JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/test/jalview/io/ClustalFileTest.java b/test/jalview/io/ClustalFileTest.java
deleted file mode 100644 (file)
index 1da2c75..0000000
--- a/test/jalview/io/ClustalFileTest.java
+++ /dev/null
@@ -1,67 +0,0 @@
-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"));
-  }
-}