X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fhtsjdk%2FTestHtsContigDb.java;h=28c5cf0ddaf1fe0ca052b08b819129ea1580e336;hb=d8720fc191cba996c440171ef8e07462ef9f7035;hp=bdc14db3c8d0c5cb14bf42e80ec1b1c40a753090;hpb=956deeb079bf76f9a0e9dc076154ff4865743e63;p=jalview.git

diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java
index bdc14db..28c5cf0 100644
--- a/test/jalview/ext/htsjdk/TestHtsContigDb.java
+++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java
@@ -20,11 +20,19 @@
  */
 package jalview.ext.htsjdk;
 
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
 import jalview.datamodel.SequenceI;
 
 import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.StandardCopyOption;
 
-import org.testng.Assert;
 import org.testng.annotations.Test;
 
 /**
@@ -34,16 +42,107 @@ import org.testng.annotations.Test;
 public class TestHtsContigDb
 {
   @Test(groups = "Functional")
-  public final void testHTSReferenceSequence() throws Exception
+  public final void testGetSequenceProxy() throws Exception
   {
-    HtsContigDb remmadb = new HtsContigDb("REEMADB", new File(
-            "test/jalview/ext/htsjdk/pgmb.fasta"));
+    String pathname = "test/jalview/ext/htsjdk/pgmb.fasta";
+    HtsContigDb db = new HtsContigDb("ADB", new File(pathname));
+    
+    assertTrue(db.isValid());
+    assertTrue(db.isIndexed()); // htsjdk opens the .fai file
+    
+    SequenceI sq = db.getSequenceProxy("Deminut");
+    assertNotNull(sq);
+    assertEquals(sq.getLength(), 606);
 
-    Assert.assertTrue(remmadb.isValid());
+    /*
+     * read a sequence earlier in the file
+     */
+    sq = db.getSequenceProxy("PPL_06716");
+    assertNotNull(sq);
+    assertEquals(sq.getLength(), 602);
+    
+    // dict = db.getDictionary(f, truncate))
+  }
 
-    SequenceI sq = remmadb.getSequenceProxy("Deminut");
-    Assert.assertNotNull(sq);
-    Assert.assertNotEquals(0, sq.getLength());
+  /**
+   * Trying to open a .fai file directly results in IllegalArgumentException -
+   * have to provide the unindexed file name instead
+   */
+  @Test(
+    groups = "Functional",
+    expectedExceptions = java.lang.IllegalArgumentException.class)
+  public final void testGetSequenceProxy_indexed()
+  {
+    String pathname = "test/jalview/ext/htsjdk/pgmb.fasta.fai";
+    new HtsContigDb("ADB", new File(pathname));
+    fail("Expected exception opening .fai file");
   }
 
+  /**
+   * Tests that exercise
+   * <ul>
+   * <li>opening an unindexed fasta file</li>
+   * <li>creating a .fai index</li>
+   * <li>opening the fasta file, now using the index</li>
+   * <li>error on creating index if overwrite not allowed</li>
+   * </ul>
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testCreateFastaSequenceIndex() throws IOException
+  {
+    File fasta = new File("test/jalview/ext/htsjdk/pgmb.fasta");
+    
+    /*
+     * create .fai with no overwrite fails if it exists
+     */
+    try {
+      HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false);
+      fail("Expected exception");
+    } catch (IOException e)
+    {
+      // expected
+    }
+
+    /*
+     * create a copy of the .fasta (as a temp file)
+     */
+    File copyFasta = File.createTempFile("copyFasta", ".fasta");
+    copyFasta.deleteOnExit();
+    assertTrue(copyFasta.exists());
+    Files.copy(fasta.toPath(), copyFasta.toPath(),
+            StandardCopyOption.REPLACE_EXISTING);
+
+    /*
+     * open the Fasta file - not indexed, as no .fai file yet exists
+     */
+    HtsContigDb db = new HtsContigDb("ADB", copyFasta);
+    assertTrue(db.isValid());
+    assertFalse(db.isIndexed());
+    db.close();
+
+    /*
+     * create the .fai index, re-open the .fasta file - now indexed
+     */
+    HtsContigDb.createFastaSequenceIndex(copyFasta.toPath(), true);
+    db = new HtsContigDb("ADB", copyFasta);
+    assertTrue(db.isValid());
+    assertTrue(db.isIndexed());
+    db.close();
+  }
+
+  /**
+   * A convenience 'test' that may be run to create a .fai file for any given
+   * fasta file
+   * 
+   * @throws IOException
+   */
+  @Test(enabled = false)
+  public void testCreateIndex() throws IOException
+  {
+
+    File fasta = new File("test/jalview/io/vcf/contigs.fasta");
+    HtsContigDb.createFastaSequenceIndex(fasta.toPath(), true);
+  }
 }