+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.structures.models;
import static org.testng.AssertJUnit.assertEquals;
/**
* Set up test conditions with three aligned sequences,
*/
- @BeforeMethod
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
SequenceI seq1 = new Sequence("1YCS", "-VPSQK");
SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
- al = new Alignment(new SequenceI[]
- { seq1, seq2, seq3 });
+ al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
al.setDataset(null);
PDBEntry[] pdbFiles = new PDBEntry[3];
pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "1OOT.pdb");
String[][] chains = new String[3][];
SequenceI[][] seqs = new SequenceI[3][];
- seqs[0] = new SequenceI[]
- { seq1 };
- seqs[1] = new SequenceI[]
- { seq2 };
- seqs[2] = new SequenceI[]
- { seq3 };
+ seqs[0] = new SequenceI[] { seq1 };
+ seqs[1] = new SequenceI[] { seq2 };
+ seqs[2] = new SequenceI[] { seq3 };
StructureSelectionManager ssm = new StructureSelectionManager();
- ssm.setMapping(new SequenceI[]
- { seq1 }, null, PDB_1, AppletFormatAdapter.PASTE);
- ssm.setMapping(new SequenceI[]
- { seq2 }, null, PDB_2, AppletFormatAdapter.PASTE);
- ssm.setMapping(new SequenceI[]
- { seq3 }, null, PDB_3, AppletFormatAdapter.PASTE);
+ ssm.setMapping(new SequenceI[] { seq1 }, null, PDB_1,
+ AppletFormatAdapter.PASTE);
+ ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
+ AppletFormatAdapter.PASTE);
+ ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
+ AppletFormatAdapter.PASTE);
testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null)
{
* fudge 'filenames' to match those generated when PDBFile parses PASTE
* data
*/
- return new String[]
- { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
+ return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
}
+
@Override
public void updateColours(Object source)
{
}
+
@Override
public void releaseReferences(Object svl)
{
}
+
@Override
public void highlightAtoms(List<AtomSpec> atoms)
{
}
/**
- * Verify that the method determines that columns 2, 5 and 6 of the aligment
+ * Verify that the method determines that columns 2, 5 and 6 of the alignment
* are alignable in structure
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testFindSuperposableResidues()
{
SuperposeData[] structs = new SuperposeData[al.getHeight()];
assertTrue(matched[5]);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testFindSuperposableResidues_hiddenColumn()
{
SuperposeData[] structs = new SuperposeData[al.getHeight()];