X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fhtsjdk%2FTestHtsContigDb.java;h=ad9bf0342ff180e766ff2ba9b360eeb953e0503f;hb=5ddab6dda9d0e32e9b2d36cea1b41a7cd4a5371e;hp=29303d0ee9bc931b3d4504d4039a968d70875d69;hpb=d53f86449820b92534376bd383e92a083037ec90;p=jalview.git

diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java
index 29303d0..ad9bf03 100644
--- a/test/jalview/ext/htsjdk/TestHtsContigDb.java
+++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java
@@ -44,12 +44,12 @@ public class TestHtsContigDb
   @Test(groups = "Functional")
   public final void testGetSequenceProxy() throws Exception
   {
-    String pathname = "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);
@@ -60,7 +60,7 @@ public class TestHtsContigDb
     sq = db.getSequenceProxy("PPL_06716");
     assertNotNull(sq);
     assertEquals(sq.getLength(), 602);
-    
+
     // dict = db.getDictionary(f, truncate))
   }
 
@@ -73,24 +73,39 @@ public class TestHtsContigDb
     expectedExceptions = java.lang.IllegalArgumentException.class)
   public final void testGetSequenceProxy_indexed()
   {
-    String pathname = "test/jalview/ext/htsjdk/pgmb.fasta.fai";
+    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");
-    
+    File fasta = new File("test/jalview/ext/htsjdk/pgmB.fasta");
+
     /*
      * create .fai with no overwrite fails if it exists
      */
-    try {
+    try
+    {
       HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false);
       fail("Expected exception");
     } catch (IOException e)
     {
+      System.out.println(
+              "Caught IOException in testCreateFastaSequenceIndex");
+      e.printStackTrace();
       // expected
     }
 
@@ -120,4 +135,18 @@ public class TestHtsContigDb
     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);
+  }
 }