Merge branch 'develop' into bug/JAL-1841rnaSecStr

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

diff --git a/test/jalview/io/FormatAdapterTest.java b/test/jalview/io/FormatAdapterTest.java
new file mode 100644 (file)
index 0000000..81e336e
--- /dev/null
+++ b/test/jalview/io/FormatAdapterTest.java
@@ -0,0 +1,138 @@
+package jalview.io;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.fail;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+public class FormatAdapterTest
+{
+
+  /**
+   * Test saving and re-reading in a specified format
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" }, dataProvider = "formats")
+  public void testRoundTrip(String format) throws IOException
+  {
+    try
+    {
+      AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
+              FormatAdapter.FILE, "FASTA");
+
+      /*
+       * 'gap' is the gap character used in the alignment data file here,
+       * not the user preferred gap character
+       */
+      char gap = al.getGapCharacter();
+      assertNotNull(al);
+
+      SequenceI[] seqs = al.getSequencesArray();
+      String formatted = new FormatAdapter().formatSequences(format, al,
+              false);
+
+      AlignmentI reloaded = new FormatAdapter().readFile(formatted,
+              FormatAdapter.PASTE, format);
+      List<SequenceI> reread = reloaded.getSequences();
+      assertEquals("Wrong number of reloaded sequences", seqs.length,
+              reread.size());
+
+      int i = 0;
+      for (SequenceI seq : reread)
+      {
+        String sequenceString = seq.getSequenceAsString();
+
+        /*
+         * special case: MSF always uses '.' as gap character
+         */
+        sequenceString = adjustForGapTreatment(sequenceString, gap, format);
+        assertEquals(
+                String.format("Sequence %d: %s", i,
+                        seqs[i].getName()), seqs[i].getSequenceAsString(),
+                sequenceString);
+        i++;
+      }
+    } catch (IOException e)
+    {
+      fail(String
+              .format("Format %s failed with %s", format, e.getMessage()));
+    }
+  }
+
+  /**
+   * Optionally change the gap character in the string to the given character,
+   * depending on the sequence file format
+   * 
+   * @param sequenceString
+   *          a sequence (as written in 'format' format)
+   * @param gap
+   *          the sequence's original gap character
+   * @param format
+   * @return
+   */
+  String adjustForGapTreatment(String sequenceString, char gap,
+          String format)
+  {
+    if ("MSF".equals(format))
+    {
+      /*
+       * MSF forces gap character to '.', so change it back
+       * for comparison purposes
+       */
+      sequenceString = sequenceString.replace('.', gap);
+    }
+    return sequenceString;
+  }
+
+  /**
+   * Data provider that serves alignment formats that are both readable and
+   * writable
+   * 
+   * @return
+   */
+  @DataProvider(name = "formats")
+  static Object[][] getFormats()
+  {
+    List<String> both = new ArrayList<String>();
+    String[] readable = FormatAdapter.READABLE_FORMATS;
+    List<String> writeable = Arrays.asList(FormatAdapter.WRITEABLE_FORMATS);
+    for (String r : readable)
+    {
+      if (writeable.contains(r))
+      {
+        both.add(r);
+      }
+    }
+
+    Object[][] formats = new Object[both.size()][];
+    int i = 0;
+    for (String format : both)
+    {
+      formats[i] = new Object[] { format };
+      i++;
+    }
+    return formats;
+  }
+
+  /**
+   * Enable this to isolate testing to a single file format
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" }, enabled = false)
+  public void testOneFormatRoundTrip() throws IOException
+  {
+    testRoundTrip("JSON");
+  }
+}