*/
package jalview.io;
-import static org.junit.Assert.*;
import jalview.io.TCoffeeScoreFile.Block;
import jalview.io.TCoffeeScoreFile.Header;
import java.io.IOException;
import java.util.List;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.junit.Test;
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
public class TCoffeeScoreFileTest
{
final static File ALIGN_FILE = new File(
"test/jalview/io/tcoffee.fasta_aln");
- @Test
+ @Test(groups = { "Functional" })
public void testReadHeader() throws IOException
{
TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
AppletFormatAdapter.FILE);
- assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
+ AssertJUnit.assertTrue(scoreFile.getWarningMessage(),
+ scoreFile.isValid());
Header header = scoreFile.header;
- assertNotNull(header);
- assertEquals(
- "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
- header.head);
- assertEquals(90, header.score);
- assertEquals(89, header.getScoreFor("1PHT"));
- assertEquals(90, header.getScoreFor("1BB9"));
- assertEquals(94, header.getScoreFor("1UHC"));
- assertEquals(94, header.getScoreFor("1YCS"));
- assertEquals(93, header.getScoreFor("1OOT"));
- assertEquals(94, header.getScoreFor("1ABO"));
- assertEquals(94, header.getScoreFor("1FYN"));
- assertEquals(94, header.getScoreFor("1QCF"));
- assertEquals(90, header.getScoreFor("cons"));
+ AssertJUnit.assertNotNull(header);
+ AssertJUnit
+ .assertEquals(
+ "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
+ header.head);
+ AssertJUnit.assertEquals(90, header.score);
+ AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
+ AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
+ AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
+ AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
+ AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
+ AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
+ AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
+ AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
+ AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
}
- @Test
+ @Test(groups = { "Functional" })
public void testWrongFile()
{
try
{
TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
FormatAdapter.FILE);
- assertFalse(result.isValid());
+ AssertJUnit.assertFalse(result.isValid());
} catch (IOException x)
{
- assertTrue("File not found exception thrown",
+ AssertJUnit.assertTrue("File not found exception thrown",
x instanceof FileNotFoundException);
}
}
- @Test
+ @Test(groups = { "Functional" })
public void testHeightAndWidth() throws IOException
{
TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
FormatAdapter.FILE);
- assertTrue(result.isValid());
- assertEquals(8, result.getHeight());
- assertEquals(83, result.getWidth());
+ AssertJUnit.assertTrue(result.isValid());
+ AssertJUnit.assertEquals(8, result.getHeight());
+ AssertJUnit.assertEquals(83, result.getWidth());
}
- @Test
+ @Test(groups = { "Functional" })
public void testReadBlock() throws IOException
{
FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE);
Block block = TCoffeeScoreFile.readBlock(source, 0);
- assertNotNull(block);
- assertEquals("999999999999999999999999998762112222543211112134",
+ AssertJUnit.assertNotNull(block);
+ AssertJUnit.assertEquals(
+ "999999999999999999999999998762112222543211112134",
block.getScoresFor("1PHT"));
- assertEquals("99999999999999999999999999987-------4322----2234",
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999987-------4322----2234",
block.getScoresFor("1BB9"));
- assertEquals("99999999999999999999999999987-------5321----2246",
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999987-------5321----2246",
block.getScoresFor("1UHC"));
- assertEquals("99999999999999999999999999986-------4321----1-35",
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999986-------4321----1-35",
block.getScoresFor("1YCS"));
- assertEquals("999999999999999999999999999861-------3------1135",
+ AssertJUnit.assertEquals(
+ "999999999999999999999999999861-------3------1135",
block.getScoresFor("1OOT"));
- assertEquals("99999999999999999999999999986-------422-------34",
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999986-------422-------34",
block.getScoresFor("1ABO"));
- assertEquals("99999999999999999999999999985-------32--------35",
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999985-------32--------35",
block.getScoresFor("1FYN"));
- assertEquals("99999999999999999999999999974-------2---------24",
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999974-------2---------24",
block.getScoresFor("1QCF"));
- assertEquals("999999999999999999999999999851000110321100001134",
+ AssertJUnit.assertEquals(
+ "999999999999999999999999999851000110321100001134",
block.getConsensus());
}
- @Test
+ @Test(groups = { "Functional" })
public void testParse() throws IOException
{
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
FormatAdapter.FILE);
- assertEquals(
- "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
- parser.getScoresFor("1PHT"));
- assertEquals(
- "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
- parser.getScoresFor("1BB9"));
- assertEquals(
- "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
- parser.getScoresFor("1UHC"));
- assertEquals(
- "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
- parser.getScoresFor("1YCS"));
- assertEquals(
- "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
- parser.getScoresFor("1OOT"));
- assertEquals(
- "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
- parser.getScoresFor("1ABO"));
- assertEquals(
- "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
- parser.getScoresFor("1FYN"));
- assertEquals(
- "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
- parser.getScoresFor("1QCF"));
- assertEquals(
- "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
- parser.getScoresFor("cons"));
+ AssertJUnit
+ .assertEquals(
+ "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
+ parser.getScoresFor("1PHT"));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
+ parser.getScoresFor("1BB9"));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
+ parser.getScoresFor("1UHC"));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
+ parser.getScoresFor("1YCS"));
+ AssertJUnit
+ .assertEquals(
+ "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
+ parser.getScoresFor("1OOT"));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
+ parser.getScoresFor("1ABO"));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
+ parser.getScoresFor("1FYN"));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
+ parser.getScoresFor("1QCF"));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
+ parser.getScoresFor("cons"));
}
- @Test
+ @Test(groups = { "Functional" })
public void testGetAsList() throws IOException
{
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
FormatAdapter.FILE);
- assertTrue(parser.getWarningMessage(), parser.isValid());
+ AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
List<String> scores = parser.getScoresList();
- assertEquals(
- "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
- scores.get(0));
- assertEquals(
- "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
- scores.get(1));
- assertEquals(
- "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
- scores.get(2));
- assertEquals(
- "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
- scores.get(3));
- assertEquals(
- "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
- scores.get(4));
- assertEquals(
- "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
- scores.get(5));
- assertEquals(
- "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
- scores.get(6));
- assertEquals(
- "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
- scores.get(7));
- assertEquals(
- "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
- scores.get(8));
+ AssertJUnit
+ .assertEquals(
+ "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
+ scores.get(0));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
+ scores.get(1));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
+ scores.get(2));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
+ scores.get(3));
+ AssertJUnit
+ .assertEquals(
+ "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
+ scores.get(4));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
+ scores.get(5));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
+ scores.get(6));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
+ scores.get(7));
+ AssertJUnit
+ .assertEquals(
+ "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
+ scores.get(8));
}
- @Test
+ @Test(groups = { "Functional" })
public void testGetAsArray() throws IOException
{
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
FormatAdapter.FILE);
- assertTrue(parser.getWarningMessage(), parser.isValid());
+ AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
byte[][] scores = parser.getScoresArray();
- assertEquals(9, scores[0][0]);
- assertEquals(9, scores[1][0]);
- assertEquals(9, scores[2][0]);
- assertEquals(9, scores[3][0]);
- assertEquals(9, scores[4][0]);
- assertEquals(9, scores[5][0]);
- assertEquals(9, scores[6][0]);
- assertEquals(9, scores[7][0]);
- assertEquals(9, scores[8][0]);
-
- assertEquals(5, scores[0][36]);
- assertEquals(4, scores[1][36]);
- assertEquals(5, scores[2][36]);
- assertEquals(4, scores[3][36]);
- assertEquals(-1, scores[4][36]);
- assertEquals(4, scores[5][36]);
- assertEquals(3, scores[6][36]);
- assertEquals(2, scores[7][36]);
- assertEquals(3, scores[8][36]);
+ AssertJUnit.assertEquals(9, scores[0][0]);
+ AssertJUnit.assertEquals(9, scores[1][0]);
+ AssertJUnit.assertEquals(9, scores[2][0]);
+ AssertJUnit.assertEquals(9, scores[3][0]);
+ AssertJUnit.assertEquals(9, scores[4][0]);
+ AssertJUnit.assertEquals(9, scores[5][0]);
+ AssertJUnit.assertEquals(9, scores[6][0]);
+ AssertJUnit.assertEquals(9, scores[7][0]);
+ AssertJUnit.assertEquals(9, scores[8][0]);
+
+ AssertJUnit.assertEquals(5, scores[0][36]);
+ AssertJUnit.assertEquals(4, scores[1][36]);
+ AssertJUnit.assertEquals(5, scores[2][36]);
+ AssertJUnit.assertEquals(4, scores[3][36]);
+ AssertJUnit.assertEquals(-1, scores[4][36]);
+ AssertJUnit.assertEquals(4, scores[5][36]);
+ AssertJUnit.assertEquals(3, scores[6][36]);
+ AssertJUnit.assertEquals(2, scores[7][36]);
+ AssertJUnit.assertEquals(3, scores[8][36]);
}
- @Test
+ @Test(groups = { "Functional" })
public void testHeightAndWidthWithResidueNumbers() throws Exception
{
String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
- assertTrue(result.isValid());
- assertEquals(5, result.getHeight());
- assertEquals(84, result.getWidth());
+ AssertJUnit.assertTrue(result.isValid());
+ AssertJUnit.assertEquals(5, result.getHeight());
+ AssertJUnit.assertEquals(84, result.getWidth());
}
}
git://source.jalview.org / jalview.git / blobdiff