/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import jalview.gui.JvOptionPane;
import jalview.io.TCoffeeScoreFile.Block;
import jalview.io.TCoffeeScoreFile.Header;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.List;
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(groups = { "Functional" })
public void testReadHeader() throws IOException
{
TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
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(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(),
DataSourceType.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(),
DataSourceType.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, DataSourceType.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(),
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"));
}
@Test(groups = { "Functional" })
public void testGetAsList() throws IOException
{
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
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));
}
@Test(groups = { "Functional" })
public void testGetAsArray() throws IOException
{
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
DataSourceType.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,
DataSourceType.FILE);
AssertJUnit.assertTrue(result.isValid());
AssertJUnit.assertEquals(5, result.getHeight());
AssertJUnit.assertEquals(84, result.getWidth());
}
}