+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
import jalview.datamodel.AlignmentAnnotation;
import java.util.Map;
import javax.swing.JButton;
-import javax.swing.JCheckBox;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
* @author gmcarstairs
*
*/
+@SuppressWarnings("serial")
public class AnnotationChooser extends JPanel
{
// currently selected 'annotation type' checkboxes
private Map<String, String> selectedTypes = new HashMap<String, String>();
-
+
/**
* Constructor.
*
for (final String type : annotationTypes)
{
- final JCheckBox check = new JCheckBox(type);
+ final Checkbox check = new Checkbox(type);
check.setFont(CHECKBOX_FONT);
check.addItemListener(new ItemListener()
{
{
AnnotationChooser.this.selectedTypes.remove(type);
}
- repaintAnnotations(false);
+ changeTypeSelected_actionPerformed(type);
}
});
jp.add(check);
}
/**
- * Set visibility flags on annotation rows then repaint the alignment panel.
+ * Update display when scope (All/Selected sequences/Unselected) is changed.
* <p>
- * Optionally, update all rows, including those not in the 'apply to' scope.
- * This makes more sense when switching between selected and unselected
- * sequences. When selecting annotation types, or show/hide, we only apply the
- * settings to the selected sequences.
+ * Set annotations (with one of the selected types) to the selected Show/Hide
+ * visibility, if they are in the new application scope. Set to the opposite
+ * if outside the scope.
* <p>
* Note this only affects sequence-specific annotations, others are left
* unchanged.
*/
- protected void repaintAnnotations(boolean updateAllRows)
+ protected void changeApplyTo_actionPerformed()
{
+ setAnnotationVisibility(true);
+
+ // copied from AnnotationLabel.actionPerformed (after show/hide row)...
+ // TODO should drive this functionality into AlignmentPanel
+ ap.updateAnnotation();
+ // this.ap.annotationPanel.adjustPanelHeight();
+ // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
+ // this.ap.annotationPanel.getSize().height);
+ // this.ap.validate();
+ this.ap.paintAlignment(true);
+ }
+
+ /**
+ * Update display when an annotation type is selected or deselected.
+ * <p>
+ * If the type is selected, set visibility of annotations of that type which
+ * are in the application scope (all, selected or unselected sequences).
+ * <p>
+ * If the type is unselected, set visibility to the opposite value. That is,
+ * treat select/deselect as a 'toggle' operation.
+ *
+ * @param type
+ */
+ protected void changeTypeSelected_actionPerformed(String type)
+ {
+ boolean typeSelected = this.selectedTypes.containsKey(type);
for (AlignmentAnnotation aa : this.ap.getAlignment()
.getAlignmentAnnotation())
{
- if (aa.sequenceRef != null)
+ if (aa.sequenceRef != null && type.equals(aa.label)
+ && isInActionScope(aa))
{
- setAnnotationVisibility(aa, updateAllRows);
+ aa.visible = typeSelected ? this.showSelected : !this.showSelected;
}
}
- // copied from AnnotationLabel.actionPerformed (after show/hide row)...
- // TODO should drive this functionality into AlignmentPanel
ap.updateAnnotation();
- this.ap.annotationPanel.adjustPanelHeight();
- this.ap.alabels.setSize(this.ap.alabels.getSize().width,
- this.ap.annotationPanel.getSize().height);
- this.ap.validate();
+ // // this.ap.annotationPanel.adjustPanelHeight();
+ // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
+ // this.ap.annotationPanel.getSize().height);
+ // this.ap.validate();
+ this.ap.paintAlignment(true);
+ }
+
+ /**
+ * Update display on change of choice of Show or Hide
+ * <p>
+ * For annotations of any selected type, set visibility of annotations of that
+ * type which are in the application scope (all, selected or unselected
+ * sequences).
+ *
+ * @param type
+ */
+ protected void changeShowHide_actionPerformed()
+ {
+ setAnnotationVisibility(false);
+
+ this.ap.updateAnnotation();
+ // this.ap.annotationPanel.adjustPanelHeight();
this.ap.paintAlignment(true);
}
/**
+ * Update visibility flags on annotation rows as per the current user choices.
+ *
+ * @param updateAllRows
+ */
+ protected void setAnnotationVisibility(boolean updateAllRows)
+ {
+ for (AlignmentAnnotation aa : this.ap.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (aa.sequenceRef != null)
+ {
+ setAnnotationVisibility(aa, updateAllRows);
+ }
+ }
+ }
+
+ /**
* Determine and set the visibility of the given annotation from the currently
* selected options.
* <p>
- * If its sequence is in the selected application scope
- * (all/selected/unselected sequences), then we set its visibility.
+ * Only update annotations whose type is one of the selected types.
* <p>
- * If the annotation type is one of those currently selected by checkbox, set
- * its visibility to the selected value. If it is not currently selected, set
- * it to the opposite value. So, unselecting an annotation type with 'hide'
- * selected, will cause those annotations to be unhidden.
+ * If its sequence is in the selected application scope
+ * (all/selected/unselected sequences), then we set its visibility according
+ * to the current choice of Show or Hide.
* <p>
* If force update of all rows is wanted, then set rows not in the sequence
* selection scope to the opposite visibility to those in scope.
protected void setAnnotationVisibility(AlignmentAnnotation aa,
boolean updateAllRows)
{
- boolean setToVisible = false;
if (this.selectedTypes.containsKey(aa.label))
{
- setToVisible = this.showSelected;
- }
- else
- {
- setToVisible = !this.showSelected;
- }
- if (isInActionScope(aa))
- {
- aa.visible = setToVisible;
- }
- else if (updateAllRows)
- {
- aa.visible = !setToVisible;
+ if (isInActionScope(aa))
+ {
+ aa.visible = this.showSelected;
+ }
+ else if (updateAllRows)
+ {
+ aa.visible = !this.showSelected;
+ }
}
// TODO force not visible if associated sequence is hidden?
// currently hiding a sequence does not hide its annotation rows
// we don't care if the annotation's sequence is selected or not
result = true;
}
+ else if (this.sg == null)
+ {
+ // shouldn't happen - defensive programming
+ result = true;
+ }
else if (this.sg.getSequences().contains(aa.sequenceRef))
{
// annotation is for a member of the selection group
public static List<String> getAnnotationTypes(AlignmentI alignment,
boolean sequenceSpecificOnly)
{
- // stub
List<String> result = new ArrayList<String>();
for (AlignmentAnnotation aa : alignment.getAlignmentAnnotation())
{
final boolean wholeAlignment = this.sg == null;
JPanel applyToOptions = new JPanel(new FlowLayout(FlowLayout.LEFT));
CheckboxGroup actingOn = new CheckboxGroup();
-
+
String forAll = MessageManager.getString("label.all_sequences");
final Checkbox allSequences = new Checkbox(forAll, actingOn,
wholeAlignment);
@Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getStateChange() == ItemEvent.SELECTED) {
+ if (evt.getStateChange() == ItemEvent.SELECTED)
+ {
AnnotationChooser.this.setApplyToSelectedSequences(true);
AnnotationChooser.this.setApplyToUnselectedSequences(true);
- AnnotationChooser.this.repaintAnnotations(true);
+ AnnotationChooser.this.changeApplyTo_actionPerformed();
}
}
});
applyToOptions.add(allSequences);
-
+
String forSelected = MessageManager
.getString("label.selected_sequences");
final Checkbox selectedSequences = new Checkbox(forSelected, actingOn,
{
AnnotationChooser.this.setApplyToSelectedSequences(true);
AnnotationChooser.this.setApplyToUnselectedSequences(false);
- AnnotationChooser.this.repaintAnnotations(true);
+ AnnotationChooser.this.changeApplyTo_actionPerformed();
}
}
});
applyToOptions.add(selectedSequences);
-
+
String exceptSelected = MessageManager
.getString("label.except_selected_sequences");
- final Checkbox unselectedSequences = new Checkbox(exceptSelected, actingOn, false);
+ final Checkbox unselectedSequences = new Checkbox(exceptSelected,
+ actingOn, false);
unselectedSequences.setEnabled(!wholeAlignment);
unselectedSequences.addItemListener(new ItemListener()
{
{
AnnotationChooser.this.setApplyToSelectedSequences(false);
AnnotationChooser.this.setApplyToUnselectedSequences(true);
- AnnotationChooser.this.repaintAnnotations(true);
+ AnnotationChooser.this.changeApplyTo_actionPerformed();
}
}
});
applyToOptions.add(unselectedSequences);
-
+
// set member variables to match the initial selection state
this.applyToSelectedSequences = selectedSequences.getState()
|| allSequences.getState();
}
/**
- * Build a panel with radio buttons options to show or hide selected
+ * Build a panel with radio button options to show or hide selected
* annotations.
*
* @return
@Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getStateChange() == ItemEvent.SELECTED) {
+ if (evt.getStateChange() == ItemEvent.SELECTED)
+ {
AnnotationChooser.this.setShowSelected(true);
- AnnotationChooser.this.repaintAnnotations(false);
+ AnnotationChooser.this.changeShowHide_actionPerformed();
}
}
});
if (evt.getStateChange() == ItemEvent.SELECTED)
{
AnnotationChooser.this.setShowSelected(false);
- AnnotationChooser.this.repaintAnnotations(false);
+ AnnotationChooser.this.changeShowHide_actionPerformed();
}
}
});
{
JPanel jp = new JPanel();
final Font labelFont = JvSwingUtils.getLabelFont();
-
+
JButton ok = new JButton(MessageManager.getString("action.ok"));
ok.setFont(labelFont);
ok.addActionListener(new ActionListener()
}
});
jp.add(ok);
-
+
JButton cancel = new JButton(MessageManager.getString("action.cancel"));
cancel.setFont(labelFont);
cancel.addActionListener(new ActionListener()
this.applyToUnselectedSequences = applyToUnselectedSequences;
}
+ protected boolean isShowSelected()
+ {
+ return showSelected;
+ }
+
+ protected boolean isApplyToSelectedSequences()
+ {
+ return applyToSelectedSequences;
+ }
+
+ protected boolean isApplyToUnselectedSequences()
+ {
+ return applyToUnselectedSequences;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff