/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * 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;
-import static org.junit.Assert.*;
import jalview.io.TCoffeeScoreFile.Block;
import jalview.io.TCoffeeScoreFile.Header;
-import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
-import java.io.FileReader;
import java.io.IOException;
-import java.io.StringReader;
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;
-
-public class TCoffeeScoreFileTest {
-
- 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
- public void testReadHeader() throws IOException, FileNotFoundException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
-
- TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
- 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") );
- }
-
-
- @Test
- public void testWrongFile() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
- try {
- TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
- assertFalse(result.isValid());
- } catch (IOException x)
- {
- assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
- }
- }
-
- @Test
- public void testHeightAndWidth() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
- TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
- assertTrue(result.isValid());
- assertEquals( 8, result.getHeight() );
- assertEquals( 83, result.getWidth() );
- }
-
- @Test
- public void testReadBlock( ) throws IOException {
-
- String BLOCK = "\n" +
- "\n" +
- "\n" +
- "1PHT 999999999999999999999999998762112222543211112134\n" +
- "1BB9 99999999999999999999999999987-------4322----2234 \n" +
- "1UHC 99999999999999999999999999987-------5321----2246\n" +
- "1YCS 99999999999999999999999999986-------4321----1-35\n" +
- "1OOT 999999999999999999999999999861-------3------1135 \n" +
- "1ABO 99999999999999999999999999986-------422-------34\n" +
- "1FYN 99999999999999999999999999985-------32--------35\n" +
- "1QCF 99999999999999999999999999974-------2---------24\n" +
- "cons 999999999999999999999999999851000110321100001134\n" +
- "\n" +
- "\n";
- FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
- Block block = TCoffeeScoreFile.readBlock(source, 0);
-
- assertNotNull(block);
- assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
- assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
- assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
- assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
- assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
- assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
- assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
- assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
- assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
- }
-
- @Test
- public void testParse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
-
- 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") );
- }
-
-
- @Test
- public void testGetAsList() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
-
- TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
- 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) );
-
- }
-
-
- @Test
- public void testGetAsArray() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
-
- TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
- 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] );
-
- }
-
-
-
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+public class TCoffeeScoreFileTest
+{
+
+ 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(groups = { "Functional" })
+ public void testReadHeader() throws IOException
+ {
+
+ TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
+ AppletFormatAdapter.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(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(groups = { "Functional" })
+ public void testWrongFile()
+ {
+ try
+ {
+ TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
+ FormatAdapter.FILE);
+ AssertJUnit.assertFalse(result.isValid());
+ } catch (IOException x)
+ {
+ AssertJUnit.assertTrue("File not found exception thrown",
+ x instanceof FileNotFoundException);
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void testHeightAndWidth() throws IOException
+ {
+ TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
+ FormatAdapter.FILE);
+ AssertJUnit.assertTrue(result.isValid());
+ AssertJUnit.assertEquals(8, result.getHeight());
+ AssertJUnit.assertEquals(83, result.getWidth());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testReadBlock() throws IOException
+ {
+
+ String BLOCK = "\n" + "\n" + "\n"
+ + "1PHT 999999999999999999999999998762112222543211112134\n"
+ + "1BB9 99999999999999999999999999987-------4322----2234 \n"
+ + "1UHC 99999999999999999999999999987-------5321----2246\n"
+ + "1YCS 99999999999999999999999999986-------4321----1-35\n"
+ + "1OOT 999999999999999999999999999861-------3------1135 \n"
+ + "1ABO 99999999999999999999999999986-------422-------34\n"
+ + "1FYN 99999999999999999999999999985-------32--------35\n"
+ + "1QCF 99999999999999999999999999974-------2---------24\n"
+ + "cons 999999999999999999999999999851000110321100001134\n"
+ + "\n" + "\n";
+ FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE);
+ Block block = TCoffeeScoreFile.readBlock(source, 0);
+
+ AssertJUnit.assertNotNull(block);
+ AssertJUnit.assertEquals(
+ "999999999999999999999999998762112222543211112134",
+ block.getScoresFor("1PHT"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999987-------4322----2234",
+ block.getScoresFor("1BB9"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999987-------5321----2246",
+ block.getScoresFor("1UHC"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999986-------4321----1-35",
+ block.getScoresFor("1YCS"));
+ AssertJUnit.assertEquals(
+ "999999999999999999999999999861-------3------1135",
+ block.getScoresFor("1OOT"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999986-------422-------34",
+ block.getScoresFor("1ABO"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999985-------32--------35",
+ block.getScoresFor("1FYN"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999974-------2---------24",
+ block.getScoresFor("1QCF"));
+ AssertJUnit.assertEquals(
+ "999999999999999999999999999851000110321100001134",
+ block.getConsensus());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testParse() throws IOException
+ {
+
+ TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
+ FormatAdapter.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"));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetAsList() throws IOException
+ {
+
+ TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
+ FormatAdapter.FILE);
+ AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
+ List<String> 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));
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetAsArray() throws IOException
+ {
+
+ TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
+ FormatAdapter.FILE);
+ AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
+ byte[][] scores = parser.getScoresArray();
+
+ 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(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);
+ AssertJUnit.assertTrue(result.isValid());
+ AssertJUnit.assertEquals(5, result.getHeight());
+ AssertJUnit.assertEquals(84, result.getWidth());
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff