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package jalview.gui; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertFalse; |
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import static org.testng.AssertJUnit.assertTrue; |
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import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; |
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import jalview.bin.Cache; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Annotation; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileFormat; |
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import jalview.io.FormatAdapter; |
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import jalview.util.MessageManager; |
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import java.awt.BorderLayout; |
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import java.awt.Checkbox; |
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import java.awt.Component; |
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import java.awt.Container; |
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import java.awt.FlowLayout; |
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import java.awt.event.ItemEvent; |
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import java.io.IOException; |
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import java.util.List; |
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import javax.swing.JButton; |
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import javax.swing.JPanel; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.BeforeMethod; |
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import org.testng.annotations.Test; |
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@author |
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| 99.7% |
Uncovered Elements: 1 (350) |
Complexity: 32 |
Complexity Density: 0.1 |
|
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public class AnnotationChooserTest |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n" |
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+ "TIETHKEAELVG-\n" |
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+ ">FER_CAPAN Ferredoxin, chloroplast precursor\n" |
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+ "TIETHKEAELVG-\n" |
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+ ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n" |
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+ "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n" |
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+ "TIETHKEEELTA-\n"; |
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AnnotationChooser testee; |
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AlignmentPanel parentPanel; |
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AlignFrame af; |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
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@BeforeMethod(alwaysRun = true)... |
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public void setUp() throws IOException |
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{ |
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Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
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Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS, |
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SequenceAnnotationOrder.NONE.name()); |
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final String TRUE = Boolean.TRUE.toString(); |
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Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE, |
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TRUE); |
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Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE); |
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Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE); |
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Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE); |
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AlignmentI al = new FormatAdapter().readFile(TEST_DATA, |
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DataSourceType.PASTE, FileFormat.Fasta); |
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af = new AlignFrame(al, 700, 500); |
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parentPanel = new AlignmentPanel(af, af.getViewport()); |
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addAnnotations(); |
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} |
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| 100% |
Uncovered Elements: 0 (17) |
Complexity: 1 |
Complexity Density: 0.06 |
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private void addAnnotations()... |
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{ |
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Annotation an = new Annotation(2f); |
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Annotation[] anns = new Annotation[] { an, an, an }; |
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AlignmentAnnotation ann0 = new AlignmentAnnotation("IUPRED", "", anns); |
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AlignmentAnnotation ann1 = new AlignmentAnnotation("Beauty", "", anns); |
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AlignmentAnnotation ann2 = new AlignmentAnnotation("JMol", "", anns); |
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AlignmentAnnotation ann3 = new AlignmentAnnotation("IUPRED", "", anns); |
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AlignmentAnnotation ann4 = new AlignmentAnnotation("JMol", "", anns); |
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SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray(); |
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ann0.setSequenceRef(seqs[0]); |
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ann2.setSequenceRef(seqs[3]); |
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ann3.setSequenceRef(seqs[2]); |
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ann4.setSequenceRef(seqs[1]); |
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parentPanel.getAlignment().addAnnotation(ann0); |
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parentPanel.getAlignment().addAnnotation(ann1); |
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parentPanel.getAlignment().addAnnotation(ann2); |
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parentPanel.getAlignment().addAnnotation(ann3); |
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parentPanel.getAlignment().addAnnotation(ann4); |
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} |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testBuildActionButtonsPanel() |
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{ |
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testee = new AnnotationChooser(parentPanel); |
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JPanel jp = testee.buildActionButtonsPanel(); |
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assertTrue("Wrong layout", jp.getLayout() instanceof FlowLayout); |
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Component[] comps = jp.getComponents(); |
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assertEquals("Not 2 action buttons", 2, comps.length); |
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final Component jb1 = comps[0]; |
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final Component jb2 = comps[1]; |
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assertEquals("Not 'OK' button", MessageManager.getString("action.ok"), |
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((JButton) jb1).getText()); |
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assertEquals("Wrong button font", JvSwingUtils.getLabelFont(), |
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jb1.getFont()); |
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assertEquals("Not 'Cancel' button", |
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MessageManager.getString("action.cancel"), |
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((JButton) jb2).getText()); |
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assertEquals("Wrong button font", JvSwingUtils.getLabelFont(), |
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jb2.getFont()); |
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} |
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167 |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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1 |
@Test(groups = { "Functional" })... |
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public void testBuildApplyToOptionsPanel_withSelectionGroup() |
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{ |
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selectSequences(0, 2, 3); |
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testee = new AnnotationChooser(parentPanel); |
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JPanel jp = testee.buildApplyToOptionsPanel(); |
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Component[] comps = jp.getComponents(); |
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assertEquals("Not 3 radio buttons", 3, comps.length); |
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final Checkbox cb1 = (Checkbox) comps[0]; |
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final Checkbox cb2 = (Checkbox) comps[1]; |
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final Checkbox cb3 = (Checkbox) comps[2]; |
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assertTrue("Not enabled", cb1.isEnabled()); |
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assertTrue("Not enabled", cb2.isEnabled()); |
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assertTrue("Not enabled", cb3.isEnabled()); |
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assertEquals("Option not selected", cb2, |
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cb2.getCheckboxGroup().getSelectedCheckbox()); |
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assertTrue(testee.isApplyToSelectedSequences()); |
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assertFalse(testee.isApplyToUnselectedSequences()); |
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} |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
200 |
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private void selectSequences(int... selected)... |
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{ |
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SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray(); |
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SequenceGroup sg = new SequenceGroup(); |
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for (int i : selected) |
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{ |
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sg.addSequence(seqs[i], false); |
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} |
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parentPanel.av.setSelectionGroup(sg); |
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} |
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214 |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testBuildApplyToOptionsPanel_noSelectionGroup() |
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{ |
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testee = new AnnotationChooser(parentPanel); |
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JPanel jp = testee.buildApplyToOptionsPanel(); |
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verifyApplyToOptionsPanel_noSelectionGroup(jp); |
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} |
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| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
|
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protected void verifyApplyToOptionsPanel_noSelectionGroup(JPanel jp)... |
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{ |
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assertTrue("Wrong layout", jp.getLayout() instanceof FlowLayout); |
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Component[] comps = jp.getComponents(); |
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assertEquals("Not 3 radio buttons", 3, comps.length); |
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final Checkbox cb1 = (Checkbox) comps[0]; |
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final Checkbox cb2 = (Checkbox) comps[1]; |
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final Checkbox cb3 = (Checkbox) comps[2]; |
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assertTrue("Not enabled", cb1.isEnabled()); |
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assertFalse("Enabled", cb2.isEnabled()); |
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assertFalse("Enabled", cb3.isEnabled()); |
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assertEquals("Not selected", cb1, |
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cb1.getCheckboxGroup().getSelectedCheckbox()); |
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assertTrue(testee.isApplyToSelectedSequences()); |
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assertTrue(testee.isApplyToUnselectedSequences()); |
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assertEquals("Wrong text", |
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MessageManager.getString("label.all_sequences"), |
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cb1.getLabel()); |
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assertEquals("Wrong text", |
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MessageManager.getString("label.selected_sequences"), |
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cb2.getLabel()); |
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assertEquals("Wrong text", |
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MessageManager.getString("label.except_selected_sequences"), |
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cb3.getLabel()); |
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} |
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256 |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
1PASS
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257 |
1 |
@Test(groups = { "Functional" })... |
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public void testBuildShowHidePanel() |
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{ |
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testee = new AnnotationChooser(parentPanel); |
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JPanel jp = testee.buildShowHidePanel(); |
262 |
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verifyShowHidePanel(jp); |
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} |
265 |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
|
266 |
2 |
protected void verifyShowHidePanel(JPanel jp)... |
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{ |
268 |
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assertTrue("Wrong layout", jp.getLayout() instanceof FlowLayout); |
269 |
2 |
Component[] comps = jp.getComponents(); |
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assertEquals("Not 2 radio buttons", 2, comps.length); |
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final Checkbox cb1 = (Checkbox) comps[0]; |
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final Checkbox cb2 = (Checkbox) comps[1]; |
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assertTrue("Show not enabled", cb1.isEnabled()); |
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assertTrue("Hide not enabled", cb2.isEnabled()); |
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assertEquals("Not selected", cb2, |
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cb2.getCheckboxGroup().getSelectedCheckbox()); |
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282 |
2 |
assertTrue("Show is flagged", !testee.isShowSelected()); |
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2 |
assertEquals("Wrong text", |
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MessageManager.getString("label.show_selected_annotations"), |
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cb1.getLabel()); |
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2 |
assertEquals("Wrong text", |
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MessageManager.getString("label.hide_selected_annotations"), |
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cb2.getLabel()); |
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} |
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292 |
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293 |
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294 |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
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295 |
1 |
@Test(groups = { "Functional" })... |
296 |
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public void testBuildShowHideOptionsPanel() |
297 |
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{ |
298 |
1 |
testee = new AnnotationChooser(parentPanel); |
299 |
1 |
JPanel jp = testee.buildShowHideOptionsPanel(); |
300 |
1 |
assertTrue("Wrong layout", jp.getLayout() instanceof BorderLayout); |
301 |
1 |
Component[] comps = jp.getComponents(); |
302 |
1 |
assertEquals("Not 2 sub-panels", 2, comps.length); |
303 |
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304 |
1 |
verifyShowHidePanel((JPanel) comps[0]); |
305 |
1 |
verifyApplyToOptionsPanel_noSelectionGroup((JPanel) comps[1]); |
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} |
307 |
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308 |
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309 |
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310 |
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311 |
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| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
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312 |
1 |
@Test(groups = { "Functional" })... |
313 |
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public void testGetAnnotationTypes() |
314 |
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{ |
315 |
1 |
selectSequences(1); |
316 |
1 |
testee = new AnnotationChooser(parentPanel); |
317 |
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318 |
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319 |
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320 |
1 |
List<String> types = AnnotationChooser |
321 |
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.getAnnotationTypes(parentPanel.getAlignment(), true); |
322 |
1 |
assertEquals("Not two annotation types", 2, types.size()); |
323 |
1 |
assertTrue("IUPRED missing", types.contains("IUPRED")); |
324 |
1 |
assertTrue("JMol missing", types.contains("JMol")); |
325 |
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|
326 |
1 |
types = AnnotationChooser.getAnnotationTypes(parentPanel.getAlignment(), |
327 |
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false); |
328 |
1 |
assertEquals("Not six annotation types", 7, types.size()); |
329 |
1 |
assertTrue("IUPRED missing", types.contains("IUPRED")); |
330 |
1 |
assertTrue("JMol missing", types.contains("JMol")); |
331 |
1 |
assertTrue("Beauty missing", types.contains("Beauty")); |
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|
333 |
1 |
assertTrue("Consensus missing", types.contains("Consensus")); |
334 |
1 |
assertTrue("Quality missing", types.contains("Quality")); |
335 |
1 |
assertTrue("Conservation missing", types.contains("Conservation")); |
336 |
1 |
assertTrue("Occupancy missing", types.contains("Occupancy")); |
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} |
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339 |
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340 |
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341 |
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342 |
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343 |
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344 |
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| 100% |
Uncovered Elements: 0 (20) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
|
345 |
1 |
@Test(groups = { "Functional" })... |
346 |
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public void testSelectType_hideForAll() |
347 |
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{ |
348 |
1 |
selectSequences(1, 2); |
349 |
1 |
testee = new AnnotationChooser(parentPanel); |
350 |
1 |
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1); |
351 |
1 |
setSelected(hideCheckbox, true); |
352 |
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|
353 |
1 |
final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1, |
354 |
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1, 0); |
355 |
1 |
setSelected(allSequencesCheckbox, true); |
356 |
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|
357 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
358 |
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.getAlignmentAnnotation(); |
359 |
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|
360 |
1 |
int autocalc = countAutocalc(anns); |
361 |
1 |
assertTrue(anns[autocalc + 2].visible); |
362 |
1 |
assertTrue(anns[autocalc + 4].visible); |
363 |
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|
364 |
1 |
setSelected(getTypeCheckbox("JMol"), true); |
365 |
1 |
assertTrue(anns[0].visible); |
366 |
1 |
assertTrue(anns[1].visible); |
367 |
1 |
assertTrue(anns[2].visible); |
368 |
1 |
assertTrue(anns[3].visible); |
369 |
1 |
assertTrue(anns[4].visible); |
370 |
1 |
assertTrue(anns[5].visible); |
371 |
1 |
assertFalse(anns[6].visible); |
372 |
1 |
assertTrue(anns[7].visible); |
373 |
1 |
assertFalse(anns[8].visible); |
374 |
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} |
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376 |
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377 |
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378 |
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379 |
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380 |
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381 |
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382 |
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| 100% |
Uncovered Elements: 0 (17) |
Complexity: 1 |
Complexity Density: 0.06 |
1PASS
|
|
383 |
1 |
@Test(groups = { "Functional" })... |
384 |
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public void testSelectType_hideForSelected() |
385 |
|
{ |
386 |
1 |
selectSequences(1, 2); |
387 |
1 |
testee = new AnnotationChooser(parentPanel); |
388 |
1 |
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1); |
389 |
1 |
setSelected(hideCheckbox, true); |
390 |
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391 |
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392 |
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393 |
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394 |
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395 |
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396 |
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|
397 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
398 |
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.getAlignmentAnnotation(); |
399 |
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|
400 |
1 |
int autocalc = countAutocalc(anns); |
401 |
1 |
assertTrue(anns[autocalc + 4].visible); |
402 |
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|
403 |
1 |
setSelected(getTypeCheckbox("JMol"), true); |
404 |
1 |
assertTrue(anns[0].visible); |
405 |
1 |
assertTrue(anns[1].visible); |
406 |
1 |
assertTrue(anns[2].visible); |
407 |
1 |
assertTrue(anns[3].visible); |
408 |
1 |
assertTrue(anns[4].visible); |
409 |
1 |
assertTrue(anns[5].visible); |
410 |
1 |
assertTrue(anns[6].visible); |
411 |
1 |
assertTrue(anns[7].visible); |
412 |
1 |
assertFalse(anns[8].visible); |
413 |
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} |
414 |
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415 |
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416 |
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417 |
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418 |
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419 |
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420 |
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|
421 |
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|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
422 |
1 |
@Test(groups = { "Functional" })... |
423 |
|
public void testDeselectType_hideForAll() |
424 |
|
{ |
425 |
1 |
selectSequences(1, 2); |
426 |
1 |
testee = new AnnotationChooser(parentPanel); |
427 |
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|
428 |
1 |
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1); |
429 |
1 |
setSelected(hideCheckbox, true); |
430 |
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|
431 |
1 |
final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1, |
432 |
|
1, 0); |
433 |
1 |
setSelected(allSequencesCheckbox, true); |
434 |
|
|
435 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
436 |
|
.getAlignmentAnnotation(); |
437 |
|
|
438 |
1 |
final Checkbox typeCheckbox = getTypeCheckbox("JMol"); |
439 |
|
|
440 |
|
|
441 |
1 |
setSelected(typeCheckbox, true); |
442 |
1 |
int autocalc = countAutocalc(anns); |
443 |
1 |
assertFalse(anns[autocalc + 2].visible); |
444 |
1 |
assertFalse(anns[autocalc + 4].visible); |
445 |
|
|
446 |
|
|
447 |
1 |
setSelected(typeCheckbox, false); |
448 |
1 |
for (AlignmentAnnotation ann : anns) |
449 |
|
{ |
450 |
9 |
assertTrue(ann.visible); |
451 |
|
} |
452 |
|
} |
453 |
|
|
454 |
|
|
455 |
|
|
456 |
|
|
457 |
|
@param |
458 |
|
@return |
459 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
460 |
9 |
private int countAutocalc(AlignmentAnnotation[] anns)... |
461 |
|
{ |
462 |
9 |
int count = 0; |
463 |
9 |
for (AlignmentAnnotation ann : anns) |
464 |
|
{ |
465 |
81 |
if (ann.autoCalculated) |
466 |
|
{ |
467 |
36 |
count++; |
468 |
|
} |
469 |
|
} |
470 |
9 |
return count; |
471 |
|
} |
472 |
|
|
473 |
|
|
474 |
|
|
475 |
|
|
476 |
|
|
477 |
|
|
478 |
|
|
479 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
480 |
1 |
@Test(groups = { "Functional" })... |
481 |
|
public void testDeselectType_hideForSelected() |
482 |
|
{ |
483 |
1 |
selectSequences(1, 2); |
484 |
1 |
testee = new AnnotationChooser(parentPanel); |
485 |
1 |
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1); |
486 |
1 |
setSelected(hideCheckbox, true); |
487 |
|
|
488 |
|
|
489 |
|
|
490 |
|
|
491 |
|
|
492 |
|
|
493 |
|
|
494 |
1 |
setSelected(getTypeCheckbox("JMol"), true); |
495 |
1 |
setSelected(getTypeCheckbox("JMol"), false); |
496 |
|
|
497 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
498 |
|
.getAlignmentAnnotation(); |
499 |
1 |
assertTrue(anns[0].visible); |
500 |
1 |
assertTrue(anns[1].visible); |
501 |
1 |
assertTrue(anns[2].visible); |
502 |
1 |
assertTrue(anns[3].visible); |
503 |
1 |
assertTrue(anns[4].visible); |
504 |
1 |
assertTrue(anns[5].visible); |
505 |
1 |
assertTrue(anns[6].visible); |
506 |
1 |
assertTrue(anns[7].visible); |
507 |
|
} |
508 |
|
|
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
|
513 |
|
|
514 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
515 |
1 |
@Test(groups = { "Functional" })... |
516 |
|
public void testSelectType_showForAll() |
517 |
|
{ |
518 |
1 |
selectSequences(1, 2); |
519 |
1 |
testee = new AnnotationChooser(parentPanel); |
520 |
1 |
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0); |
521 |
1 |
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1); |
522 |
|
|
523 |
1 |
final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1, |
524 |
|
1, 0); |
525 |
|
|
526 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
527 |
|
.getAlignmentAnnotation(); |
528 |
|
|
529 |
|
|
530 |
1 |
setSelected(allSequencesCheckbox, true); |
531 |
1 |
setSelected(hideCheckbox, true); |
532 |
1 |
setSelected(getTypeCheckbox("JMol"), true); |
533 |
1 |
int autocalc = countAutocalc(anns); |
534 |
1 |
assertFalse(anns[autocalc + 2].visible); |
535 |
1 |
assertFalse(anns[autocalc + 4].visible); |
536 |
|
|
537 |
1 |
setSelected(showCheckbox, true); |
538 |
1 |
for (AlignmentAnnotation ann : anns) |
539 |
|
{ |
540 |
9 |
assertTrue(ann.visible); |
541 |
|
} |
542 |
|
} |
543 |
|
|
544 |
|
|
545 |
|
|
546 |
|
|
547 |
|
|
548 |
|
|
549 |
|
|
550 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
551 |
1 |
@Test(groups = { "Functional" })... |
552 |
|
public void testSelectType_showForSelected() |
553 |
|
{ |
554 |
|
|
555 |
1 |
selectSequences(1, 2); |
556 |
1 |
testee = new AnnotationChooser(parentPanel); |
557 |
1 |
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0); |
558 |
1 |
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1); |
559 |
|
|
560 |
1 |
final Checkbox selectedSequencesCheckbox = (Checkbox) getComponent( |
561 |
|
testee, 1, 1, 1); |
562 |
|
|
563 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
564 |
|
.getAlignmentAnnotation(); |
565 |
|
|
566 |
|
|
567 |
1 |
setSelected(selectedSequencesCheckbox, true); |
568 |
1 |
setSelected(hideCheckbox, true); |
569 |
1 |
setSelected(getTypeCheckbox("JMol"), true); |
570 |
|
|
571 |
1 |
int autocalc = countAutocalc(anns); |
572 |
1 |
assertTrue(anns[autocalc + 2].visible); |
573 |
1 |
assertFalse(anns[autocalc + 4].visible); |
574 |
|
|
575 |
1 |
setSelected(showCheckbox, true); |
576 |
|
|
577 |
1 |
for (AlignmentAnnotation ann : anns) |
578 |
|
{ |
579 |
9 |
assertTrue(ann.visible); |
580 |
|
} |
581 |
|
} |
582 |
|
|
583 |
|
|
584 |
|
|
585 |
|
|
586 |
|
|
587 |
|
|
588 |
|
|
589 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
|
590 |
1 |
@Test(groups = { "Functional" })... |
591 |
|
public void testDeselectType_showForAll() |
592 |
|
{ |
593 |
1 |
selectSequences(1, 2); |
594 |
1 |
testee = new AnnotationChooser(parentPanel); |
595 |
|
|
596 |
1 |
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0); |
597 |
1 |
setSelected(showCheckbox, true); |
598 |
|
|
599 |
1 |
final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1, |
600 |
|
1, 0); |
601 |
1 |
setSelected(allSequencesCheckbox, true); |
602 |
|
|
603 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
604 |
|
.getAlignmentAnnotation(); |
605 |
|
|
606 |
1 |
final Checkbox typeCheckbox = getTypeCheckbox("JMol"); |
607 |
|
|
608 |
1 |
setSelected(typeCheckbox, true); |
609 |
1 |
int autocalc = countAutocalc(anns); |
610 |
1 |
assertTrue(anns[autocalc + 2].visible); |
611 |
1 |
assertTrue(anns[autocalc + 4].visible); |
612 |
|
|
613 |
|
|
614 |
1 |
setSelected(typeCheckbox, false); |
615 |
1 |
assertTrue(anns[0].visible); |
616 |
1 |
assertTrue(anns[1].visible); |
617 |
1 |
assertTrue(anns[2].visible); |
618 |
1 |
assertTrue(anns[3].visible); |
619 |
1 |
assertTrue(anns[4].visible); |
620 |
1 |
assertTrue(anns[5].visible); |
621 |
1 |
assertFalse(anns[6].visible); |
622 |
1 |
assertTrue(anns[7].visible); |
623 |
1 |
assertFalse(anns[8].visible); |
624 |
|
} |
625 |
|
|
626 |
|
|
627 |
|
|
628 |
|
|
629 |
|
|
630 |
|
|
631 |
|
|
632 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
|
633 |
1 |
@Test(groups = { "Functional" })... |
634 |
|
public void testDeselectType_showForSelected() |
635 |
|
{ |
636 |
1 |
selectSequences(1, 2); |
637 |
1 |
testee = new AnnotationChooser(parentPanel); |
638 |
1 |
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0); |
639 |
1 |
setSelected(showCheckbox, true); |
640 |
|
|
641 |
|
|
642 |
|
|
643 |
|
|
644 |
|
|
645 |
|
|
646 |
|
|
647 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
648 |
|
.getAlignmentAnnotation(); |
649 |
|
|
650 |
|
|
651 |
1 |
setSelected(getTypeCheckbox("JMol"), true); |
652 |
1 |
int autocalc = countAutocalc(anns); |
653 |
1 |
assertTrue(anns[autocalc + 2].visible); |
654 |
1 |
assertTrue(anns[autocalc + 4].visible); |
655 |
|
|
656 |
|
|
657 |
1 |
setSelected(getTypeCheckbox("JMol"), false); |
658 |
1 |
assertTrue(anns[0].visible); |
659 |
1 |
assertTrue(anns[1].visible); |
660 |
1 |
assertTrue(anns[2].visible); |
661 |
1 |
assertTrue(anns[3].visible); |
662 |
1 |
assertTrue(anns[4].visible); |
663 |
1 |
assertTrue(anns[5].visible); |
664 |
1 |
assertTrue(anns[6].visible); |
665 |
1 |
assertTrue(anns[7].visible); |
666 |
1 |
assertFalse(anns[8].visible); |
667 |
|
} |
668 |
|
|
669 |
|
|
670 |
|
|
671 |
|
|
672 |
|
@param |
673 |
|
@param |
674 |
|
@param |
675 |
|
@param |
676 |
|
@return |
677 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
678 |
19 |
public static Component getComponent(Container cont, int... positions)... |
679 |
|
{ |
680 |
19 |
Component comp = cont; |
681 |
19 |
for (int i : positions) |
682 |
|
{ |
683 |
57 |
comp = ((Container) comp).getComponent(i); |
684 |
|
} |
685 |
19 |
return comp; |
686 |
|
} |
687 |
|
|
688 |
|
|
689 |
|
|
690 |
|
|
691 |
|
@param |
692 |
|
@param |
693 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
694 |
33 |
protected void setSelected(Checkbox cb, boolean select)... |
695 |
|
{ |
696 |
|
|
697 |
33 |
cb.setState(select); |
698 |
|
|
699 |
33 |
cb.getItemListeners()[0].itemStateChanged( |
700 |
|
new ItemEvent(cb, ItemEvent.ITEM_STATE_CHANGED, cb, |
701 |
33 |
select ? ItemEvent.SELECTED : ItemEvent.DESELECTED)); |
702 |
|
} |
703 |
|
|
704 |
|
|
705 |
|
|
706 |
|
|
707 |
|
|
708 |
|
@return |
709 |
|
|
|
|
| 87.5% |
Uncovered Elements: 1 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
710 |
12 |
private Checkbox getTypeCheckbox(String forLabel)... |
711 |
|
{ |
712 |
12 |
Component[] cbs = ((JPanel) testee.getComponent(0)).getComponents(); |
713 |
12 |
for (Component comp : cbs) |
714 |
|
{ |
715 |
23 |
final Checkbox cb = (Checkbox) comp; |
716 |
23 |
if (cb.getLabel().equals(forLabel)) |
717 |
|
{ |
718 |
12 |
return cb; |
719 |
|
} |
720 |
|
} |
721 |
0 |
return null; |
722 |
|
} |
723 |
|
|
724 |
|
|
725 |
|
|
726 |
|
|
727 |
|
|
728 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
1PASS
|
|
729 |
1 |
@Test(groups = { "Functional" })... |
730 |
|
public void testIsInActionScope_selectedScope() |
731 |
|
{ |
732 |
|
|
733 |
1 |
selectSequences(1, 2); |
734 |
1 |
testee = new AnnotationChooser(parentPanel); |
735 |
|
|
736 |
1 |
final Checkbox selectedSequencesCheckbox = (Checkbox) getComponent( |
737 |
|
testee, 1, 1, 1); |
738 |
1 |
setSelected(selectedSequencesCheckbox, true); |
739 |
|
|
740 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
741 |
|
.getAlignmentAnnotation(); |
742 |
1 |
int autocalc = countAutocalc(anns); |
743 |
1 |
assertFalse(testee.isInActionScope(anns[autocalc])); |
744 |
1 |
assertFalse(testee.isInActionScope(anns[autocalc + 1])); |
745 |
1 |
assertFalse(testee.isInActionScope(anns[autocalc + 2])); |
746 |
1 |
assertTrue(testee.isInActionScope(anns[autocalc + 3])); |
747 |
1 |
assertTrue(testee.isInActionScope(anns[autocalc + 4])); |
748 |
|
} |
749 |
|
|
750 |
|
|
751 |
|
|
752 |
|
|
753 |
|
|
754 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
1PASS
|
|
755 |
1 |
@Test(groups = { "Functional" })... |
756 |
|
public void testIsInActionScope_unselectedScope() |
757 |
|
{ |
758 |
|
|
759 |
1 |
selectSequences(1, 2); |
760 |
1 |
testee = new AnnotationChooser(parentPanel); |
761 |
|
|
762 |
1 |
final Checkbox unselectedSequencesCheckbox = (Checkbox) getComponent( |
763 |
|
testee, 1, 1, 2); |
764 |
1 |
setSelected(unselectedSequencesCheckbox, true); |
765 |
|
|
766 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
767 |
|
.getAlignmentAnnotation(); |
768 |
1 |
int autocalc = countAutocalc(anns); |
769 |
1 |
assertTrue(testee.isInActionScope(anns[autocalc])); |
770 |
1 |
assertTrue(testee.isInActionScope(anns[autocalc + 1])); |
771 |
1 |
assertTrue(testee.isInActionScope(anns[autocalc + 2])); |
772 |
1 |
assertFalse(testee.isInActionScope(anns[autocalc + 3])); |
773 |
1 |
assertFalse(testee.isInActionScope(anns[autocalc + 4])); |
774 |
|
} |
775 |
|
|
776 |
|
|
777 |
|
|
778 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (26) |
Complexity: 3 |
Complexity Density: 0.14 |
1PASS
|
|
779 |
1 |
@Test(groups = { "Functional" })... |
780 |
|
public void testResetOriginalState() |
781 |
|
{ |
782 |
1 |
testee = new AnnotationChooser(parentPanel); |
783 |
|
|
784 |
1 |
AlignmentAnnotation[] anns = parentPanel.getAlignment() |
785 |
|
.getAlignmentAnnotation(); |
786 |
|
|
787 |
10 |
for (int i = 0; i < anns.length; i++) |
788 |
|
{ |
789 |
9 |
assertTrue(i + "'th sequence not visible", anns[i].visible); |
790 |
|
} |
791 |
|
|
792 |
|
|
793 |
|
|
794 |
|
|
795 |
1 |
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1); |
796 |
1 |
setSelected(hideCheckbox, true); |
797 |
|
|
798 |
1 |
final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1, |
799 |
|
1, 0); |
800 |
1 |
setSelected(allSequencesCheckbox, true); |
801 |
|
|
802 |
1 |
setSelected(getTypeCheckbox("JMol"), true); |
803 |
1 |
setSelected(getTypeCheckbox("IUPRED"), true); |
804 |
|
|
805 |
1 |
assertTrue(anns[0].visible); |
806 |
1 |
assertTrue(anns[1].visible); |
807 |
1 |
assertTrue(anns[2].visible); |
808 |
1 |
assertTrue(anns[3].visible); |
809 |
1 |
assertFalse(anns[4].visible); |
810 |
1 |
assertTrue(anns[5].visible); |
811 |
1 |
assertFalse(anns[6].visible); |
812 |
1 |
assertFalse(anns[7].visible); |
813 |
1 |
assertFalse(anns[8].visible); |
814 |
|
|
815 |
|
|
816 |
1 |
testee.resetOriginalState(); |
817 |
10 |
for (int i = 0; i < anns.length; i++) |
818 |
|
{ |
819 |
9 |
assertTrue(i + "'th sequence not visible", anns[i].visible); |
820 |
|
} |
821 |
|
} |
822 |
|
} |