develop merge

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

diff --git a/test/jalview/io/gff/GffHelperBaseTest.java b/test/jalview/io/gff/GffHelperBaseTest.java
new file mode 100644 (file)
index 0000000..fe8f88e
--- /dev/null
+++ b/test/jalview/io/gff/GffHelperBaseTest.java
@@ -0,0 +1,168 @@
+package jalview.io.gff;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.Test;
+
+public class GffHelperBaseTest
+{
+
+  /**
+   * Test the method that parses lines like <br>
+   * ID=2345;Name=Something,Another thing;Notes=Hello;Notes=World
+   */
+  @Test(groups = { "Functional" })
+  public void testParseNameValuePairs()
+  {
+    assertTrue(GffHelperBase.parseNameValuePairs(null, ";", ' ', ",")
+            .isEmpty());
+    assertTrue(GffHelperBase.parseNameValuePairs("", ";", ' ', ",")
+            .isEmpty());
+    assertTrue(GffHelperBase.parseNameValuePairs("hello=world", ";", ' ',
+            ",").isEmpty());
+
+    Map<String, List<String>> map = GffHelperBase.parseNameValuePairs(
+            "hello world", ";", ' ', ", ");
+    assertEquals(1, map.size());
+    assertEquals(1, map.get("hello").size());
+    assertEquals("world", map.get("hello").get(0));
+
+    map = GffHelperBase
+            .parseNameValuePairs(
+                    "Method= manual curation ;nothing; Notes=F2 S ; Notes=Metal,Shiny; Type=",
+                    ";", '=', ",");
+
+    // Type is ignored as no value was supplied
+    assertEquals(2, map.size());
+
+    assertEquals(1, map.get("Method").size());
+    assertEquals("manual curation", map.get("Method").get(0)); // trimmed
+
+    assertEquals(3, map.get("Notes").size());
+    assertEquals("F2 S", map.get("Notes").get(0));
+    assertEquals("Metal", map.get("Notes").get(1));
+    assertEquals("Shiny", map.get("Notes").get(2));
+  }
+
+  /**
+   * Test for the method that tries to trim mappings to equivalent lengths
+   */
+  @Test(groups = "Functional")
+  public void testTrimMapping()
+  {
+    int[] from = { 1, 12 };
+    int[] to = { 20, 31 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
+    assertEquals("[1, 12]", Arrays.toString(from)); // unchanged
+    assertEquals("[20, 31]", Arrays.toString(to)); // unchanged
+
+    // from too long:
+    from = new int[] { 1, 13 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
+    assertEquals("[1, 12]", Arrays.toString(from)); // trimmed
+    assertEquals("[20, 31]", Arrays.toString(to)); // unchanged
+
+    // to too long:
+    to = new int[] { 20, 33 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
+    assertEquals("[1, 12]", Arrays.toString(from)); // unchanged
+    assertEquals("[20, 31]", Arrays.toString(to)); // trimmed
+
+    // from reversed:
+    from = new int[] { 12, 1 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
+    assertEquals("[12, 1]", Arrays.toString(from)); // unchanged
+    assertEquals("[20, 31]", Arrays.toString(to)); // unchanged
+
+    // to reversed:
+    to = new int[] { 31, 20 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
+    assertEquals("[12, 1]", Arrays.toString(from)); // unchanged
+    assertEquals("[31, 20]", Arrays.toString(to)); // unchanged
+
+    // from reversed and too long:
+    from = new int[] { 14, 1 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
+    assertEquals("[14, 3]", Arrays.toString(from)); // end trimmed
+    assertEquals("[31, 20]", Arrays.toString(to)); // unchanged
+
+    // to reversed and too long:
+    to = new int[] { 31, 10 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
+    assertEquals("[14, 3]", Arrays.toString(from)); // unchanged
+    assertEquals("[31, 20]", Arrays.toString(to)); // end trimmed
+
+    // cdna to peptide (matching)
+    from = new int[] { 1, 18 };
+    to = new int[] { 4, 9 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
+    assertEquals("[1, 18]", Arrays.toString(from)); // unchanged
+    assertEquals("[4, 9]", Arrays.toString(to)); // unchanged
+
+    // overlong cdna to peptide
+    from = new int[] { 1, 20 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
+    assertEquals("[1, 18]", Arrays.toString(from)); // end trimmed
+    assertEquals("[4, 9]", Arrays.toString(to)); // unchanged
+
+    // overlong cdna (reversed) to peptide
+    from = new int[] { 20, 1 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
+    assertEquals("[20, 3]", Arrays.toString(from)); // end trimmed
+    assertEquals("[4, 9]", Arrays.toString(to)); // unchanged
+
+    // overlong cdna (reversed) to peptide (reversed)
+    from = new int[] { 20, 1 };
+    to = new int[] { 9, 4 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
+    assertEquals("[20, 3]", Arrays.toString(from)); // end trimmed
+    assertEquals("[9, 4]", Arrays.toString(to)); // unchanged
+
+    // peptide to cdna (matching)
+    from = new int[] { 4, 9 };
+    to = new int[] { 1, 18 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
+    assertEquals("[4, 9]", Arrays.toString(from)); // unchanged
+    assertEquals("[1, 18]", Arrays.toString(to)); // unchanged
+
+    // peptide to overlong cdna
+    to = new int[] { 1, 20 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
+    assertEquals("[4, 9]", Arrays.toString(from)); // unchanged
+    assertEquals("[1, 18]", Arrays.toString(to)); // end trimmed
+
+    // peptide to overlong cdna (reversed)
+    to = new int[] { 20, 1 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
+    assertEquals("[4, 9]", Arrays.toString(from)); // unchanged
+    assertEquals("[20, 3]", Arrays.toString(to)); // end trimmed
+
+    // peptide (reversed) to overlong cdna (reversed)
+    from = new int[] { 9, 4 };
+    to = new int[] { 20, 1 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
+    assertEquals("[9, 4]", Arrays.toString(from)); // unchanged
+    assertEquals("[20, 3]", Arrays.toString(to)); // end trimmed
+
+    // overlong peptide to word-length cdna
+    from = new int[] { 4, 10 };
+    to = new int[] { 1, 18 };
+    assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
+    assertEquals("[4, 9]", Arrays.toString(from)); // end trimmed
+    assertEquals("[1, 18]", Arrays.toString(to)); // unchanged
+
+    // overlong peptide to non-word-length cdna
+    from = new int[] { 4, 10 };
+    to = new int[] { 1, 19 };
+    assertFalse(GffHelperBase.trimMapping(from, to, 1, 3));
+    assertEquals("[4, 10]", Arrays.toString(from)); // unchanged
+    assertEquals("[1, 19]", Arrays.toString(to)); // unchanged
+
+  }
+}