X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FClustalFileTest.java;fp=test%2Fjalview%2Fio%2FClustalFileTest.java;h=1da2c75a33ba2e237dd6af7cc6e37202e72dda7a;hb=252ddd218b716396b003b3fcbe0f8da499bde8c8;hp=0000000000000000000000000000000000000000;hpb=d716c9b072f989bef39c6eba038f779ce98396a8;p=jalview.git

diff --git a/test/jalview/io/ClustalFileTest.java b/test/jalview/io/ClustalFileTest.java
new file mode 100644
index 0000000..1da2c75
--- /dev/null
+++ b/test/jalview/io/ClustalFileTest.java
@@ -0,0 +1,67 @@
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+
+import org.testng.annotations.Test;
+
+public class ClustalFileTest
+{
+  @Test(groups="Functional")
+  public void testParse_withNumbering() throws IOException
+  {
+    //@formatter:off
+    String data = "CLUSTAL\n\n"
+            + "FER_CAPAA/1-8      -----------------------------------------------------------A\t1\n"
+            + "FER_CAPAN/1-55     MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA 48\n"
+            + "FER1_SOLLC/1-55    MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
+            + "Q93XJ9_SOLTU/1-55  MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
+            + "FER1_PEA/1-60      MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA 53\n\n"
+            + "FER_CAPAA/1-8      SYKVKLI 8\n"
+            + "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"
+            + "                   .*     .:....*******..** ..........**  ********...*:::*  ...\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();
+    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"));
+  }
+}