+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.ws.jabaws;
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.List;
-
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.io.AnnotationFile;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import java.util.ArrayList;
+import java.util.List;
+
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
;
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
- // NOTE: Consensus annotation row cannot be exported and reimported faithfully - so we remove them
+ // NOTE: Consensus annotation row cannot be exported and reimported
+ // faithfully - so we remove them
List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation())
+ for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
{
if (aa.autoCalculated)
{
toremove.add(aa);
}
}
- for (AlignmentAnnotation aa:toremove)
+ for (AlignmentAnnotation aa : toremove)
{
orig_alig.deleteAnnotation(aa);
}
{
String aligfileout = new FormatAdapter().formatSequences("PFAM",
al.getSequencesArray());
- String anfileout = new AnnotationFile().printAnnotations(
- al.getAlignmentAnnotation(), al.getGroups(),
- al.getProperties());
+ String anfileout = new AnnotationFile()
+ .printAnnotationsForAlignment(al);
assertTrue(
"Test "
+ testname