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JAL-1264 unit test corrected
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 13 Oct 2014 08:52:51 +0000
(09:52 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 13 Oct 2014 08:52:51 +0000
(09:52 +0100)
test/jalview/datamodel/AlignmentTest.java
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diff --git
a/test/jalview/datamodel/AlignmentTest.java
b/test/jalview/datamodel/AlignmentTest.java
index
5cc4f83
..
5920189
100644
(file)
--- a/
test/jalview/datamodel/AlignmentTest.java
+++ b/
test/jalview/datamodel/AlignmentTest.java
@@
-3,8
+3,6
@@
package jalview.datamodel;
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.gui.AlignFrame;
-import jalview.gui.AlignmentPanel;
import jalview.io.AppletFormatAdapter;
import java.io.IOException;
import jalview.io.AppletFormatAdapter;
import java.io.IOException;
@@
-32,7
+30,8
@@
public class AlignmentTest
"D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
"#=GR D.melanogaster.2 SS ................((((\n" +
"D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
"D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
"#=GR D.melanogaster.2 SS ................((((\n" +
"D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
- "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n";
+ "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
+ "//";
// @formatter:on
// @formatter:on
@@
-47,8
+46,14
@@
public class AlignmentTest
{
al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
AppletFormatAdapter.PASTE, "STH");
{
al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
AppletFormatAdapter.PASTE, "STH");
- AlignFrame af = new AlignFrame(al, 700, 500);
- new AlignmentPanel(af, af.getViewport());
+ for (int i = 0; i < al.getSequencesArray().length; ++i)
+ {
+ al.getSequenceAt(i).setDatasetSequence(
+ al.getSequenceAt(i).createDatasetSequence());
+ al.addAnnotation(al.getSequenceAt(i).getAnnotation()[0]);
+ al.getSequenceAt(i).getAnnotation()[0].setCalcId("CalcIdFor"
+ + al.getSequenceAt(i).getName());
+ }
}
/**
}
/**
@@
-58,11
+63,11
@@
public class AlignmentTest
public void testFindAnnotation_byCalcId()
{
Iterable<AlignmentAnnotation> anns = al
public void testFindAnnotation_byCalcId()
{
Iterable<AlignmentAnnotation> anns = al
- .findAnnotation("D.melanogaster.3");
+ .findAnnotation("CalcIdForD.melanogaster.2");
Iterator<AlignmentAnnotation> iter = anns.iterator();
assertTrue(iter.hasNext());
AlignmentAnnotation ann = iter.next();
Iterator<AlignmentAnnotation> iter = anns.iterator();
assertTrue(iter.hasNext());
AlignmentAnnotation ann = iter.next();
- assertEquals("D.melanogaster.3", ann.sequenceRef.getName());
+ assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
assertFalse(iter.hasNext());
}
}
assertFalse(iter.hasNext());
}
}