+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+
import jalview.analysis.AlignSeq;
import jalview.io.AppletFormatAdapter;
+import org.testng.annotations.Test;
+
public class AlignmentAnnotationTests
{
- @Test
+ @Test(groups = { "Functional" })
public void testCopyConstructor()
{
SequenceI sq = new Sequence("Foo", "ARAARARARAWEAWEAWRAWEAWE");
alc.getProperty(key));
}
}
+
/**
* create some dummy annotation derived from the sequence
*
* different dataset frames (annotation transferred by mapping between
* sequences)
*/
- @Test
+ @Test(groups = { "Functional" })
public void testLiftOver()
{
SequenceI sqFrom = new Sequence("fromLong", "QQQCDEWGH");
alSeq2.setStart(sqTo.getStart() + align.getSeq2Start() - 1);
alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1);
alSeq2.setDatasetSequence(sqTo);
- System.out.println(new AppletFormatAdapter().formatSequences("STH",
- new Alignment(new SequenceI[]
- { sqFrom, alSeq1, sqTo, alSeq2 }), true));
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences("STH", new Alignment(new SequenceI[] { sqFrom,
+ alSeq1, sqTo, alSeq2 }), true));
Mapping mp = align.getMappingFromS1(false);
almap2.setSequenceRef(alSeq2);
almap2.adjustForAlignment();
- AlignmentI all = new Alignment(new SequenceI[]
- { alSeq1, alSeq2 });
+ AlignmentI all = new Alignment(new SequenceI[] { alSeq1, alSeq2 });
all.addAnnotation(almap1);
all.addAnnotation(almap2);
System.out.println(new AppletFormatAdapter().formatSequences("STH",
}
}
- @Test
+ @Test(groups = { "Functional" })
public void testAdjustForAlignment()
{
SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
/*
* Annotate positions 3/4/5 (CDE) with values 1/2/3
*/
- Annotation[] anns = new Annotation[]
- { null, null, new Annotation(1), new Annotation(2), new Annotation(3) };
+ Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
+ new Annotation(2), new Annotation(3) };
AlignmentAnnotation ann = new AlignmentAnnotation("SS",
"secondary structure", anns);
seq.addAlignmentAnnotation(ann);