+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class GffHelperBaseTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test the method that parses lines like <br>
* ID=2345;Name=Something,Another thing;Notes=Hello;Notes=World
{
assertTrue(GffHelperBase.parseNameValuePairs(null, ";", ' ', ",")
.isEmpty());
- assertTrue(GffHelperBase.parseNameValuePairs("", ";", ' ', ",")
- .isEmpty());
- assertTrue(GffHelperBase.parseNameValuePairs("hello=world", ";", ' ',
- ",").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<String, List<String>> map = GffHelperBase
+ .parseNameValuePairs("hello world", ";", ' ', ", ");
+ 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=",
- ";", '=', ",");
+ map = GffHelperBase.parseNameValuePairs(
+ "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(map.size(), 2);
+
+ assertEquals(map.get("Method").size(), 1);
+ assertEquals(map.get("Method").get(0), "manual curation"); // trimmed
- assertEquals(1, map.get("Method").size());
- assertEquals("manual curation", map.get("Method").get(0)); // 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
- 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));
+ /*
+ * 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);
}
/**
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,X=Y");
+ assertEquals(map.size(), 2);
+ // value of A is everything up to and excluding ,X=
+ assertEquals(map.get("A"), "B,C,=;\t%D");
+ assertEquals(map.get("X"), "Y");
+
+ /*
+ * malformed cases should result in an empty map
+ */
+ map = GffHelperBase.parseAttributeMap("=B=Y");
+ assertTrue(map.isEmpty());
+ // first token should be an attribute name only, no commas
+ map = GffHelperBase.parseAttributeMap("A,B=C");
+ assertTrue(map.isEmpty());
+ // intermediate tokens need at least one comma (value,name=)
+ map = GffHelperBase.parseAttributeMap("A=B=C");
+ assertTrue(map.isEmpty());
+ // last token may have a comma or not
+ map = GffHelperBase.parseAttributeMap("A=B");
+ assertEquals(map.get("A"), "B");
+ map = GffHelperBase.parseAttributeMap("A=B,C");
+ assertEquals(map.get("A"), "B,C");
+ map = GffHelperBase.parseAttributeMap("A");
+ assertTrue(map.isEmpty());
+ map = GffHelperBase.parseAttributeMap("A=");
+ assertTrue(map.isEmpty());
+ map = GffHelperBase.parseAttributeMap("A==C");
+ assertTrue(map.isEmpty());
+ map = GffHelperBase.parseAttributeMap("=A");
+ assertTrue(map.isEmpty());
+ map = GffHelperBase.parseAttributeMap("=");
+ assertTrue(map.isEmpty());
+ map = GffHelperBase.parseAttributeMap(",");
+ assertTrue(map.isEmpty());
+ map = GffHelperBase.parseAttributeMap(" ");
+ assertTrue(map.isEmpty());
+ map = GffHelperBase.parseAttributeMap("");
+ assertTrue(map.isEmpty());
+ map = GffHelperBase.parseAttributeMap("A=B, =C");
+ assertTrue(map.isEmpty());
+ try
+ {
+ GffHelperBase.parseAttributeMap(null);
+ fail("expected exception");
+ } catch (NullPointerException e)
+ {
+ // expected
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff