JAL-4101 Updated Rfam* tests

[jalview.git] / test / jalview / io / ClustalFileTest.java

diff --git a/test/jalview/io/ClustalFileTest.java b/test/jalview/io/ClustalFileTest.java
index a912d96..0277ce6 100644 (file)
--- a/test/jalview/io/ClustalFileTest.java
+++ b/test/jalview/io/ClustalFileTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -11,7 +31,7 @@ import org.testng.annotations.Test;
 
 public class ClustalFileTest
 {
-  @Test(groups="Functional")
+  @Test(groups = "Functional")
   public void testParse_withNumbering() throws IOException
   {
     //@formatter:off
@@ -25,7 +45,35 @@ public class ClustalFileTest
             + "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();