+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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.gui;
import static org.testng.AssertJUnit.assertEquals;
{
AlignmentI al;
+
AlignViewport testee;
@BeforeClass(alwaysRun = true)
"test/jalview/testProps.jvprops" });
}
- @BeforeMethod(alwaysRun = true)
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
SequenceI seq1 = new Sequence("Seq1", "ABC");
SequenceI seq2 = new Sequence("Seq2", "ABC");
SequenceI seq3 = new Sequence("Seq3", "ABC");
- SequenceI[] seqs = new SequenceI[]
- { seq1, seq2, seq3 };
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
al = new Alignment(seqs);
al.setDataset(null);
testee = new AlignViewport(al);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testCollateForPdb()
{
/*
* seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC
*/
al.getSequenceAt(0).getDatasetSequence()
- .addPDBId(
- new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
+ .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
al.getSequenceAt(2).getDatasetSequence()
- .addPDBId(
- new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
+ .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
al.getSequenceAt(1).getDatasetSequence()
- .addPDBId(
- new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
+ .addPDBId(new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
/*
* Add a second chain PDB xref to Seq2 - should not result in a duplicate in
* the results
/*
* run method under test
*/
- SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[]
- { pdb1, pdb2, pdb3 });
+ SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2,
+ pdb3 });
// seq1 and seq3 refer to PDBEntry[0]
assertEquals(2, seqs[0].length);
* Test that a mapping is not deregistered when a second view is closed but
* the first still holds a reference to the mapping
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testDeregisterMapping_onCloseView()
{
/*
*/
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
">Seq1\nCAGT\n", FormatAdapter.PASTE);
-
+
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
-
+
Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
mappings.add(acf1);
mappings.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings);
af1.newView_actionPerformed(null);
-
+
/*
* Verify that creating the alignment for the new View has registered the
* mappings
assertEquals(2, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
-
+
/*
* Close the second view. Verify that mappings are not removed as the first
* view still holds a reference to them.
/**
* Test that a mapping is deregistered if no alignment holds a reference to it
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testDeregisterMapping_withNoReference()
{
Desktop d = Desktop.instance;
">Seq1\nRSVQ\n", FormatAdapter.PASTE);
AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
">Seq2\nDGEL\n", FormatAdapter.PASTE);
-
+
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
AlignedCodonFrame acf3 = new AlignedCodonFrame();
-
+
Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
mappings1.add(acf1);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
-
+
/*
* AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
*/
* Test that a mapping is not deregistered if another alignment holds a
* reference to it
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testDeregisterMapping_withReference()
{
Desktop d = Desktop.instance;
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
ssm.resetAll();
-
+
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
">Seq1\nRSVQ\n", FormatAdapter.PASTE);
AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
">Seq2\nDGEL\n", FormatAdapter.PASTE);
-
+
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
AlignedCodonFrame acf3 = new AlignedCodonFrame();
-
+
Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
mappings1.add(acf1);
mappings1.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
-
+
Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
-
+
/*
* AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
*/
-
+
Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
assertEquals(0, ssmMappings.size());
ssm.registerMapping(acf1);
assertEquals(2, ssmMappings.size());
ssm.registerMapping(acf3);
assertEquals(3, ssmMappings.size());
-
+
/*
* Closing AlignFrame2 should remove mapping acf3 from
* StructureSelectionManager, but not acf2, since AlignFrame1 still has a
git://source.jalview.org / jalview.git / blobdiff