+/*
+ * 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.gui;
import static org.testng.AssertJUnit.assertEquals;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.util.MessageManager;
PopupMenu testee = null;
- @BeforeMethod(alwaysRun = true)
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
alignment = new FormatAdapter().readFile(TEST_DATA,
- AppletFormatAdapter.PASTE, "FASTA");
+ DataSourceType.PASTE, FileFormat.Fasta);
AlignFrame af = new AlignFrame(alignment, 700, 500);
parentPanel = new AlignmentPanel(af, af.getViewport());
testee = new PopupMenu(parentPanel, null, null);
int i = 0;
for (SequenceI seq : alignment.getSequences())
{
- final AlignmentAnnotation annotation = new AlignmentAnnotation("label" + i,
- "desc" + i, i);
+ final AlignmentAnnotation annotation = new AlignmentAnnotation(
+ "label" + i, "desc" + i, i);
annotation.setCalcId("calcId" + i);
seq.addAlignmentAnnotation(annotation);
annotation.setSequenceRef(seq);
}
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
{
JMenuItem menu = new JMenuItem();
* are no reference annotations to add to the alignment. The menu item should
* be disabled.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
{
JMenuItem menu = new JMenuItem();
* reference annotations are already on the alignment. The menu item should be
* disabled.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
{
JMenuItem menu = new JMenuItem();
* The menu item should be enabled, and acquire a tooltip which lists the
* annotation sources (calcIds) and type (labels).
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu()
{
JMenuItem menu = new JMenuItem();
* on the alignment. The menu item should be enabled, and acquire a tooltip
* which lists the annotation sources (calcIds) and type (labels).
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
{
JMenuItem menu = new JMenuItem();
* The menu item should be enabled, and acquire a tooltip which lists the
* annotation sources (calcIds) and type (labels).
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testConfigureReferenceAnnotationsMenu_twoViews()
{
}
* Test for building menu options including 'show' and 'hide' annotation
* types.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testBuildAnnotationTypesMenus()
{
JMenu showMenu = new JMenu();
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
- "secondary structure", "", new Annotation[]
- {});
+ "secondary structure", "", new Annotation[] {});
annotation.setCalcId("PDB");
annotation.visible = true;
seqs.get(0).addAlignmentAnnotation(annotation);
parentPanel.getAlignment().addAnnotation(annotation);
// JMOL.secondary structure on Sequence0 - hidden
- annotation = new AlignmentAnnotation("secondary structure", "", new Annotation[]
- {});
+ annotation = new AlignmentAnnotation("secondary structure", "",
+ new Annotation[] {});
annotation.setCalcId("JMOL");
annotation.visible = false;
seqs.get(0).addAlignmentAnnotation(annotation);
parentPanel.getAlignment().addAnnotation(annotation);
// Jpred.SSP on Sequence0 - hidden
- annotation = new AlignmentAnnotation("SSP", "", new Annotation[]
- {});
+ annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
annotation.setCalcId("JPred");
annotation.visible = false;
seqs.get(0).addAlignmentAnnotation(annotation);
parentPanel.getAlignment().addAnnotation(annotation);
// PDB.Temp on Sequence1
- annotation = new AlignmentAnnotation("Temp", "", new Annotation[]
- {});
+ annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
annotation.setCalcId("PDB");
annotation.visible = true;
seqs.get(1).addAlignmentAnnotation(annotation);
assertEquals(4, showOptions.length); // includes 'All' and separator
assertEquals(4, hideOptions.length);
- assertEquals("All",
- ((JMenuItem) showOptions[0]).getText());
+ assertEquals("All", ((JMenuItem) showOptions[0]).getText());
assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) showOptions[1]).getOrientation());
assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
- assertEquals("All",
- ((JMenuItem) hideOptions[0]).getText());
+ assertEquals("All", ((JMenuItem) hideOptions[0]).getText());
assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) hideOptions[1]).getOrientation());
/**
* Test for building menu options with only 'hide' annotation types enabled.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testBuildAnnotationTypesMenus_showDisabled()
{
JMenu showMenu = new JMenu();
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
- "secondary structure", "", new Annotation[]
- {});
+ "secondary structure", "", new Annotation[] {});
annotation.setCalcId("PDB");
annotation.visible = true;
seqs.get(0).addAlignmentAnnotation(annotation);
parentPanel.getAlignment().addAnnotation(annotation);
// PDB.Temp on Sequence1
- annotation = new AlignmentAnnotation("Temp", "", new Annotation[]
- {});
+ annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
annotation.setCalcId("PDB");
annotation.visible = true;
seqs.get(1).addAlignmentAnnotation(annotation);
/**
* Test for building menu options with only 'show' annotation types enabled.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testBuildAnnotationTypesMenus_hideDisabled()
{
JMenu showMenu = new JMenu();
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
- "secondary structure", "", new Annotation[]
- {});
+ "secondary structure", "", new Annotation[] {});
annotation.setCalcId("PDB");
annotation.visible = false;
seqs.get(0).addAlignmentAnnotation(annotation);
parentPanel.getAlignment().addAnnotation(annotation);
// PDB.Temp on Sequence1
- annotation = new AlignmentAnnotation("Temp", "", new Annotation[]
- {});
+ annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
annotation.setCalcId("PDB2");
annotation.visible = false;
seqs.get(1).addAlignmentAnnotation(annotation);
git://source.jalview.org / jalview.git / blobdiff