JAL-1296 JAL-1291 JAL-1297 JAL-1295 JAL-1294

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

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
new file mode 100644 (file)
index 0000000..2aed08b
--- /dev/null
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -0,0 +1,90 @@
+package jalview.io;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import jalview.datamodel.AlignmentI;
+
+import java.io.File;
+
+import org.junit.Test;
+
+public class AnnotationFileIOTest
+{
+
+  static String TestFiles[][] = {{ "Test example annotation import/export","examples/uniref50.fa", "examples/testdata/example_annot_file.jva" }
+          ,{"Test multiple combine annotation statements import/export","examples/uniref50.fa", "examples/testdata/test_combine_annot.jva"}};
+
+  @Test
+  public void exampleAnnotationFileIO() throws Exception
+  {
+    for (String[] testPair:TestFiles)
+    {
+      testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(testPair[2]));
+    }
+  }
+
+  public static AlignmentI readAlignmentFile(File f)
+  {
+    System.out.println("Reading file: " + f);
+    String ff = f.getPath();
+    try
+    {
+      FormatAdapter rf = new FormatAdapter();
+
+      AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
+              new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+      
+      // make sure dataset is initialised ? not sure about this
+      for (int i = 0; i < al.getSequencesArray().length; ++i)
+      {
+        al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence());
+      }
+      assertNotNull("Couldn't read supplied alignment data.", al);
+      return al;
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    fail("Couln't read the alignment in file '"+f.toString()+"'");
+    return null;
+  }
+  /**
+   * test alignment data in given file can be imported, exported and reimported
+   * with no dataloss
+   * 
+   * @param f
+   *          - source datafile (IdentifyFile.identify() should work with it)
+   * @param ioformat
+   *          - label for IO class used to write and read back in the data from
+   *          f
+   */
+  public static void testAnnotationFileIO(String testname, File f, File annotFile)
+  {
+    System.out.println("Test: "+testname+"\nReading annotation file '"+annotFile+"' onto : " + f);
+    String af = annotFile.getPath();
+    try
+    {
+      AlignmentI al = readAlignmentFile(f);
+      
+      assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
+      
+      String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
+      assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null);
+      assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Empty string",anfileout.length()>"JALVIEW_ANNOTATION".length());
+
+      System.out.println("Output annotation file:\n"+anfileout+"\n<<EOF\n");
+      
+      AlignmentI al_new = readAlignmentFile(f);
+      assertTrue("Test "+testname+"\nregenerated annotation file did not annotate alignment.",new AnnotationFile().readAnnotationFile(al_new, anfileout, FormatAdapter.PASTE));
+      
+      // test for consistency in io
+      StockholmFileTest.testAlignmentEquivalence(al, al_new);
+      return;
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");
+  }
+}