X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2Fgff%2FGffHelperBaseTest.java;h=de4e8205ea358c65db965b3a1e42aa931d100176;hb=9135cbb74bbff06ea60485540194515ebcc018b0;hp=7fb716f3bfddf9a087aca71aff52dfbe51648343;hpb=d90461d46979dda9326255b1e1e85ce34c465ea3;p=jalview.git

diff --git a/test/jalview/io/gff/GffHelperBaseTest.java b/test/jalview/io/gff/GffHelperBaseTest.java
index 7fb716f..de4e820 100644
--- a/test/jalview/io/gff/GffHelperBaseTest.java
+++ b/test/jalview/io/gff/GffHelperBaseTest.java
@@ -20,9 +20,10 @@
  */
 package jalview.io.gff;
 
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
 
 import jalview.gui.JvOptionPane;
 
@@ -59,25 +60,38 @@ public class GffHelperBaseTest
 
     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));
+    assertEquals(map.size(), 1);
+    assertEquals(map.get("hello").size(), 1);
+    assertEquals(map.get("hello").get(0), "world");
 
     map = GffHelperBase
             .parseNameValuePairs(
-                    "Method= manual curation ;nothing; Notes=F2 S ; Notes=Metal,Shiny; Type=",
+                    "Method= manual curation ;nothing; Notes=F2 S ; Notes=Metal,Shiny%2Csmooth; 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));
+    assertEquals(map.size(), 2);
+
+    assertEquals(map.get("Method").size(), 1);
+    assertEquals(map.get("Method").get(0), "manual curation"); // trimmed
+
+    assertEquals(map.get("Notes").size(), 3);
+    assertEquals(map.get("Notes").get(0), "F2 S");
+    assertEquals(map.get("Notes").get(1), "Metal");
+    assertEquals(map.get("Notes").get(2), "Shiny%2Csmooth"); // not decoded here
+
+    /*
+     * gff3 style with nested attribute values
+     */
+    String csqValue = "POLYPHEN=possibly_damaging,probably_damaging,SIFT=tolerated%2Cdeleterious";
+    map = GffHelperBase.parseNameValuePairs("hello=world;CSQ=" + csqValue,
+            ";", '=', ",");
+    assertEquals(map.size(), 2); // keys hello, CSQ
+    assertEquals(map.get("hello").size(), 1);
+    assertEquals(map.get("hello").get(0), "world");
+    // CSQ values is read 'raw' here, and parsed further elsewhere
+    assertEquals(map.get("CSQ").size(), 1);
+    assertEquals(map.get("CSQ").get(0), csqValue);
   }
 
   /**
@@ -89,110 +103,126 @@ public class GffHelperBaseTest
     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
+    assertEquals(Arrays.toString(from), "[1, 12]"); // unchanged
+    assertEquals(Arrays.toString(to), "[20, 31]"); // 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
+    assertEquals(Arrays.toString(from), "[1, 12]"); // trimmed
+    assertEquals(Arrays.toString(to), "[20, 31]"); // 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
+    assertEquals(Arrays.toString(from), "[1, 12]"); // unchanged
+    assertEquals(Arrays.toString(to), "[20, 31]"); // 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
+    assertEquals(Arrays.toString(from), "[12, 1]"); // unchanged
+    assertEquals(Arrays.toString(to), "[20, 31]"); // 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
+    assertEquals(Arrays.toString(from), "[12, 1]"); // unchanged
+    assertEquals(Arrays.toString(to), "[31, 20]"); // 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
+    assertEquals(Arrays.toString(from), "[14, 3]"); // end trimmed
+    assertEquals(Arrays.toString(to), "[31, 20]"); // 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
+    assertEquals(Arrays.toString(from), "[14, 3]"); // unchanged
+    assertEquals(Arrays.toString(to), "[31, 20]"); // 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
+    assertEquals(Arrays.toString(from), "[1, 18]"); // unchanged
+    assertEquals(Arrays.toString(to), "[4, 9]"); // 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
+    assertEquals(Arrays.toString(from), "[1, 18]"); // end trimmed
+    assertEquals(Arrays.toString(to), "[4, 9]"); // 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
+    assertEquals(Arrays.toString(from), "[20, 3]"); // end trimmed
+    assertEquals(Arrays.toString(to), "[4, 9]"); // 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
+    assertEquals(Arrays.toString(from), "[20, 3]"); // end trimmed
+    assertEquals(Arrays.toString(to), "[9, 4]"); // 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
+    assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
+    assertEquals(Arrays.toString(to), "[1, 18]"); // 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
+    assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
+    assertEquals(Arrays.toString(to), "[1, 18]"); // 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
+    assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
+    assertEquals(Arrays.toString(to), "[20, 3]"); // 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
+    assertEquals(Arrays.toString(from), "[9, 4]"); // unchanged
+    assertEquals(Arrays.toString(to), "[20, 3]"); // 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
+    assertEquals(Arrays.toString(from), "[4, 9]"); // end trimmed
+    assertEquals(Arrays.toString(to), "[1, 18]"); // 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
+    assertEquals(Arrays.toString(from), "[4, 10]"); // unchanged
+    assertEquals(Arrays.toString(to), "[1, 19]"); // unchanged
+  }
 
+  @Test(groups = { "Functional" })
+  public void testParseAttributeMap()
+  {
+    Map<String, String> map = GffHelperBase
+            .parseAttributeMap("A=B,C%2C%3D%3B%09%25D");
+    assertEquals(map.get("A"), "B,C,=;\t%D");
+
+    try
+    {
+      GffHelperBase.parseAttributeMap(null);
+      fail("expected exception");
+    } catch (NullPointerException e)
+    {
+      // expected
+    }
   }
 }