File FileFormatsTest.java

Branches:

Statements:

Methods:

Classes:

LOC:

191

NCLOC:

129

Total complexity:

Complexity density:

0.15

Statements/Method:

6.89

Methods/Class:

Average method complexity:

Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FileFormatsTest	38	62	9	0.00%

Class FileFormatsTest

Class FileFormatsTest	Line # 38	Total Statements 62	Complexity 9	TOTAL Coverage 0.00%
tearDown() : void tearDown() : void	4040	1.01	1.01	0.0 0.00%
setUp() : void setUp() : void	4646	1.01	1.01	0.0 0.00%
testIsIdentifiable() : void testIsIdentifiable() : void	5252	11.011	1.01	0.0 0.00%
testGetReadableFormats() : void testGetReadableFormats() : void	7878	3.03	1.01	0.0 0.00%
testGetWritableFormats() : void testGetWritableFormats() : void	8686	5.05	1.01	0.0 0.00%
testDeregisterFileFormat() : void testDeregisterFileFormat() : void	9696	15.015	1.01	0.0 0.00%
testForName() : void testForName() : void	121121	7.07	1.01	0.0 0.00%
testRegisterFileFormat() : void testRegisterFileFormat() : void	137137	10.010	1.01	0.0 0.00%
testGetFormats() : void testGetFormats() : void	165165	9.09	1.01	0.0 0.00%

Contributing tests

No tests hitting this source file were found.

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* 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 <http://www.gnu.org/licenses/>.

* The Jalview Authors are detailed in the 'AUTHORS' file.

package jalview.io;

import java.util.Locale;

import static org.testng.Assert.assertEquals;

import static org.testng.Assert.assertFalse;

import static org.testng.Assert.assertNotEquals;

import static org.testng.Assert.assertNull;

import static org.testng.Assert.assertSame;

import static org.testng.Assert.assertTrue;

import java.util.Iterator;

import org.testng.annotations.AfterMethod;

import org.testng.annotations.BeforeMethod;

import org.testng.annotations.Test;

public class FileFormatsTest

{

@AfterMethod(alwaysRun = true)

public void tearDown()

{

FileFormats.getInstance().reset();

}

@BeforeMethod(alwaysRun = true)

public void setUp()

{

FileFormats.getInstance().reset();

}

@Test(groups = "Functional")

public void testIsIdentifiable()

{

FileFormats formats = FileFormats.getInstance();

assertTrue(formats

.isIdentifiable(formats.forName(FileFormat.Fasta.getName())));

assertTrue(formats

.isIdentifiable(formats.forName(FileFormat.MMCif.getName())));

assertTrue(formats

.isIdentifiable(formats.forName(FileFormat.Jnet.getName())));

assertTrue(formats

.isIdentifiable(formats.forName(FileFormat.Jalview.getName())));

// GenBank/ENA

assertFalse(formats.isIdentifiable(null));

* remove and re-add a format: it is still 'identifiable'

formats.deregisterFileFormat(FileFormat.Fasta.getName());

assertNull(formats.forName(FileFormat.Fasta.getName()));

formats.registerFileFormat(FileFormat.Fasta);

assertSame(FileFormat.Fasta,

formats.forName(FileFormat.Fasta.getName()));

assertTrue(formats.isIdentifiable(FileFormat.Fasta));

}

@Test(groups = "Functional")

public void testGetReadableFormats()

{

String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";

FileFormats formats = FileFormats.getInstance();

assertEquals(formats.getReadableFormats().toString(), expected);

}

@Test(groups = "Functional")

public void testGetWritableFormats()

{

String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";

FileFormats formats = FileFormats.getInstance();

assertEquals(formats.getWritableFormats(true).toString(), expected);

expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview]";

assertEquals(formats.getWritableFormats(false).toString(), expected);

}

@Test(groups = "Functional")

public void testDeregisterFileFormat()

{

String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";

100

String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";

101

FileFormats formats = FileFormats.getInstance();

102

assertEquals(formats.getWritableFormats(true).toString(), writable);

103

assertEquals(formats.getReadableFormats().toString(), readable);

104

105

formats.deregisterFileFormat(FileFormat.Fasta.getName());

106

writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";

107

readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";

108

assertEquals(formats.getWritableFormats(true).toString(), writable);

109

assertEquals(formats.getReadableFormats().toString(), readable);

110

111

112

* re-register the format: it gets added to the end of the list

113

114

formats.registerFileFormat(FileFormat.Fasta);

115

writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";

116

readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";

117

assertEquals(formats.getWritableFormats(true).toString(), writable);

118

assertEquals(formats.getReadableFormats().toString(), readable);

119

}

120