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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
/*
* SimpleSymbolPropertyTableDBTest.java
*/
package org.biojava.bio.proteomics.aaindex;
import java.util.ArrayList;
import java.util.Set;
import junit.framework.TestCase;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.seq.db.IllegalIDException;
import org.biojava.bio.symbol.SimpleSymbolPropertyTable;
import org.biojava.bio.symbol.SymbolPropertyTable;
/**
* Test class for {@link org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB}.
* @author <a href="mailto:Martin.Szugat@GMX.net">Martin Szugat</a>
* @version $Revision: 4023 $
*/
public class SimpleSymbolPropertyTableDBTest extends TestCase {
/**
* Main entry point.
* @param args command line arguments
*/
public static void main(String[] args) {
junit.textui.TestRunner.run(SimpleSymbolPropertyTableDBTest.class);
}
/**
* Test constructor to create an empty database.
*/
public void testEmptyConstructor() {
SymbolPropertyTableDB db = new SimpleSymbolPropertyTableDB();
assertEquals("Database is not empty.", 0, db.numTables());
assertFalse("Database does not return an empty iterator.",
db.tableIterator().hasNext());
}
/**
* Test constructor to create a non-empty database.
* @throws BioException if iterator fails.
*/
public void testNonEmptyConstructor() throws BioException {
SimpleSymbolPropertyTableDB dbInit = new SimpleSymbolPropertyTableDB();
SymbolPropertyTable t1 = new SimpleSymbolPropertyTable(
ProteinTools.getAlphabet(), "protein");
SymbolPropertyTable t2 = new SimpleSymbolPropertyTable(
DNATools.getDNA(), "dna");
dbInit.addTable(t1);
dbInit.addTable(t2);
SymbolPropertyTableDB db = new SimpleSymbolPropertyTableDB(
dbInit.tableIterator());
assertEquals("Database has wrong number of tables.", 2, db.numTables());
SymbolPropertyTableIterator iterator = db.tableIterator();
ArrayList tables = new ArrayList(2);
while (iterator.hasNext()) {
tables.add(iterator.nextTable());
}
assertEquals("Iterator returned wrong number of tables.",
2, tables.size());
assertEquals("Iterator returned wrong table.", t1, tables.get(0));
assertEquals("Iterator returned wrong table.", t2, tables.get(1));
}
/**
* Test for {@link SimpleSymbolPropertyTableDB#addTable(SymbolPropertyTable)}.
* @throws IllegalIDException if {@link SymbolPropertyTableDB#table(String)}
* fails.
*/
public void testAddTable() throws IllegalIDException {
SimpleSymbolPropertyTableDB db = new SimpleSymbolPropertyTableDB();
SymbolPropertyTable t1 = new SimpleSymbolPropertyTable(
ProteinTools.getAlphabet(), "protein");
SymbolPropertyTable t2 = new SimpleSymbolPropertyTable(
DNATools.getDNA(), "dna");
db.addTable(t1);
assertEquals("Database has wrong number of tables.", 1, db.numTables());
db.addTable(t2);
assertEquals("Database has wrong number of tables.", 2, db.numTables());
assertEquals("Database returned wrong table.", t1, db.table("protein"));
assertEquals("Database returned wrong table.", t2, db.table("dna"));
Set names = db.names();
assertTrue("Table is missing.", names.contains("protein"));
assertTrue("Table is missing.", names.contains("dna"));
assertEquals("Database has wrong number of tables.", 2, names.size());
try {
db.addTable(null);
fail("addTable must throw NullPointerException.");
} catch (NullPointerException e) {
e.printStackTrace();
}
}
/**
* Test for {@link SimpleSymbolPropertyTableDB#table(String)}.
*/
public void testTable() {
SimpleSymbolPropertyTableDB db = new SimpleSymbolPropertyTableDB();
try {
db.table(null);
fail("table must throw NullPointerException.");
} catch (NullPointerException e) {
e.printStackTrace();
} catch (IllegalIDException e) {
fail("table throwed IllegalIDException instead of NullPointerException.");
}
try {
db.table("test");
fail("table must throw IllegalIDException.");
} catch (IllegalIDException e) {
e.printStackTrace();
}
}
}
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