JAL-2997 additional tests

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

diff --git a/test/jalview/io/ClustalFileTest.java b/test/jalview/io/ClustalFileTest.java
index a912d96..1da2c75 100644 (file)
--- a/test/jalview/io/ClustalFileTest.java
+++ b/test/jalview/io/ClustalFileTest.java
@@ -25,7 +25,35 @@ 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();