2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 import jalview.datamodel.HiddenColumns;
25 import jalview.schemes.AnnotationColourGradient;
26 import jalview.util.MessageManager;
27 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
29 import java.awt.BorderLayout;
30 import java.awt.CardLayout;
31 import java.awt.Color;
32 import java.awt.Dimension;
33 import java.awt.event.ActionEvent;
34 import java.awt.event.ActionListener;
35 import java.awt.event.ItemEvent;
36 import java.awt.event.ItemListener;
37 import java.util.Iterator;
39 import javax.swing.ButtonGroup;
40 import javax.swing.JCheckBox;
41 import javax.swing.JComboBox;
42 import javax.swing.JInternalFrame;
43 import javax.swing.JLayeredPane;
44 import javax.swing.JPanel;
45 import javax.swing.JRadioButton;
46 import javax.swing.JTextField;
47 import javax.swing.border.TitledBorder;
48 import javax.swing.event.DocumentEvent;
49 import javax.swing.event.DocumentListener;
51 import net.miginfocom.swing.MigLayout;
53 @SuppressWarnings("serial")
54 public class AnnotationColumnChooser extends AnnotationRowFilter implements
57 private JPanel switchableViewsPanel = new JPanel(new CardLayout());
59 private JPanel annotationComboBoxPanel = new JPanel();
61 private StructureFilterPanel gStructureFilterPanel;
63 private StructureFilterPanel ngStructureFilterPanel;
65 private StructureFilterPanel currentStructureFilterPanel;
67 private SearchPanel currentSearchPanel;
69 private SearchPanel gSearchPanel;
71 private SearchPanel ngSearchPanel;
73 private FurtherActionPanel currentFurtherActionPanel;
75 private FurtherActionPanel gFurtherActionPanel;
77 private FurtherActionPanel ngFurtherActionPanel;
79 public static final int ACTION_OPTION_SELECT = 1;
81 public static int ACTION_OPTION_HIDE = 2;
83 public static String NO_GRAPH_VIEW = "0";
85 public static String GRAPH_VIEW = "1";
87 private int actionOption = ACTION_OPTION_SELECT;
89 private HiddenColumns oldHiddenColumns;
91 protected int MIN_WIDTH = 420;
93 protected int MIN_HEIGHT = 430;
95 public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
98 frame = new JInternalFrame();
99 frame.setContentPane(this);
100 frame.setLayer(JLayeredPane.PALETTE_LAYER);
101 Desktop.addInternalFrame(frame,
102 MessageManager.getString("label.select_by_annotation"), 520,
104 frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
106 addSliderChangeListener();
107 addSliderMouseListeners();
109 if (av.getAlignment().getAlignmentAnnotation() == null)
113 setOldHiddenColumns(av.getAlignment().getHiddenColumns());
116 setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
117 populateThresholdComboBox(threshold);
118 AnnotationColumnChooser lastChooser = av
119 .getAnnotationColumnSelectionState();
120 // restore Object state from the previous session if one exists
121 if (lastChooser != null)
123 currentSearchPanel = lastChooser
124 .getCurrentSearchPanel();
125 currentStructureFilterPanel = lastChooser
126 .getCurrentStructureFilterPanel();
127 annotations.setSelectedIndex(lastChooser
128 .getAnnotations().getSelectedIndex());
129 threshold.setSelectedIndex(lastChooser
130 .getThreshold().getSelectedIndex());
131 actionOption = lastChooser
133 percentThreshold.setSelected(lastChooser.percentThreshold
140 } catch (Exception ex)
151 protected void jbInit()
155 JPanel thresholdPanel = new JPanel();
156 thresholdPanel.setBorder(new TitledBorder(MessageManager
157 .getString("label.threshold_filter")));
158 thresholdPanel.setBackground(Color.white);
159 thresholdPanel.setFont(JvSwingUtils.getLabelFont());
160 thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
162 percentThreshold.setBackground(Color.white);
163 percentThreshold.setFont(JvSwingUtils.getLabelFont());
165 JPanel actionPanel = new JPanel();
166 actionPanel.setBackground(Color.white);
167 actionPanel.setFont(JvSwingUtils.getLabelFont());
169 JPanel graphFilterView = new JPanel();
170 graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
171 graphFilterView.setBackground(Color.white);
173 JPanel noGraphFilterView = new JPanel();
174 noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
175 noGraphFilterView.setBackground(Color.white);
177 annotationComboBoxPanel.setBackground(Color.white);
178 annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
180 gSearchPanel = new SearchPanel(this);
181 ngSearchPanel = new SearchPanel(this);
182 gFurtherActionPanel = new FurtherActionPanel(this);
183 ngFurtherActionPanel = new FurtherActionPanel(this);
184 gStructureFilterPanel = new StructureFilterPanel(this);
185 ngStructureFilterPanel = new StructureFilterPanel(this);
187 thresholdPanel.add(getThreshold());
188 thresholdPanel.add(percentThreshold, "wrap");
189 thresholdPanel.add(slider, "grow");
190 thresholdPanel.add(thresholdValue, "span, wrap");
193 actionPanel.add(cancel);
195 graphFilterView.add(gSearchPanel, "grow, span, wrap");
196 graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
197 graphFilterView.add(thresholdPanel, "grow, span, wrap");
198 graphFilterView.add(gFurtherActionPanel);
200 noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
201 noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
202 noGraphFilterView.add(ngFurtherActionPanel);
204 annotationComboBoxPanel.add(getAnnotations());
205 switchableViewsPanel.add(noGraphFilterView,
206 AnnotationColumnChooser.NO_GRAPH_VIEW);
207 switchableViewsPanel.add(graphFilterView,
208 AnnotationColumnChooser.GRAPH_VIEW);
210 this.setLayout(new BorderLayout());
211 this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
212 this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
213 this.add(actionPanel, java.awt.BorderLayout.SOUTH);
215 selectedAnnotationChanged();
216 updateThresholdPanelToolTip();
220 protected void updateThresholdPanelToolTip()
222 thresholdValue.setToolTipText("");
223 slider.setToolTipText("");
225 String defaultTtip = MessageManager
226 .getString("info.change_threshold_mode_to_enable");
228 String thresh = getThreshold().getSelectedItem().toString();
229 if (thresh.equalsIgnoreCase("No Threshold"))
231 thresholdValue.setToolTipText(defaultTtip);
232 slider.setToolTipText(defaultTtip);
237 protected void reset()
239 if (this.getOldHiddenColumns() != null)
241 av.getColumnSelection().clear();
243 if (av.getAnnotationColumnSelectionState() != null)
245 HiddenColumns oldHidden = av
246 .getAnnotationColumnSelectionState()
247 .getOldHiddenColumns();
248 if (oldHidden != null && oldHidden.getHiddenRegions() != null
249 && !oldHidden.getHiddenRegions().isEmpty())
251 for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
252 .iterator(); itr.hasNext();)
254 int positions[] = itr.next();
255 av.hideColumns(positions[0], positions[1]);
258 av.getAlignment().setHiddenColumns(oldHidden);
260 ap.paintAlignment(true);
266 public void valueChanged(boolean updateAllAnnotation)
268 if (slider.isEnabled())
270 getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
272 propagateSeqAssociatedThreshold(updateAllAnnotation,
273 getCurrentAnnotation());
274 ap.paintAlignment(false);
279 public void updateView()
281 // Check if combobox is still adjusting
287 AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
289 setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
290 .getSelectedIndex()]]);
292 int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
293 .getSelectedIndex());
295 slider.setEnabled(true);
296 thresholdValue.setEnabled(true);
297 percentThreshold.setEnabled(true);
299 if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
301 slider.setEnabled(false);
302 thresholdValue.setEnabled(false);
303 thresholdValue.setText("");
304 percentThreshold.setEnabled(false);
305 // build filter params
307 else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
309 if (getCurrentAnnotation().threshold == null)
311 getCurrentAnnotation()
313 new jalview.datamodel.GraphLine(
314 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
315 "Threshold", Color.black));
319 float range = getCurrentAnnotation().graphMax * 1000
320 - getCurrentAnnotation().graphMin * 1000;
322 slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
323 slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
324 slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
326 setThresholdValueText();
328 slider.setMajorTickSpacing((int) (range / 10f));
329 slider.setEnabled(true);
330 thresholdValue.setEnabled(true);
333 // build filter params
335 .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
336 if (getCurrentAnnotation().isQuantitative())
339 .setThresholdValue(getCurrentAnnotation().threshold.value);
341 if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
344 .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
346 else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
349 .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
354 updateThresholdPanelToolTip();
355 if (currentStructureFilterPanel != null)
357 if (currentStructureFilterPanel.alphaHelix.isSelected())
359 filterParams.setFilterAlphaHelix(true);
361 if (currentStructureFilterPanel.betaStrand.isSelected())
363 filterParams.setFilterBetaSheet(true);
365 if (currentStructureFilterPanel.turn.isSelected())
367 filterParams.setFilterTurn(true);
371 if (currentSearchPanel != null)
374 if (!currentSearchPanel.searchBox.getText().isEmpty())
376 currentSearchPanel.description.setEnabled(true);
377 currentSearchPanel.displayName.setEnabled(true);
378 filterParams.setRegexString(currentSearchPanel.searchBox.getText());
379 if (currentSearchPanel.displayName.isSelected())
382 .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
384 if (currentSearchPanel.description.isSelected())
387 .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
392 currentSearchPanel.description.setEnabled(false);
393 currentSearchPanel.displayName.setEnabled(false);
397 av.getColumnSelection().filterAnnotations(
398 getCurrentAnnotation().annotations, filterParams);
400 av.showAllHiddenColumns();
401 if (getActionOption() == ACTION_OPTION_HIDE)
403 av.hideSelectedColumns();
407 av.setAnnotationColumnSelectionState(this);
408 ap.paintAlignment(true);
411 public HiddenColumns getOldHiddenColumns()
413 return oldHiddenColumns;
416 public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
418 if (currentHiddenColumns != null)
420 this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
424 public FurtherActionPanel getCurrentFutherActionPanel()
426 return currentFurtherActionPanel;
429 public void setCurrentFutherActionPanel(
430 FurtherActionPanel currentFutherActionPanel)
432 this.currentFurtherActionPanel = currentFutherActionPanel;
435 public SearchPanel getCurrentSearchPanel()
437 return currentSearchPanel;
440 public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
442 this.currentSearchPanel = currentSearchPanel;
445 public int getActionOption()
450 public void setActionOption(int actionOption)
452 this.actionOption = actionOption;
455 public StructureFilterPanel getCurrentStructureFilterPanel()
457 return currentStructureFilterPanel;
460 public void setCurrentStructureFilterPanel(
461 StructureFilterPanel currentStructureFilterPanel)
463 this.currentStructureFilterPanel = currentStructureFilterPanel;
466 public void select_action(ActionEvent actionEvent)
468 JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
469 if (radioButton.isSelected())
471 setActionOption(ACTION_OPTION_SELECT);
476 public void hide_action(ActionEvent actionEvent)
478 JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
479 if (radioButton.isSelected())
481 setActionOption(ACTION_OPTION_HIDE);
487 public void itemStateChanged(ItemEvent e)
489 selectedAnnotationChanged();
493 public void selectedAnnotationChanged()
495 String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
496 if (av.getAlignment()
497 .getAlignmentAnnotation()[annmap[getAnnotations()
498 .getSelectedIndex()]].isQuantitative())
500 currentView = AnnotationColumnChooser.GRAPH_VIEW;
503 gSearchPanel.syncState();
504 gFurtherActionPanel.syncState();
505 gStructureFilterPanel.syncState();
507 ngSearchPanel.syncState();
508 ngFurtherActionPanel.syncState();
509 ngStructureFilterPanel.syncState();
511 CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
513 switchableViewsLayout.show(switchableViewsPanel, currentView);
517 public class FurtherActionPanel extends JPanel
519 private AnnotationColumnChooser aColChooser;
521 private JRadioButton hideOption = new JRadioButton();
523 private JRadioButton selectOption = new JRadioButton();
525 private ButtonGroup optionsGroup = new ButtonGroup();
527 public FurtherActionPanel(AnnotationColumnChooser aColChooser)
529 this.aColChooser = aColChooser;
530 JvSwingUtils.jvInitComponent(selectOption, "action.select");
531 selectOption.addActionListener(new ActionListener()
534 public void actionPerformed(ActionEvent actionEvent)
536 selectRadioAction(actionEvent);
540 JvSwingUtils.jvInitComponent(hideOption, "action.hide");
541 hideOption.addActionListener(new ActionListener()
544 public void actionPerformed(ActionEvent actionEvent)
546 hideRadioAction(actionEvent);
550 optionsGroup.add(selectOption);
551 optionsGroup.add(hideOption);
552 optionsGroup.setSelected(selectOption.getModel(), true);
554 JvSwingUtils.jvInitComponent(this);
557 this.add(selectOption);
558 this.add(hideOption);
561 public void selectRadioAction(ActionEvent actionEvent)
563 aColChooser.setCurrentFutherActionPanel(this);
564 aColChooser.select_action(actionEvent);
567 public void hideRadioAction(ActionEvent actionEvent)
569 aColChooser.setCurrentFutherActionPanel(this);
570 aColChooser.hide_action(actionEvent);
573 public void syncState()
575 if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
577 this.optionsGroup.setSelected(this.hideOption.getModel(), true);
581 this.optionsGroup.setSelected(this.selectOption.getModel(), true);
586 public class StructureFilterPanel extends JPanel
588 private AnnotationColumnChooser aColChooser;
590 private JCheckBox alphaHelix = new JCheckBox();
592 private JCheckBox betaStrand = new JCheckBox();
594 private JCheckBox turn = new JCheckBox();
596 private JCheckBox all = new JCheckBox();
598 public StructureFilterPanel(AnnotationColumnChooser aColChooser)
600 this.aColChooser = aColChooser;
602 JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
603 alphaHelix.addActionListener(new ActionListener()
606 public void actionPerformed(ActionEvent actionEvent)
608 alphaHelix_actionPerformed();
612 JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
613 betaStrand.addActionListener(new ActionListener()
616 public void actionPerformed(ActionEvent actionEvent)
618 betaStrand_actionPerformed();
622 JvSwingUtils.jvInitComponent(turn, "label.turn");
623 turn.addActionListener(new ActionListener()
626 public void actionPerformed(ActionEvent actionEvent)
628 turn_actionPerformed();
632 JvSwingUtils.jvInitComponent(all, "label.select_all");
633 all.addActionListener(new ActionListener()
636 public void actionPerformed(ActionEvent actionEvent)
638 all_actionPerformed();
642 this.setBorder(new TitledBorder(MessageManager
643 .getString("label.structures_filter")));
644 JvSwingUtils.jvInitComponent(this);
647 this.add(alphaHelix);
648 this.add(betaStrand);
652 public void alphaHelix_actionPerformed()
654 updateSelectAllState();
655 aColChooser.setCurrentStructureFilterPanel(this);
656 aColChooser.updateView();
659 public void betaStrand_actionPerformed()
661 updateSelectAllState();
662 aColChooser.setCurrentStructureFilterPanel(this);
663 aColChooser.updateView();
666 public void turn_actionPerformed()
668 updateSelectAllState();
669 aColChooser.setCurrentStructureFilterPanel(this);
670 aColChooser.updateView();
673 public void all_actionPerformed()
675 if (all.isSelected())
677 alphaHelix.setSelected(true);
678 betaStrand.setSelected(true);
679 turn.setSelected(true);
683 alphaHelix.setSelected(false);
684 betaStrand.setSelected(false);
685 turn.setSelected(false);
687 aColChooser.setCurrentStructureFilterPanel(this);
688 aColChooser.updateView();
691 public void updateSelectAllState()
693 if (alphaHelix.isSelected() && betaStrand.isSelected()
694 && turn.isSelected())
696 all.setSelected(true);
700 all.setSelected(false);
704 public void syncState()
706 StructureFilterPanel sfp = aColChooser
707 .getCurrentStructureFilterPanel();
710 alphaHelix.setSelected(sfp.alphaHelix.isSelected());
711 betaStrand.setSelected(sfp.betaStrand.isSelected());
712 turn.setSelected(sfp.turn.isSelected());
713 if (sfp.all.isSelected())
715 all.setSelected(true);
716 alphaHelix.setSelected(true);
717 betaStrand.setSelected(true);
718 turn.setSelected(true);
725 public class SearchPanel extends JPanel
727 private AnnotationColumnChooser aColChooser;
729 private JCheckBox displayName = new JCheckBox();
731 private JCheckBox description = new JCheckBox();
733 private JTextField searchBox = new JTextField(10);
735 public SearchPanel(AnnotationColumnChooser aColChooser)
738 this.aColChooser = aColChooser;
739 JvSwingUtils.jvInitComponent(this);
740 this.setBorder(new TitledBorder(MessageManager
741 .getString("label.search_filter")));
743 JvSwingUtils.jvInitComponent(searchBox);
744 searchBox.setToolTipText(MessageManager
745 .getString("info.enter_search_text_here"));
746 searchBox.getDocument().addDocumentListener(new DocumentListener()
749 public void insertUpdate(DocumentEvent e)
751 searchStringAction();
755 public void removeUpdate(DocumentEvent e)
757 searchStringAction();
761 public void changedUpdate(DocumentEvent e)
763 searchStringAction();
767 JvSwingUtils.jvInitComponent(displayName, "label.label");
768 displayName.setEnabled(false);
769 displayName.addActionListener(new ActionListener()
772 public void actionPerformed(ActionEvent actionEvent)
774 displayNameCheckboxAction();
778 JvSwingUtils.jvInitComponent(description, "label.description");
779 description.setEnabled(false);
780 description.addActionListener(new ActionListener()
783 public void actionPerformed(ActionEvent actionEvent)
785 discriptionCheckboxAction();
791 this.add(displayName);
792 this.add(description);
795 public void displayNameCheckboxAction()
797 aColChooser.setCurrentSearchPanel(this);
798 aColChooser.updateView();
801 public void discriptionCheckboxAction()
803 aColChooser.setCurrentSearchPanel(this);
804 aColChooser.updateView();
807 public void searchStringAction()
809 aColChooser.setCurrentSearchPanel(this);
810 aColChooser.updateView();
811 updateSearchPanelToolTips();
814 public void syncState()
816 SearchPanel sp = aColChooser.getCurrentSearchPanel();
819 description.setEnabled(sp.description.isEnabled());
820 description.setSelected(sp.description.isSelected());
822 displayName.setEnabled(sp.displayName.isEnabled());
823 displayName.setSelected(sp.displayName.isSelected());
825 searchBox.setText(sp.searchBox.getText());
827 updateSearchPanelToolTips();
830 public void updateSearchPanelToolTips()
832 String defaultTtip = MessageManager
833 .getString("info.enter_search_text_to_enable");
834 String labelTtip = MessageManager.formatMessage(
835 "info.search_in_annotation_label", annotations
836 .getSelectedItem().toString());
837 String descTtip = MessageManager.formatMessage(
838 "info.search_in_annotation_description", annotations
839 .getSelectedItem().toString());
840 displayName.setToolTipText(displayName.isEnabled() ? labelTtip
842 description.setToolTipText(description.isEnabled() ? descTtip