/*
* 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 jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.HiddenColumns;
import jalview.io.cache.JvCacheableInputBox;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.event.FocusEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyEvent;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.border.TitledBorder;
import net.miginfocom.swing.MigLayout;
@SuppressWarnings("serial")
public class AnnotationColumnChooser extends AnnotationRowFilter
implements ItemListener
{
private JPanel switchableViewsPanel = new JPanel(new CardLayout());
private JPanel annotationComboBoxPanel = new JPanel();
private StructureFilterPanel gStructureFilterPanel;
private StructureFilterPanel ngStructureFilterPanel;
private StructureFilterPanel currentStructureFilterPanel;
private SearchPanel currentSearchPanel;
private SearchPanel gSearchPanel;
private SearchPanel ngSearchPanel;
private FurtherActionPanel currentFurtherActionPanel;
private FurtherActionPanel gFurtherActionPanel;
private FurtherActionPanel ngFurtherActionPanel;
public static final int ACTION_OPTION_SELECT = 1;
public static int ACTION_OPTION_HIDE = 2;
public static String NO_GRAPH_VIEW = "0";
public static String GRAPH_VIEW = "1";
private int actionOption = ACTION_OPTION_SELECT;
private HiddenColumns oldHiddenColumns;
protected static int MIN_WIDTH = (Platform.isJS() ? 370 : 420);
protected static int MIN_HEIGHT = (Platform.isJS() ? 370 : 430);
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
super(av, ap);
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
MessageManager.getString("label.select_by_annotation"), 0, 0);
// BH note: MIGLayout ignores this completely,
// possibly creating a frame smaller than specified:
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
addSliderChangeListener();
addSliderMouseListeners();
if (av.getAlignment().getAlignmentAnnotation() == null)
{
return;
}
setOldHiddenColumns(av.getAlignment().getHiddenColumns());
adjusting = true;
setAnnotations(new JComboBox<>(getAnnotationItems(false)));
populateThresholdComboBox(threshold);
AnnotationColumnChooser lastChooser = av
.getAnnotationColumnSelectionState();
// restore Object state from the previous session if one exists
if (lastChooser != null)
{
currentSearchPanel = lastChooser.getCurrentSearchPanel();
currentStructureFilterPanel = lastChooser
.getCurrentStructureFilterPanel();
annotations.setSelectedIndex(
lastChooser.getAnnotations().getSelectedIndex());
threshold.setSelectedIndex(
lastChooser.getThreshold().getSelectedIndex());
actionOption = lastChooser.getActionOption();
percentThreshold
.setSelected(lastChooser.percentThreshold.isSelected());
}
try
{
jbInit();
} catch (Exception ex)
{
}
adjusting = false;
updateView();
frame.invalidate();
frame.pack();
}
@Override
protected void jbInit()
{
super.jbInit();
JPanel thresholdPanel = new JPanel();
thresholdPanel.setBorder(new TitledBorder(
MessageManager.getString("label.threshold_filter")));
thresholdPanel.setBackground(Color.white);
thresholdPanel.setFont(JvSwingUtils.getLabelFont());
thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
percentThreshold.setBackground(Color.white);
percentThreshold.setFont(JvSwingUtils.getLabelFont());
JPanel actionPanel = new JPanel();
actionPanel.setBackground(Color.white);
actionPanel.setFont(JvSwingUtils.getLabelFont());
JPanel graphFilterView = new JPanel();
graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
graphFilterView.setBackground(Color.white);
JPanel noGraphFilterView = new JPanel();
noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
noGraphFilterView.setBackground(Color.white);
annotationComboBoxPanel.setBackground(Color.white);
annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
gSearchPanel = new SearchPanel(this);
ngSearchPanel = new SearchPanel(this);
gFurtherActionPanel = new FurtherActionPanel(this);
ngFurtherActionPanel = new FurtherActionPanel(this);
gStructureFilterPanel = new StructureFilterPanel(this);
ngStructureFilterPanel = new StructureFilterPanel(this);
thresholdPanel.add(getThreshold());
thresholdPanel.add(percentThreshold, "wrap");
thresholdPanel.add(slider, "grow");
thresholdPanel.add(thresholdValue, "span, wrap");
actionPanel.add(ok);
actionPanel.add(cancel);
graphFilterView.add(gSearchPanel, "grow, span, wrap");
graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
graphFilterView.add(thresholdPanel, "grow, span, wrap");
graphFilterView.add(gFurtherActionPanel);
noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
noGraphFilterView.add(ngFurtherActionPanel);
annotationComboBoxPanel.add(getAnnotations());
switchableViewsPanel.add(noGraphFilterView,
AnnotationColumnChooser.NO_GRAPH_VIEW);
switchableViewsPanel.add(graphFilterView,
AnnotationColumnChooser.GRAPH_VIEW);
this.setLayout(new BorderLayout());
this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
this.add(actionPanel, java.awt.BorderLayout.SOUTH);
selectedAnnotationChanged();
updateThresholdPanelToolTip();
this.validate();
}
protected void updateThresholdPanelToolTip()
{
thresholdValue.setToolTipText("");
slider.setToolTipText("");
String defaultTtip = MessageManager
.getString("info.change_threshold_mode_to_enable");
String thresh = getThreshold().getSelectedItem().toString();
if (thresh.equalsIgnoreCase("No Threshold"))
{
thresholdValue.setToolTipText(defaultTtip);
slider.setToolTipText(defaultTtip);
}
}
@Override
protected void reset()
{
if (this.getOldHiddenColumns() != null)
{
av.getColumnSelection().clear();
if (av.getAnnotationColumnSelectionState() != null)
{
HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
.getOldHiddenColumns();
av.getAlignment().setHiddenColumns(oldHidden);
}
av.sendSelection();
ap.paintAlignment(true, true);
}
}
@Override
public void valueChanged(boolean updateAllAnnotation)
{
if (slider.isEnabled())
{
getCurrentAnnotation().threshold.value = getSliderValue();
updateView();
propagateSeqAssociatedThreshold(updateAllAnnotation,
getCurrentAnnotation());
ap.paintAlignment(false, false);
}
}
@Override
public void updateView()
{
// Check if combobox is still adjusting
if (adjusting)
{
return;
}
AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
setCurrentAnnotation(av.getAlignment()
.getAlignmentAnnotation()[annmap[getAnnotations()
.getSelectedIndex()]]);
int selectedThresholdItem = getSelectedThresholdItem(
getThreshold().getSelectedIndex());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
percentThreshold.setEnabled(true);
final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
percentThreshold.setEnabled(false);
// build filter params
}
else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
{
if (currentAnnotation.threshold == null)
{
currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
(currentAnnotation.graphMax - currentAnnotation.graphMin)
/ 2f,
"Threshold", Color.black));
}
adjusting = true;
setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
currentAnnotation.threshold.value);
setThresholdValueText();
slider.setEnabled(true);
thresholdValue.setEnabled(true);
adjusting = false;
// build filter params
filterParams.setThresholdType(
AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
if (currentAnnotation.isQuantitative())
{
filterParams.setThresholdValue(currentAnnotation.threshold.value);
if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
{
filterParams.setThresholdType(
AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
}
else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
{
filterParams.setThresholdType(
AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
}
}
}
updateThresholdPanelToolTip();
if (currentStructureFilterPanel != null)
{
if (currentStructureFilterPanel.alphaHelix.isSelected())
{
filterParams.setFilterAlphaHelix(true);
}
if (currentStructureFilterPanel.betaStrand.isSelected())
{
filterParams.setFilterBetaSheet(true);
}
if (currentStructureFilterPanel.turn.isSelected())
{
filterParams.setFilterTurn(true);
}
}
if (currentSearchPanel != null)
{
if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
{
filterParams.setRegexString(
currentSearchPanel.searchBox.getUserInput());
if (currentSearchPanel.displayName.isSelected())
{
filterParams.addRegexSearchField(
AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
}
if (currentSearchPanel.description.isSelected())
{
filterParams.addRegexSearchField(
AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
}
}
}
// show hidden columns here, before changing the column selection in
// filterAnnotations, because showing hidden columns has the side effect of
// adding them to the selection
av.showAllHiddenColumns();
av.getColumnSelection().filterAnnotations(currentAnnotation.annotations,
filterParams);
boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
if (hideCols)
{
av.hideSelectedColumns();
}
av.sendSelection();
filterParams = null;
av.setAnnotationColumnSelectionState(this);
// only update overview and structures if columns were hidden
ap.paintAlignment(hideCols, hideCols);
}
public HiddenColumns getOldHiddenColumns()
{
return oldHiddenColumns;
}
public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
{
if (currentHiddenColumns != null)
{
this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
}
}
public FurtherActionPanel getCurrentFutherActionPanel()
{
return currentFurtherActionPanel;
}
public void setCurrentFutherActionPanel(
FurtherActionPanel currentFutherActionPanel)
{
this.currentFurtherActionPanel = currentFutherActionPanel;
}
public SearchPanel getCurrentSearchPanel()
{
return currentSearchPanel;
}
public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
{
this.currentSearchPanel = currentSearchPanel;
}
public int getActionOption()
{
return actionOption;
}
public void setActionOption(int actionOption)
{
this.actionOption = actionOption;
}
public StructureFilterPanel getCurrentStructureFilterPanel()
{
return currentStructureFilterPanel;
}
public void setCurrentStructureFilterPanel(
StructureFilterPanel currentStructureFilterPanel)
{
this.currentStructureFilterPanel = currentStructureFilterPanel;
}
public void select_action(ActionEvent actionEvent)
{
JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
if (radioButton.isSelected())
{
setActionOption(ACTION_OPTION_SELECT);
updateView();
}
}
public void hide_action(ActionEvent actionEvent)
{
JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
if (radioButton.isSelected())
{
setActionOption(ACTION_OPTION_HIDE);
updateView();
}
}
@Override
public void itemStateChanged(ItemEvent e)
{
selectedAnnotationChanged();
}
@Override
public void selectedAnnotationChanged()
{
String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
.getSelectedIndex()]].isQuantitative())
{
currentView = AnnotationColumnChooser.GRAPH_VIEW;
}
saveCache();
gSearchPanel.syncState();
gFurtherActionPanel.syncState();
gStructureFilterPanel.syncState();
ngSearchPanel.syncState();
ngFurtherActionPanel.syncState();
ngStructureFilterPanel.syncState();
CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
.getLayout();
switchableViewsLayout.show(switchableViewsPanel, currentView);
updateView();
}
public class FurtherActionPanel extends JPanel
{
private AnnotationColumnChooser aColChooser;
private JRadioButton hideOption = new JRadioButton();
private JRadioButton selectOption = new JRadioButton();
private ButtonGroup optionsGroup = new ButtonGroup();
public FurtherActionPanel(AnnotationColumnChooser aColChooser)
{
this.aColChooser = aColChooser;
JvSwingUtils.jvInitComponent(selectOption, "action.select");
selectOption.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
selectRadioAction(actionEvent);
}
});
JvSwingUtils.jvInitComponent(hideOption, "action.hide");
hideOption.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
hideRadioAction(actionEvent);
}
});
optionsGroup.add(selectOption);
optionsGroup.add(hideOption);
optionsGroup.setSelected(selectOption.getModel(), true);
JvSwingUtils.jvInitComponent(this);
syncState();
this.add(selectOption);
this.add(hideOption);
}
public void selectRadioAction(ActionEvent actionEvent)
{
aColChooser.setCurrentFutherActionPanel(this);
aColChooser.select_action(actionEvent);
}
public void hideRadioAction(ActionEvent actionEvent)
{
aColChooser.setCurrentFutherActionPanel(this);
aColChooser.hide_action(actionEvent);
}
public void syncState()
{
if (aColChooser
.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
{
this.optionsGroup.setSelected(this.hideOption.getModel(), true);
}
else
{
this.optionsGroup.setSelected(this.selectOption.getModel(), true);
}
}
}
public class StructureFilterPanel extends JPanel
{
private AnnotationColumnChooser aColChooser;
private JCheckBox alphaHelix = new JCheckBox();
private JCheckBox betaStrand = new JCheckBox();
private JCheckBox turn = new JCheckBox();
private JCheckBox all = new JCheckBox();
public StructureFilterPanel(AnnotationColumnChooser aColChooser)
{
this.aColChooser = aColChooser;
JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
alphaHelix.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
alphaHelix_actionPerformed();
}
});
JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
betaStrand.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
betaStrand_actionPerformed();
}
});
JvSwingUtils.jvInitComponent(turn, "label.turn");
turn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
turn_actionPerformed();
}
});
JvSwingUtils.jvInitComponent(all, "label.select_all");
all.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
all_actionPerformed();
}
});
this.setBorder(new TitledBorder(
MessageManager.getString("label.structures_filter")));
JvSwingUtils.jvInitComponent(this);
this.add(all);
this.add(alphaHelix);
this.add(betaStrand);
this.add(turn);
}
public void alphaHelix_actionPerformed()
{
updateSelectAllState();
aColChooser.setCurrentStructureFilterPanel(this);
aColChooser.updateView();
}
public void betaStrand_actionPerformed()
{
updateSelectAllState();
aColChooser.setCurrentStructureFilterPanel(this);
aColChooser.updateView();
}
public void turn_actionPerformed()
{
updateSelectAllState();
aColChooser.setCurrentStructureFilterPanel(this);
aColChooser.updateView();
}
public void all_actionPerformed()
{
if (all.isSelected())
{
alphaHelix.setSelected(true);
betaStrand.setSelected(true);
turn.setSelected(true);
}
else
{
alphaHelix.setSelected(false);
betaStrand.setSelected(false);
turn.setSelected(false);
}
aColChooser.setCurrentStructureFilterPanel(this);
aColChooser.updateView();
}
public void updateSelectAllState()
{
if (alphaHelix.isSelected() && betaStrand.isSelected()
&& turn.isSelected())
{
all.setSelected(true);
}
else
{
all.setSelected(false);
}
}
public void syncState()
{
StructureFilterPanel sfp = aColChooser
.getCurrentStructureFilterPanel();
if (sfp != null)
{
alphaHelix.setSelected(sfp.alphaHelix.isSelected());
betaStrand.setSelected(sfp.betaStrand.isSelected());
turn.setSelected(sfp.turn.isSelected());
if (sfp.all.isSelected())
{
all.setSelected(true);
alphaHelix.setSelected(true);
betaStrand.setSelected(true);
turn.setSelected(true);
}
}
}
}
public class SearchPanel extends JPanel
{
private AnnotationColumnChooser aColChooser;
private JCheckBox displayName = new JCheckBox();
private JCheckBox description = new JCheckBox();
private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
public JvCacheableInputBox searchBox = new JvCacheableInputBox<>(
FILTER_BY_ANN_CACHE_KEY, 23);
public SearchPanel(AnnotationColumnChooser aColChooser)
{
this.aColChooser = aColChooser;
JvSwingUtils.jvInitComponent(this);
this.setBorder(new TitledBorder(
MessageManager.getString("label.search_filter")));
searchBox.getComponent().setToolTipText(
MessageManager.getString("info.enter_search_text_here"));
searchBox.addKeyListener(new java.awt.event.KeyAdapter()
{
@Override
public void keyPressed(KeyEvent e)
{
if (e.getKeyCode() == KeyEvent.VK_ENTER)
{
e.consume();
searchStringAction();
}
}
});
searchBox.addFocusListener(new FocusAdapter()
{
@Override
public void focusLost(FocusEvent e)
{
searchStringAction();
}
});
JvSwingUtils.jvInitComponent(displayName, "label.label");
displayName.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
displayNameCheckboxAction();
}
});
JvSwingUtils.jvInitComponent(description, "label.description");
description.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
descriptionCheckboxAction();
}
});
syncState();
this.add(searchBox.getComponent());
this.add(displayName);
this.add(description);
}
public void displayNameCheckboxAction()
{
aColChooser.setCurrentSearchPanel(this);
aColChooser.updateView();
}
public void descriptionCheckboxAction()
{
aColChooser.setCurrentSearchPanel(this);
aColChooser.updateView();
}
public void searchStringAction()
{
aColChooser.setCurrentSearchPanel(this);
aColChooser.updateView();
updateSearchPanelToolTips();
searchBox.updateCache();
}
public void syncState()
{
SearchPanel sp = aColChooser.getCurrentSearchPanel();
if (sp != null)
{
description.setEnabled(sp.description.isEnabled());
description.setSelected(sp.description.isSelected());
displayName.setEnabled(sp.displayName.isEnabled());
displayName.setSelected(sp.displayName.isSelected());
searchBox.setSelectedItem(sp.searchBox.getUserInput());
}
updateSearchPanelToolTips();
}
public void updateSearchPanelToolTips()
{
String defaultTtip = MessageManager
.getString("info.enter_search_text_to_enable");
String labelTtip = MessageManager.formatMessage(
"info.search_in_annotation_label",
annotations.getSelectedItem().toString());
String descTtip = MessageManager.formatMessage(
"info.search_in_annotation_description",
annotations.getSelectedItem().toString());
displayName.setToolTipText(
displayName.isEnabled() ? labelTtip : defaultTtip);
description.setToolTipText(
description.isEnabled() ? descTtip : defaultTtip);
}
}
@Override
public void ok_actionPerformed()
{
saveCache();
super.ok_actionPerformed();
}
@Override
public void cancel_actionPerformed()
{
saveCache();
super.cancel_actionPerformed();
}
private void saveCache()
{
gSearchPanel.searchBox.persistCache();
ngSearchPanel.searchBox.persistCache();
gSearchPanel.searchBox.updateCache();
ngSearchPanel.searchBox.updateCache();
}
}