X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FTCoffeeScoreFileTest.java;h=38c9a892df4a65df70fa457142d3fe0e6458056b;hb=9745565701f82e6a975ac71254bcf07822d6d9dd;hp=df4b6600e4ada539c8a2bb0e141ce6b70a1cb745;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java index df4b660..38c9a89 100644 --- a/test/jalview/io/TCoffeeScoreFileTest.java +++ b/test/jalview/io/TCoffeeScoreFileTest.java @@ -20,8 +20,7 @@ */ package jalview.io; -import org.testng.annotations.Test; -import org.testng.AssertJUnit; +import jalview.gui.JvOptionPane; import jalview.io.TCoffeeScoreFile.Block; import jalview.io.TCoffeeScoreFile.Header; @@ -30,37 +29,41 @@ import java.io.FileNotFoundException; import java.io.IOException; import java.util.List; -import javax.xml.parsers.ParserConfigurationException; - -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.BeforeClass; +import org.testng.annotations.Test; public class TCoffeeScoreFileTest { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + final static File SCORE_FILE = new File( "test/jalview/io/tcoffee.score_ascii"); 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); - AssertJUnit.assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid()); + DataSourceType.FILE); + AssertJUnit.assertTrue(scoreFile.getWarningMessage(), + scoreFile.isValid()); Header header = scoreFile.header; 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( + "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")); @@ -73,13 +76,13 @@ public class TCoffeeScoreFileTest AssertJUnit.assertEquals(90, header.getScoreFor("cons")); } - @Test + @Test(groups = { "Functional" }) public void testWrongFile() { try { TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), - FormatAdapter.FILE); + DataSourceType.FILE); AssertJUnit.assertFalse(result.isValid()); } catch (IOException x) { @@ -88,17 +91,17 @@ public class TCoffeeScoreFileTest } } - @Test + @Test(groups = { "Functional" }) public void testHeightAndWidth() throws IOException { TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), - FormatAdapter.FILE); + DataSourceType.FILE); AssertJUnit.assertTrue(result.isValid()); AssertJUnit.assertEquals(8, result.getHeight()); AssertJUnit.assertEquals(83, result.getWidth()); } - @Test + @Test(groups = { "Functional" }) public void testReadBlock() throws IOException { @@ -113,110 +116,137 @@ public class TCoffeeScoreFileTest + "1QCF 99999999999999999999999999974-------2---------24\n" + "cons 999999999999999999999999999851000110321100001134\n" + "\n" + "\n"; - FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE); + FileParse source = new FileParse(BLOCK, DataSourceType.PASTE); Block block = TCoffeeScoreFile.readBlock(source, 0); AssertJUnit.assertNotNull(block); - AssertJUnit.assertEquals("999999999999999999999999998762112222543211112134", + AssertJUnit.assertEquals( + "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT")); - AssertJUnit.assertEquals("99999999999999999999999999987-------4322----2234", + AssertJUnit.assertEquals( + "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9")); - AssertJUnit.assertEquals("99999999999999999999999999987-------5321----2246", + AssertJUnit.assertEquals( + "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC")); - AssertJUnit.assertEquals("99999999999999999999999999986-------4321----1-35", + AssertJUnit.assertEquals( + "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS")); - AssertJUnit.assertEquals("999999999999999999999999999861-------3------1135", + AssertJUnit.assertEquals( + "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT")); - AssertJUnit.assertEquals("99999999999999999999999999986-------422-------34", + AssertJUnit.assertEquals( + "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO")); - AssertJUnit.assertEquals("99999999999999999999999999985-------32--------35", + AssertJUnit.assertEquals( + "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN")); - AssertJUnit.assertEquals("99999999999999999999999999974-------2---------24", + AssertJUnit.assertEquals( + "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF")); - AssertJUnit.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); + DataSourceType.FILE); - 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")); + 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); + DataSourceType.FILE); AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid()); List scores = parser.getScoresList(); - 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)); + 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); + DataSourceType.FILE); AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid()); byte[][] scores = parser.getScoresArray(); @@ -242,11 +272,11 @@ public class TCoffeeScoreFileTest } - @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); + TCoffeeScoreFile result = new TCoffeeScoreFile(file, DataSourceType.FILE); AssertJUnit.assertTrue(result.isValid()); AssertJUnit.assertEquals(5, result.getHeight()); AssertJUnit.assertEquals(84, result.getWidth());