/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
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.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.Checkbox;
import java.awt.Component;
import java.awt.Container;
import java.awt.FlowLayout;
import java.awt.event.ItemEvent;
import java.io.IOException;
import java.util.List;
import javax.swing.JButton;
import javax.swing.JPanel;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
/**
* Unit tests for AnnotationChooser
*
* @author gmcarstairs
*
*/
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"
+ ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
+ "TIETHKEAELVG-\n"
+ ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
+ "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
+ "TIETHKEEELTA-\n";
AnnotationChooser testee;
AlignmentPanel parentPanel;
AlignFrame af;
@BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
// pin down annotation sort order for test
Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name());
final String TRUE = Boolean.TRUE.toString();
Cache.applicationProperties.setProperty(
Preferences.SHOW_AUTOCALC_ABOVE, TRUE);
Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
Cache.applicationProperties.setProperty("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();
}
/**
* Add 4 annotations, 3 of them sequence-specific.
*
*
* ann1 - for sequence 0 - label 'IUPRED'
* ann2 - not sequence related - label 'Beauty'
* ann3 - for sequence 3 - label 'JMol'
* ann4 - for sequence 2 - label 'IUPRED'
* ann5 - for sequence 1 - label 'JMol'
*/
private void addAnnotations()
{
Annotation an = new Annotation(2f);
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);
AlignmentAnnotation ann3 = new AlignmentAnnotation("IUPRED", "", anns);
AlignmentAnnotation ann4 = new AlignmentAnnotation("JMol", "", anns);
SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
ann0.setSequenceRef(seqs[0]);
ann2.setSequenceRef(seqs[3]);
ann3.setSequenceRef(seqs[2]);
ann4.setSequenceRef(seqs[1]);
parentPanel.getAlignment().addAnnotation(ann0);
parentPanel.getAlignment().addAnnotation(ann1);
parentPanel.getAlignment().addAnnotation(ann2);
parentPanel.getAlignment().addAnnotation(ann3);
parentPanel.getAlignment().addAnnotation(ann4);
}
/**
* Test creation of panel with OK and Cancel buttons
*/
@Test(groups = { "Functional" })
public void testBuildActionButtonsPanel()
{
testee = new AnnotationChooser(parentPanel);
JPanel jp = testee.buildActionButtonsPanel();
assertTrue("Wrong layout", jp.getLayout() instanceof FlowLayout);
Component[] comps = jp.getComponents();
assertEquals("Not 2 action buttons", 2, comps.length);
final Component jb1 = comps[0];
final Component jb2 = comps[1];
assertEquals("Not 'OK' button", MessageManager.getString("action.ok"),
((JButton) jb1).getText());
assertEquals("Wrong button font", JvSwingUtils.getLabelFont(),
jb1.getFont());
assertEquals("Not 'Cancel' button",
MessageManager.getString("action.cancel"),
((JButton) jb2).getText());
assertEquals("Wrong button font", JvSwingUtils.getLabelFont(),
jb2.getFont());
}
/**
* Test 'Apply to' has 3 radio buttons enabled, 'Selected Sequences' selected,
* when there is a current selection group.
*/
@Test(groups = { "Functional" })
public void testBuildApplyToOptionsPanel_withSelectionGroup()
{
selectSequences(0, 2, 3);
testee = new AnnotationChooser(parentPanel);
JPanel jp = testee.buildApplyToOptionsPanel();
Component[] comps = jp.getComponents();
assertEquals("Not 3 radio buttons", 3, comps.length);
final Checkbox cb1 = (Checkbox) comps[0];
final Checkbox cb2 = (Checkbox) comps[1];
final Checkbox cb3 = (Checkbox) comps[2];
assertTrue("Not enabled", cb1.isEnabled());
assertTrue("Not enabled", cb2.isEnabled());
assertTrue("Not enabled", cb3.isEnabled());
assertEquals("Option not selected", cb2, cb2.getCheckboxGroup()
.getSelectedCheckbox());
// check state variables match checkbox selection
assertTrue(testee.isApplyToSelectedSequences());
assertFalse(testee.isApplyToUnselectedSequences());
}
/**
* Add a sequence group to the alignment with the specified sequences (base 0)
* in it
*
* @param i
* @param more
*/
private void selectSequences(int... selected)
{
SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
SequenceGroup sg = new SequenceGroup();
for (int i : selected)
{
sg.addSequence(seqs[i], false);
}
parentPanel.av.setSelectionGroup(sg);
}
/**
* Test 'Apply to' has 1 radio button enabled, 'All Sequences' selected, when
* there is no current selection group.
*/
@Test(groups = { "Functional" })
public void testBuildApplyToOptionsPanel_noSelectionGroup()
{
testee = new AnnotationChooser(parentPanel);
JPanel jp = testee.buildApplyToOptionsPanel();
verifyApplyToOptionsPanel_noSelectionGroup(jp);
}
protected void verifyApplyToOptionsPanel_noSelectionGroup(JPanel jp)
{
assertTrue("Wrong layout", jp.getLayout() instanceof FlowLayout);
Component[] comps = jp.getComponents();
assertEquals("Not 3 radio buttons", 3, comps.length);
final Checkbox cb1 = (Checkbox) comps[0];
final Checkbox cb2 = (Checkbox) comps[1];
final Checkbox cb3 = (Checkbox) comps[2];
assertTrue("Not enabled", cb1.isEnabled());
assertFalse("Enabled", cb2.isEnabled());
assertFalse("Enabled", cb3.isEnabled());
assertEquals("Not selected", cb1, cb1.getCheckboxGroup()
.getSelectedCheckbox());
// check state variables match checkbox selection
assertTrue(testee.isApplyToSelectedSequences());
assertTrue(testee.isApplyToUnselectedSequences());
assertEquals("Wrong text",
MessageManager.getString("label.all_sequences"), cb1.getLabel());
assertEquals("Wrong text",
MessageManager.getString("label.selected_sequences"),
cb2.getLabel());
assertEquals("Wrong text",
MessageManager.getString("label.except_selected_sequences"),
cb3.getLabel());
}
/**
* Test Show and Hide radio buttons created, with Hide initially selected.
*/
@Test(groups = { "Functional" })
public void testBuildShowHidePanel()
{
testee = new AnnotationChooser(parentPanel);
JPanel jp = testee.buildShowHidePanel();
verifyShowHidePanel(jp);
}
protected void verifyShowHidePanel(JPanel jp)
{
assertTrue("Wrong layout", jp.getLayout() instanceof FlowLayout);
Component[] comps = jp.getComponents();
assertEquals("Not 2 radio buttons", 2, comps.length);
final Checkbox cb1 = (Checkbox) comps[0];
final Checkbox cb2 = (Checkbox) comps[1];
assertTrue("Show not enabled", cb1.isEnabled());
assertTrue("Hide not enabled", cb2.isEnabled());
// Hide (button 2) selected; note this may change to none (null)
assertEquals("Not selected", cb2, cb2.getCheckboxGroup()
.getSelectedCheckbox());
assertTrue("Show is flagged", !testee.isShowSelected());
assertEquals("Wrong text",
MessageManager.getString("label.show_selected_annotations"),
cb1.getLabel());
assertEquals("Wrong text",
MessageManager.getString("label.hide_selected_annotations"),
cb2.getLabel());
}
/**
* Test construction of panel containing two sub-panels
*/
@Test(groups = { "Functional" })
public void testBuildShowHideOptionsPanel()
{
testee = new AnnotationChooser(parentPanel);
JPanel jp = testee.buildShowHideOptionsPanel();
assertTrue("Wrong layout", jp.getLayout() instanceof BorderLayout);
Component[] comps = jp.getComponents();
assertEquals("Not 2 sub-panels", 2, comps.length);
verifyShowHidePanel((JPanel) comps[0]);
verifyApplyToOptionsPanel_noSelectionGroup((JPanel) comps[1]);
}
/**
* Test that annotation types are (uniquely) identified.
*
*/
@Test(groups = { "Functional" })
public void testGetAnnotationTypes()
{
selectSequences(1);
testee = new AnnotationChooser(parentPanel);
// selection group should make no difference to the result
// as all annotation types for the alignment are considered
List types = AnnotationChooser.getAnnotationTypes(
parentPanel.getAlignment(), true);
assertEquals("Not two annotation types", 2, types.size());
assertTrue("IUPRED missing", types.contains("IUPRED"));
assertTrue("JMol missing", types.contains("JMol"));
types = AnnotationChooser.getAnnotationTypes(
parentPanel.getAlignment(), false);
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"));
// These are added by viewmodel.AlignViewport.initAutoAnnotation():
assertTrue("Consensus missing", types.contains("Consensus"));
assertTrue("Quality missing", types.contains("Quality"));
assertTrue("Conservation missing", types.contains("Conservation"));
assertTrue("Occupancy missing", types.contains("Occupancy"));
}
/**
* Test result of selecting an annotation type, with 'Hide for all sequences'.
*
* We expect all annotations of that type to be set hidden. Other annotations
* should be left visible.
*/
@Test(groups = { "Functional" })
public void testSelectType_hideForAll()
{
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
setSelected(hideCheckbox, true);
final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
1, 1, 0);
setSelected(allSequencesCheckbox, true);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
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); // 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
}
/**
* Test result of selecting an annotation type, with 'Hide for selected
* sequences'.
*
* We expect the annotations of that type, linked to the sequence group, to be
* set hidden. Other annotations should be left visible.
*/
@Test(groups = { "Functional" })
public void testSelectType_hideForSelected()
{
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
setSelected(hideCheckbox, true);
/*
* Don't set the 'selected sequences' radio button since this would trigger
* an update, including unselected sequences / annotation types
*/
// setSelected(getSelectedSequencesCheckbox());
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
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); // 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 result of deselecting an annotation type, with 'Hide for all
* sequences'.
*
* We expect all annotations of that type to be set visible. Other annotations
* should be left unchanged.
*/
@Test(groups = { "Functional" })
public void testDeselectType_hideForAll()
{
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
setSelected(hideCheckbox, true);
final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
1, 1, 0);
setSelected(allSequencesCheckbox, true);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
final Checkbox typeCheckbox = getTypeCheckbox("JMol");
// select JMol - all hidden
setSelected(typeCheckbox, true);
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);
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;
}
/**
* Test result of deselecting an annotation type, with 'Hide for selected
* sequences'.
*
* We expect the annotations of that type, linked to the sequence group, to be
* set visible. Other annotations should be left unchanged.
*/
@Test(groups = { "Functional" })
public void testDeselectType_hideForSelected()
{
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
setSelected(hideCheckbox, true);
/*
* Don't set the 'selected sequences' radio button since this would trigger
* an update, including unselected sequences / annotation types
*/
// setSelected(getSelectedSequencesCheckbox());
setSelected(getTypeCheckbox("JMol"), true);
setSelected(getTypeCheckbox("JMol"), false);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
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
assertTrue(anns[7].visible); // JMol for seq1 in selection group
}
/**
* Test result of selecting an annotation type, with 'Show for all sequences'.
*
* We expect all annotations of that type to be set visible. Other annotations
* should be left unchanged
*/
@Test(groups = { "Functional" })
public void testSelectType_showForAll()
{
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
1, 1, 0);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
// hide all JMol annotations
setSelected(allSequencesCheckbox, true);
setSelected(hideCheckbox, true);
setSelected(getTypeCheckbox("JMol"), true);
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);
for (AlignmentAnnotation ann : anns)
{
assertTrue(ann.visible);
}
}
/**
* Test result of selecting an annotation type, with 'Show for selected
* sequences'.
*
* We expect all annotations of that type, linked to the sequence group, to be
* set visible. Other annotations should be left unchanged
*/
@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);
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
final Checkbox selectedSequencesCheckbox = (Checkbox) getComponent(
testee, 1, 1, 1);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
// hide all JMol annotations in the selection region (== annotation 7)
setSelected(selectedSequencesCheckbox, true);
setSelected(hideCheckbox, true);
setSelected(getTypeCheckbox("JMol"), true);
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);
for (AlignmentAnnotation ann : anns)
{
assertTrue(ann.visible);
}
}
/**
* Test result of deselecting an annotation type, with 'Show for all
* sequences'.
*
* We expect all annotations of that type to be set hidden. Other annotations
* should be left unchanged.
*/
@Test(groups = { "Functional" })
public void testDeselectType_showForAll()
{
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
setSelected(showCheckbox, true);
final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
1, 1, 0);
setSelected(allSequencesCheckbox, true);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
final Checkbox typeCheckbox = getTypeCheckbox("JMol");
// select JMol - all shown
setSelected(typeCheckbox, true);
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); // 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
}
/**
* Test result of deselecting an annotation type, with 'Show for selected
* sequences'.
*
* We expect the annotations of that type, linked to the sequence group, to be
* set hidden. Other annotations should be left unchanged.
*/
@Test(groups = { "Functional" })
public void testDeselectType_showForSelected()
{
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
setSelected(showCheckbox, true);
/*
* Don't set the 'selected sequences' radio button since this would trigger
* an update, including unselected sequences / annotation types
*/
// setSelected(getSelectedSequencesCheckbox());
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
// select JMol - should remain visible
setSelected(getTypeCheckbox("JMol"), true);
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); // 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
}
/**
* Helper method to drill down to a sub-component in a Container hierarchy.
*
* @param cont
* @param i
* @param j
* @param k
* @return
*/
public static Component getComponent(Container cont, int... positions)
{
Component comp = cont;
for (int i : positions)
{
comp = ((Container) comp).getComponent(i);
}
return comp;
}
/**
* Helper method to set or unset a checkbox and fire its action listener.
*
* @param cb
* @param select
*/
protected void setSelected(Checkbox cb, boolean select)
{
// TODO refactor to a test utility class
cb.setState(select);
// have to manually fire the action listener
cb.getItemListeners()[0].itemStateChanged(new ItemEvent(cb,
ItemEvent.ITEM_STATE_CHANGED, cb, select ? ItemEvent.SELECTED
: ItemEvent.DESELECTED));
}
/**
* Helper method to drill down to the 'Annotation type' checkbox with given
* label.
*
* @return
*/
private Checkbox getTypeCheckbox(String forLabel)
{
Component[] cbs = ((JPanel) testee.getComponent(0)).getComponents();
for (Component comp : cbs)
{
final Checkbox cb = (Checkbox) comp;
if (cb.getLabel().equals(forLabel))
{
return cb;
}
}
return null;
}
/**
* Test isInActionScope for the case where the scope is selected sequences.
* Test cases include sequences in the selection group, and others not in the
* group.
*/
@Test(groups = { "Functional" })
public void testIsInActionScope_selectedScope()
{
// sequences 1 and 2 have annotations 4 and 3 respectively
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox selectedSequencesCheckbox = (Checkbox) getComponent(
testee, 1, 1, 1);
setSelected(selectedSequencesCheckbox, true);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
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 isInActionScope for the case where the scope is unselected sequences.
* Test cases include sequences in the selection group, and others not in the
* group.
*/
@Test(groups = { "Functional" })
public void testIsInActionScope_unselectedScope()
{
// sequences 1 and 2 have annotations 4 and 3 respectively
selectSequences(1, 2);
testee = new AnnotationChooser(parentPanel);
final Checkbox unselectedSequencesCheckbox = (Checkbox) getComponent(
testee, 1, 1, 2);
setSelected(unselectedSequencesCheckbox, true);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
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(groups = { "Functional" })
public void testResetOriginalState()
{
testee = new AnnotationChooser(parentPanel);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
// all start visible
for (int i = 0; i < anns.length; i++)
{
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);
final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
1, 1, 0);
setSelected(allSequencesCheckbox, true);
setSelected(getTypeCheckbox("JMol"), true);
setSelected(getTypeCheckbox("IUPRED"), true);
assertTrue(anns[0].visible); // Conservation
assertTrue(anns[1].visible); // Quality
assertTrue(anns[2].visible); // Consensus
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();
for (int i = 0; i < anns.length; i++)
{
assertTrue(i + "'th sequence not visible", anns[i].visible);
}
}
}