+/*
+ * 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.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import javax.swing.JButton;
import javax.swing.JPanel;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
/**
* Unit tests for AnnotationChooser
*/
public class AnnotationChooserTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// 4 sequences x 13 positions
final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
+ "TIETHKEAELVG-\n"
AlignFrame af;
- @Before
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
- AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
- AppletFormatAdapter.PASTE, "FASTA");
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ // pin down annotation sort order for test
+ Cache.setPropertyNoSave(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name());
+ final String TRUE = Boolean.TRUE.toString();
+ Cache.setPropertyNoSave(
+ Preferences.SHOW_AUTOCALC_ABOVE, TRUE);
+ Cache.setPropertyNoSave("SHOW_QUALITY", TRUE);
+ Cache.setPropertyNoSave("SHOW_CONSERVATION", TRUE);
+ Cache.setPropertyNoSave("SHOW_IDENTITY", TRUE);
+
+ AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
+ DataSourceType.PASTE, FileFormat.Fasta);
af = new AlignFrame(al, 700, 500);
parentPanel = new AlignmentPanel(af, af.getViewport());
addAnnotations();
private void addAnnotations()
{
Annotation an = new Annotation(2f);
- Annotation[] anns = new Annotation[]
- { an, an, an };
+ Annotation[] anns = new Annotation[] { an, an, an };
AlignmentAnnotation ann0 = new AlignmentAnnotation("IUPRED", "", anns);
AlignmentAnnotation ann1 = new AlignmentAnnotation("Beauty", "", anns);
AlignmentAnnotation ann2 = new AlignmentAnnotation("JMol", "", anns);
/**
* Test creation of panel with OK and Cancel buttons
*/
- @Test
+ @Test(groups = { "Functional" })
public void testBuildActionButtonsPanel()
{
testee = new AnnotationChooser(parentPanel);
* Test 'Apply to' has 3 radio buttons enabled, 'Selected Sequences' selected,
* when there is a current selection group.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testBuildApplyToOptionsPanel_withSelectionGroup()
{
selectSequences(0, 2, 3);
* Test 'Apply to' has 1 radio button enabled, 'All Sequences' selected, when
* there is no current selection group.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testBuildApplyToOptionsPanel_noSelectionGroup()
{
testee = new AnnotationChooser(parentPanel);
/**
* Test Show and Hide radio buttons created, with Hide initially selected.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testBuildShowHidePanel()
{
testee = new AnnotationChooser(parentPanel);
/**
* Test construction of panel containing two sub-panels
*/
- @Test
+ @Test(groups = { "Functional" })
public void testBuildShowHideOptionsPanel()
{
testee = new AnnotationChooser(parentPanel);
* Test that annotation types are (uniquely) identified.
*
*/
- @Test
+ @Test(groups = { "Functional" })
public void testGetAnnotationTypes()
{
selectSequences(1);
types = AnnotationChooser.getAnnotationTypes(
parentPanel.getAlignment(), false);
- assertEquals("Not six annotation types", 6, types.size());
+ assertEquals("Not six annotation types", 7, types.size());
assertTrue("IUPRED missing", types.contains("IUPRED"));
assertTrue("JMol missing", types.contains("JMol"));
assertTrue("Beauty missing", types.contains("Beauty"));
assertTrue("Consensus missing", types.contains("Consensus"));
assertTrue("Quality missing", types.contains("Quality"));
assertTrue("Conservation missing", types.contains("Conservation"));
+ assertTrue("Occupancy missing", types.contains("Occupancy"));
}
/**
* We expect all annotations of that type to be set hidden. Other annotations
* should be left visible.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testSelectType_hideForAll()
{
selectSequences(1, 2);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
- assertTrue(anns[5].visible); // JMol for seq3
- assertTrue(anns[7].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+ assertTrue(anns[autocalc + 4].visible); // JMol for seq1
setSelected(getTypeCheckbox("JMol"), true);
assertTrue(anns[0].visible); // Conservation
assertTrue(anns[1].visible); // Quality
assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // IUPred for seq0
- assertTrue(anns[4].visible); // Beauty
- assertFalse(anns[5].visible); // JMol for seq3 - not selected but hidden
- assertTrue(anns[6].visible); // IUPRED for seq2
- assertFalse(anns[7].visible); // JMol for seq1 - selected and hidden
+ assertTrue(anns[3].visible); // Occupancy
+ assertTrue(anns[4].visible); // IUPred for seq0
+ assertTrue(anns[5].visible); // Beauty
+ assertFalse(anns[6].visible); // JMol for seq3 - not selected but hidden
+ assertTrue(anns[7].visible); // IUPRED for seq2
+ assertFalse(anns[8].visible); // JMol for seq1 - selected and hidden
}
/**
* We expect the annotations of that type, linked to the sequence group, to be
* set hidden. Other annotations should be left visible.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testSelectType_hideForSelected()
{
selectSequences(1, 2);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
- assertTrue(anns[7].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertTrue(anns[autocalc + 4].visible); // JMol for seq1
setSelected(getTypeCheckbox("JMol"), true);
assertTrue(anns[0].visible); // Conservation
assertTrue(anns[1].visible); // Quality
assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // IUPred for seq0
- assertTrue(anns[4].visible); // Beauty
- assertTrue(anns[5].visible); // JMol for seq3 not in selection group
- assertTrue(anns[6].visible); // IUPRED for seq2
- assertFalse(anns[7].visible); // JMol for seq1 in selection group
+ assertTrue(anns[3].visible); // Occupancy
+ assertTrue(anns[4].visible); // IUPred for seq0
+ assertTrue(anns[5].visible); // Beauty
+ assertTrue(anns[6].visible); // JMol for seq3 not in selection group
+ assertTrue(anns[7].visible); // IUPRED for seq2
+ assertFalse(anns[8].visible); // JMol for seq1 in selection group
}
/**
* We expect all annotations of that type to be set visible. Other annotations
* should be left unchanged.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testDeselectType_hideForAll()
{
selectSequences(1, 2);
// select JMol - all hidden
setSelected(typeCheckbox, true);
- assertFalse(anns[5].visible); // JMol for seq3
- assertFalse(anns[7].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertFalse(anns[autocalc + 2].visible); // JMol for seq3
+ assertFalse(anns[autocalc + 4].visible); // JMol for seq1
// deselect JMol - all unhidden
setSelected(typeCheckbox, false);
- assertTrue(anns[0].visible); // Conservation
- assertTrue(anns[1].visible); // Quality
- assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // IUPred for seq0
- assertTrue(anns[4].visible); // Beauty
- assertTrue(anns[5].visible); // JMol for seq3
- assertTrue(anns[6].visible); // IUPRED for seq2
- assertTrue(anns[7].visible); // JMol for seq1
+ for (AlignmentAnnotation ann : anns)
+ {
+ assertTrue(ann.visible);
+ }
+ }
+
+ /**
+ * Returns a count of autocalculated annotations in the set provided
+ *
+ * @param anns
+ * @return
+ */
+ private int countAutocalc(AlignmentAnnotation[] anns)
+ {
+ int count = 0;
+ for (AlignmentAnnotation ann : anns)
+ {
+ if (ann.autoCalculated)
+ {
+ count++;
+ }
+ }
+ return count;
}
/**
* We expect the annotations of that type, linked to the sequence group, to be
* set visible. Other annotations should be left unchanged.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testDeselectType_hideForSelected()
{
selectSequences(1, 2);
* We expect all annotations of that type to be set visible. Other annotations
* should be left unchanged
*/
- @Test
+ @Test(groups = { "Functional" })
public void testSelectType_showForAll()
{
selectSequences(1, 2);
setSelected(allSequencesCheckbox, true);
setSelected(hideCheckbox, true);
setSelected(getTypeCheckbox("JMol"), true);
- assertFalse(anns[5].visible); // JMol for seq3
- assertFalse(anns[7].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertFalse(anns[autocalc + 2].visible); // JMol for seq3
+ assertFalse(anns[autocalc + 4].visible); // JMol for seq1
// ...now show them...
setSelected(showCheckbox, true);
- assertTrue(anns[0].visible); // Conservation
- assertTrue(anns[1].visible); // Quality
- assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // IUPred for seq0
- assertTrue(anns[4].visible); // Beauty
- assertTrue(anns[5].visible); // JMol for seq3
- assertTrue(anns[6].visible); // IUPRED for seq2
- assertTrue(anns[7].visible); // JMol for seq1
+ for (AlignmentAnnotation ann : anns)
+ {
+ assertTrue(ann.visible);
+ }
}
/**
* We expect all annotations of that type, linked to the sequence group, to be
* set visible. Other annotations should be left unchanged
*/
- @Test
+ @Test(groups = { "Functional" })
public void testSelectType_showForSelected()
{
+ // sequences 1 and 2 have annotations IUPred and Jmol
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
setSelected(selectedSequencesCheckbox, true);
setSelected(hideCheckbox, true);
setSelected(getTypeCheckbox("JMol"), true);
- assertTrue(anns[5].visible); // JMol for seq3
- assertFalse(anns[7].visible); // JMol for seq1
+
+ int autocalc = countAutocalc(anns);
+ assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+ assertFalse(anns[autocalc + 4].visible); // JMol for seq1
// ...now show them...
setSelected(showCheckbox, true);
- assertTrue(anns[0].visible); // Conservation
- assertTrue(anns[1].visible); // Quality
- assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // IUPred for seq0
- assertTrue(anns[4].visible); // Beauty
- assertTrue(anns[5].visible); // JMol for seq3
- assertTrue(anns[6].visible); // IUPRED for seq2
- assertTrue(anns[7].visible); // JMol for seq1
+ for (AlignmentAnnotation ann : anns)
+ {
+ assertTrue(ann.visible);
+ }
}
/**
* We expect all annotations of that type to be set hidden. Other annotations
* should be left unchanged.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testDeselectType_showForAll()
{
selectSequences(1, 2);
final Checkbox typeCheckbox = getTypeCheckbox("JMol");
// select JMol - all shown
setSelected(typeCheckbox, true);
- assertTrue(anns[5].visible); // JMol for seq3
- assertTrue(anns[7].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+ assertTrue(anns[autocalc + 4].visible); // JMol for seq1
// deselect JMol - all hidden
setSelected(typeCheckbox, false);
assertTrue(anns[0].visible); // Conservation
assertTrue(anns[1].visible); // Quality
assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // IUPred for seq0
- assertTrue(anns[4].visible); // Beauty
- assertFalse(anns[5].visible); // JMol for seq3
- assertTrue(anns[6].visible); // IUPRED for seq2
- assertFalse(anns[7].visible); // JMol for seq1
+ assertTrue(anns[3].visible); // Occupancy
+ assertTrue(anns[4].visible); // IUPred for seq0
+ assertTrue(anns[5].visible); // Beauty
+ assertFalse(anns[6].visible); // JMol for seq3
+ assertTrue(anns[7].visible); // IUPRED for seq2
+ assertFalse(anns[8].visible); // JMol for seq1
}
/**
* We expect the annotations of that type, linked to the sequence group, to be
* set hidden. Other annotations should be left unchanged.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testDeselectType_showForSelected()
{
selectSequences(1, 2);
// select JMol - should remain visible
setSelected(getTypeCheckbox("JMol"), true);
- assertTrue(anns[5].visible); // JMol for seq3
- assertTrue(anns[7].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+ assertTrue(anns[autocalc + 4].visible); // JMol for seq1
// deselect JMol - should be hidden for selected sequences only
setSelected(getTypeCheckbox("JMol"), false);
assertTrue(anns[0].visible); // Conservation
assertTrue(anns[1].visible); // Quality
assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // IUPred for seq0
- assertTrue(anns[4].visible); // Beauty
- assertTrue(anns[5].visible); // JMol for seq3 not in selection group
- assertTrue(anns[6].visible); // IUPRED for seq2
- assertFalse(anns[7].visible); // JMol for seq1 in selection group
+ assertTrue(anns[3].visible); // Occupancy
+ assertTrue(anns[4].visible); // IUPred for seq0
+ assertTrue(anns[5].visible); // Beauty
+ assertTrue(anns[6].visible); // JMol for seq3 not in selection group
+ assertTrue(anns[7].visible); // IUPRED for seq2
+ assertFalse(anns[8].visible); // JMol for seq1 in selection group
}
/**
* Test cases include sequences in the selection group, and others not in the
* group.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testIsInActionScope_selectedScope()
{
// sequences 1 and 2 have annotations 4 and 3 respectively
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
- // remember 3 annotations to skip (Conservation/Quality/Consensus)
- assertFalse(testee.isInActionScope(anns[3]));
- assertFalse(testee.isInActionScope(anns[4]));
- assertFalse(testee.isInActionScope(anns[5]));
- assertTrue(testee.isInActionScope(anns[6]));
- assertTrue(testee.isInActionScope(anns[7]));
+ int autocalc = countAutocalc(anns);
+ assertFalse(testee.isInActionScope(anns[autocalc]));
+ assertFalse(testee.isInActionScope(anns[autocalc + 1]));
+ assertFalse(testee.isInActionScope(anns[autocalc + 2]));
+ assertTrue(testee.isInActionScope(anns[autocalc + 3]));
+ assertTrue(testee.isInActionScope(anns[autocalc + 4]));
}
/**
* Test cases include sequences in the selection group, and others not in the
* group.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testIsInActionScope_unselectedScope()
{
// sequences 1 and 2 have annotations 4 and 3 respectively
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
- // remember 3 annotations to skip (Conservation/Quality/Consensus)
- assertTrue(testee.isInActionScope(anns[3]));
- assertTrue(testee.isInActionScope(anns[4]));
- assertTrue(testee.isInActionScope(anns[5]));
- assertFalse(testee.isInActionScope(anns[6]));
- assertFalse(testee.isInActionScope(anns[7]));
+ int autocalc = countAutocalc(anns);
+ assertTrue(testee.isInActionScope(anns[autocalc]));
+ assertTrue(testee.isInActionScope(anns[autocalc + 1]));
+ assertTrue(testee.isInActionScope(anns[autocalc + 2]));
+ assertFalse(testee.isInActionScope(anns[autocalc + 3]));
+ assertFalse(testee.isInActionScope(anns[autocalc + 4]));
}
/**
* Test that the reset method restores previous visibility flags.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testResetOriginalState()
{
testee = new AnnotationChooser(parentPanel);
assertTrue(i + "'th sequence not visible", anns[i].visible);
}
+ /*
+ * check options to hide JMol and IUPRED annotations for all sequences
+ */
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
setSelected(hideCheckbox, true);
assertTrue(anns[0].visible); // Conservation
assertTrue(anns[1].visible); // Quality
assertTrue(anns[2].visible); // Consensus
- assertFalse(anns[3].visible); // IUPRED
- assertTrue(anns[4].visible); // Beauty (not seq-related)
- assertFalse(anns[5].visible); // JMol
- assertFalse(anns[6].visible); // IUPRED
- assertFalse(anns[7].visible); // JMol
+ assertTrue(anns[3].visible); // Occupancy
+ assertFalse(anns[4].visible); // IUPRED
+ assertTrue(anns[5].visible); // Beauty (not seq-related)
+ assertFalse(anns[6].visible); // JMol
+ assertFalse(anns[7].visible); // IUPRED
+ assertFalse(anns[8].visible); // JMol
// reset - should all be visible
testee.resetOriginalState();
git://source.jalview.org / jalview.git / blobdiff