X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FTCoffeeScoreFileTest.java;h=181aabdd8e7bc951dbf63e899da41cb80c3895ab;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=edf7f208b4034479c66bc5f36d2a3304e4a52d3c;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java index edf7f20..181aabd 100644 --- a/test/jalview/io/TCoffeeScoreFileTest.java +++ b/test/jalview/io/TCoffeeScoreFileTest.java @@ -20,7 +20,6 @@ */ package jalview.io; -import static org.junit.Assert.*; import jalview.io.TCoffeeScoreFile.Block; import jalview.io.TCoffeeScoreFile.Header; @@ -29,15 +28,8 @@ import java.io.FileNotFoundException; 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 { @@ -48,57 +40,59 @@ 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 { @@ -116,140 +110,167 @@ public class TCoffeeScoreFileTest 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 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()); } }