+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.io;
import static org.testng.Assert.assertEquals;
import java.io.File;
import java.io.IOException;
import java.net.MalformedURLException;
-import java.util.Arrays;
import java.util.List;
import java.util.Set;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceFeature;
@BeforeClass(alwaysRun = true)
public void setUp()
{
- Cache.initLogger();
+ Console.initLogger();
}
/**
File dataFile = new File("test/jalview/io/J03321.gb");
FileParse fp = new FileParse(dataFile.getAbsolutePath(),
DataSourceType.FILE);
- FlatFile parser = new GenBankFile(fp, "GenBankTest");
- parser.parse();
+ EMBLLikeFlatFile parser = new GenBankFile(fp, "GenBankTest");
List<SequenceI> seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
* xref to self : 1
* protein products: 8
*/
- List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
+ List<DBRefEntry> dbrefs = seq.getDBRefs();
assertEquals(dbrefs.size(), 9);
// xref to 'self':
assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
assertEquals(dbref.getAccessionId(), "AAA91574.1");
mapping = dbref.getMap();
- mapTo = mapping.getTo();
+ mapTo = mapping.getTo();
assertEquals(mapTo.getName(), "AAA91574.1");
// the /product qualifier transfers to protein product description
assertEquals(mapTo.getDescription(), "hypothetical protein");
assertTrue(seqString.endsWith("FKQKS"));
map = mapping.getMap();
assertEquals(map.getFromLowest(), 6045);
- assertEquals(map.getFromHighest(), 6788);
+ assertEquals(map.getFromHighest(), 6785); // excludes stop at 6788
assertEquals(map.getToLowest(), 1);
assertEquals(map.getToHighest(), 247);
assertEquals(map.getFromRatio(), 3);