+/*
+ * 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;
public class ClustalFileTest
{
- @Test(groups="Functional")
+ @Test(groups = "Functional")
public void testParse_withNumbering() throws IOException
{
//@formatter:off
+ "FER_CAPAN/1-55 SYKVKLI 55\n"
+ "FER1_SOLLC/1-55 SYKVKLI 55\n"
+ "Q93XJ9_SOLTU/1-55 SYKVKLI 55\n"
- + "FER1_PEA/1-60 SYKVKLV 60\n";
+ + "FER1_PEA/1-60 SYKVKLV 60\n"
+ + " .* .:....*******..** ..........** ********...*:::* ...\n"
+ + "\t\t.:.::. *\n";
+ //@formatter:on
+ ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
+ cf.parse();
+ SequenceI[] seqs = cf.getSeqsAsArray();
+ assertEquals(seqs.length, 5);
+ assertEquals(seqs[0].getName(), "FER_CAPAA");
+ assertEquals(seqs[0].getStart(), 1);
+ assertEquals(seqs[0].getEnd(), 8);
+ assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
+ }
+
+ @Test(groups = "Functional")
+ public void testParse_noNumbering() throws IOException
+ {
+ //@formatter:off
+ String data = "CLUSTAL\n\n"
+ + "FER_CAPAA/1-8 -----------------------------------------------------------A\n"
+ + "FER_CAPAN/1-55 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA\n"
+ + "FER1_SOLLC/1-55 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
+ + "Q93XJ9_SOLTU/1-55 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
+ + "FER1_PEA/1-60 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA\n\n"
+ + "FER_CAPAA/1-8 SYKVKLI\n"
+ + "FER_CAPAN/1-55 SYKVKLI\n"
+ + "FER1_SOLLC/1-55 SYKVKLI\n"
+ + "Q93XJ9_SOLTU/1-55 SYKVKLI\n"
+ + "FER1_PEA/1-60 SYKVKLV\n";
//@formatter:on
ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
cf.parse();