mungo merge

[jalview.git] / test / jalview / io / gff / GffHelperFactoryTest.java

diff --git a/test/jalview/io/gff/GffHelperFactoryTest.java b/test/jalview/io/gff/GffHelperFactoryTest.java
new file mode 100644 (file)
index 0000000..657b5bd
--- /dev/null
+++ b/test/jalview/io/gff/GffHelperFactoryTest.java
@@ -0,0 +1,72 @@
+package jalview.io.gff;
+
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
+import org.testng.annotations.Test;
+
+public class GffHelperFactoryTest
+{
+
+  @Test(groups = "Functional")
+  public void testGetHelper()
+  {
+    assertNull(GffHelperFactory.getHelper(null));
+
+    String tabRegex = "\\t";
+
+    /*
+     * column 3 = 'similarity' indicates exonerate GFF alignment data
+     */
+    String gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\t";
+    // no attributes (column 9 data):
+    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof Gff2Helper);
+
+    // attributes set but unhandled featureGroup - get generic handler
+    gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
+    assertSame(GffHelperFactory.getHelper(gff.split(tabRegex)).getClass(),
+            Gff3Helper.class);
+
+    // handled featureGroup (exonerate model) values
+    gff = "submitted\texonerate:protein2dna:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
+    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+
+    gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
+    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+
+    gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
+    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+
+    gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
+    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+
+    gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
+    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+
+    gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
+    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+
+    // not case-sensitive:
+    gff = "submitted\tgenome2genome\tSIMILARITY\t20\t30\t99\t+\t.\tID=$1";
+    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+
+    /*
+     * InterProScan has 'protein_match' in column 3
+     */
+    gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154";
+    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
+
+    /*
+     * nothing specific - return the generic GFF3 class if Name=Value is present in col9
+     */
+    gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID=1";
+    GffHelperI helper = GffHelperFactory.getHelper(gff.split(tabRegex));
+    assertSame(helper.getClass(), Gff3Helper.class);
+
+    // return the generic GFF2 class if "Name Value" is present in col9
+    gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID 1";
+    helper = GffHelperFactory.getHelper(gff.split(tabRegex));
+    assertSame(helper.getClass(), Gff2Helper.class);
+  }
+}