package jalview.analysis;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
import java.io.IOException;
import java.util.ArrayList;
import java.io.IOException;
import java.util.ArrayList;
@@
-19,6
+15,12
@@
import java.util.Map;
import org.junit.Before;
import org.junit.Test;
import org.junit.Before;
import org.junit.Test;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+
public class AlignmentAnnotationUtilsTest
{
// 4 sequences x 13 positions
public class AlignmentAnnotationUtilsTest
{
// 4 sequences x 13 positions
@@
-111,6
+113,11
@@
public class AlignmentAnnotationUtilsTest
return result;
}
return result;
}
+ /**
+ * Load the test alignment and generate annotations on it
+ *
+ * @throws IOException
+ */
@Before
public void setUp() throws IOException
{
@Before
public void setUp() throws IOException
{
@@
-120,7
+127,13
@@
public class AlignmentAnnotationUtilsTest
AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT];
for (int i = 0; i < anns.length; i++)
{
AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT];
for (int i = 0; i < anns.length; i++)
{
- anns[i] = new AlignmentAnnotation("Label" + i, null, 0d);
+ /*
+ * Use the constructor for a positional annotation (with an Annotation
+ * array)
+ */
+ anns[i] = new AlignmentAnnotation("Label" + i, "Desc " + i,
+ new Annotation[]
+ {});
anns[i].setCalcId("CalcId" + i);
anns[i].visible = true;
alignment.addAnnotation(anns[i]);
anns[i].setCalcId("CalcId" + i);
anns[i].visible = true;
alignment.addAnnotation(anns[i]);
@@
-304,6
+317,11
@@
public class AlignmentAnnotationUtilsTest
anns[9].graph = AlignmentAnnotation.LINE_GRAPH;
anns[9].graphGroup = GROUP_4;
anns[9].graph = AlignmentAnnotation.LINE_GRAPH;
anns[9].graphGroup = GROUP_4;
+ /*
+ * Generate annotations[] arrays to match aligned columns
+ */
+ // adjustForAlignment(anns);
+
List<SequenceI> selected = selectSequences(0, 3);
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(anns),
List<SequenceI> selected = selectSequences(0, 3);
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(anns),