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.io.cache.JvCacheableInputBox;
26 import jalview.schemes.AnnotationColourGradient;
27 import jalview.util.MessageManager;
28 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
30 import java.awt.BorderLayout;
31 import java.awt.CardLayout;
32 import java.awt.Color;
33 import java.awt.Dimension;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.ActionListener;
36 import java.awt.event.ItemEvent;
37 import java.awt.event.ItemListener;
38 import java.awt.event.KeyEvent;
39 import java.util.Iterator;
41 import javax.swing.ButtonGroup;
42 import javax.swing.JCheckBox;
43 import javax.swing.JComboBox;
44 import javax.swing.JInternalFrame;
45 import javax.swing.JLayeredPane;
46 import javax.swing.JPanel;
47 import javax.swing.JRadioButton;
48 import javax.swing.border.TitledBorder;
50 import net.miginfocom.swing.MigLayout;
52 @SuppressWarnings("serial")
53 public class AnnotationColumnChooser extends AnnotationRowFilter implements
56 private JPanel switchableViewsPanel = new JPanel(new CardLayout());
58 private JPanel annotationComboBoxPanel = new JPanel();
60 private StructureFilterPanel gStructureFilterPanel;
62 private StructureFilterPanel ngStructureFilterPanel;
64 private StructureFilterPanel currentStructureFilterPanel;
66 private SearchPanel currentSearchPanel;
68 private SearchPanel gSearchPanel;
70 private SearchPanel ngSearchPanel;
72 private FurtherActionPanel currentFurtherActionPanel;
74 private FurtherActionPanel gFurtherActionPanel;
76 private FurtherActionPanel ngFurtherActionPanel;
78 public static final int ACTION_OPTION_SELECT = 1;
80 public static int ACTION_OPTION_HIDE = 2;
82 public static String NO_GRAPH_VIEW = "0";
84 public static String GRAPH_VIEW = "1";
86 private int actionOption = ACTION_OPTION_SELECT;
88 private HiddenColumns oldHiddenColumns;
90 protected int MIN_WIDTH = 420;
92 protected int MIN_HEIGHT = 430;
94 public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
97 frame = new JInternalFrame();
98 frame.setContentPane(this);
99 frame.setLayer(JLayeredPane.PALETTE_LAYER);
100 Desktop.addInternalFrame(frame,
101 MessageManager.getString("label.select_by_annotation"), 520,
103 frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
105 addSliderChangeListener();
106 addSliderMouseListeners();
108 if (av.getAlignment().getAlignmentAnnotation() == null)
112 setOldHiddenColumns(av.getAlignment().getHiddenColumns());
115 setAnnotations(new JComboBox<>(getAnnotationItems(false)));
116 populateThresholdComboBox(threshold);
117 AnnotationColumnChooser lastChooser = av
118 .getAnnotationColumnSelectionState();
119 // restore Object state from the previous session if one exists
120 if (lastChooser != null)
122 currentSearchPanel = lastChooser
123 .getCurrentSearchPanel();
124 currentStructureFilterPanel = lastChooser
125 .getCurrentStructureFilterPanel();
126 annotations.setSelectedIndex(lastChooser
127 .getAnnotations().getSelectedIndex());
128 threshold.setSelectedIndex(lastChooser
129 .getThreshold().getSelectedIndex());
130 actionOption = lastChooser
132 percentThreshold.setSelected(lastChooser.percentThreshold
139 } catch (Exception ex)
150 protected void jbInit()
154 JPanel thresholdPanel = new JPanel();
155 thresholdPanel.setBorder(new TitledBorder(MessageManager
156 .getString("label.threshold_filter")));
157 thresholdPanel.setBackground(Color.white);
158 thresholdPanel.setFont(JvSwingUtils.getLabelFont());
159 thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
161 percentThreshold.setBackground(Color.white);
162 percentThreshold.setFont(JvSwingUtils.getLabelFont());
164 JPanel actionPanel = new JPanel();
165 actionPanel.setBackground(Color.white);
166 actionPanel.setFont(JvSwingUtils.getLabelFont());
168 JPanel graphFilterView = new JPanel();
169 graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
170 graphFilterView.setBackground(Color.white);
172 JPanel noGraphFilterView = new JPanel();
173 noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
174 noGraphFilterView.setBackground(Color.white);
176 annotationComboBoxPanel.setBackground(Color.white);
177 annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
179 gSearchPanel = new SearchPanel(this);
180 ngSearchPanel = new SearchPanel(this);
181 gFurtherActionPanel = new FurtherActionPanel(this);
182 ngFurtherActionPanel = new FurtherActionPanel(this);
183 gStructureFilterPanel = new StructureFilterPanel(this);
184 ngStructureFilterPanel = new StructureFilterPanel(this);
186 thresholdPanel.add(getThreshold());
187 thresholdPanel.add(percentThreshold, "wrap");
188 thresholdPanel.add(slider, "grow");
189 thresholdPanel.add(thresholdValue, "span, wrap");
192 actionPanel.add(cancel);
194 graphFilterView.add(gSearchPanel, "grow, span, wrap");
195 graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
196 graphFilterView.add(thresholdPanel, "grow, span, wrap");
197 graphFilterView.add(gFurtherActionPanel);
199 noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
200 noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
201 noGraphFilterView.add(ngFurtherActionPanel);
203 annotationComboBoxPanel.add(getAnnotations());
204 switchableViewsPanel.add(noGraphFilterView,
205 AnnotationColumnChooser.NO_GRAPH_VIEW);
206 switchableViewsPanel.add(graphFilterView,
207 AnnotationColumnChooser.GRAPH_VIEW);
209 this.setLayout(new BorderLayout());
210 this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
211 this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
212 this.add(actionPanel, java.awt.BorderLayout.SOUTH);
214 selectedAnnotationChanged();
215 updateThresholdPanelToolTip();
219 protected void updateThresholdPanelToolTip()
221 thresholdValue.setToolTipText("");
222 slider.setToolTipText("");
224 String defaultTtip = MessageManager
225 .getString("info.change_threshold_mode_to_enable");
227 String thresh = getThreshold().getSelectedItem().toString();
228 if (thresh.equalsIgnoreCase("No Threshold"))
230 thresholdValue.setToolTipText(defaultTtip);
231 slider.setToolTipText(defaultTtip);
236 protected void reset()
238 if (this.getOldHiddenColumns() != null)
240 av.getColumnSelection().clear();
242 if (av.getAnnotationColumnSelectionState() != null)
244 HiddenColumns oldHidden = av
245 .getAnnotationColumnSelectionState()
246 .getOldHiddenColumns();
247 if (oldHidden != null)
249 for (Iterator<int[]> itr = oldHidden.iterator(); itr.hasNext();)
251 int positions[] = itr.next();
252 av.hideColumns(positions[0], positions[1]);
255 av.getAlignment().setHiddenColumns(oldHidden);
257 ap.paintAlignment(true);
263 public void valueChanged(boolean updateAllAnnotation)
265 if (slider.isEnabled())
267 getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
269 propagateSeqAssociatedThreshold(updateAllAnnotation,
270 getCurrentAnnotation());
271 ap.paintAlignment(false);
276 public void updateView()
278 // Check if combobox is still adjusting
284 AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
286 setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
287 .getSelectedIndex()]]);
289 int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
290 .getSelectedIndex());
292 slider.setEnabled(true);
293 thresholdValue.setEnabled(true);
294 percentThreshold.setEnabled(true);
296 if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
298 slider.setEnabled(false);
299 thresholdValue.setEnabled(false);
300 thresholdValue.setText("");
301 percentThreshold.setEnabled(false);
302 // build filter params
304 else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
306 if (getCurrentAnnotation().threshold == null)
308 getCurrentAnnotation()
310 new jalview.datamodel.GraphLine(
311 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
312 "Threshold", Color.black));
316 float range = getCurrentAnnotation().graphMax * 1000
317 - getCurrentAnnotation().graphMin * 1000;
319 slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
320 slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
321 slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
323 setThresholdValueText();
325 slider.setMajorTickSpacing((int) (range / 10f));
326 slider.setEnabled(true);
327 thresholdValue.setEnabled(true);
330 // build filter params
332 .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
333 if (getCurrentAnnotation().isQuantitative())
336 .setThresholdValue(getCurrentAnnotation().threshold.value);
338 if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
341 .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
343 else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
346 .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
351 updateThresholdPanelToolTip();
352 if (currentStructureFilterPanel != null)
354 if (currentStructureFilterPanel.alphaHelix.isSelected())
356 filterParams.setFilterAlphaHelix(true);
358 if (currentStructureFilterPanel.betaStrand.isSelected())
360 filterParams.setFilterBetaSheet(true);
362 if (currentStructureFilterPanel.turn.isSelected())
364 filterParams.setFilterTurn(true);
368 if (currentSearchPanel != null)
370 if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
372 filterParams.setRegexString(currentSearchPanel.searchBox
374 if (currentSearchPanel.displayName.isSelected())
377 .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
379 if (currentSearchPanel.description.isSelected())
382 .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
387 // show hidden columns here, before changing the column selection in
388 // filterAnnotations, because showing hidden columns has the side effect of
389 // adding them to the selection
390 av.showAllHiddenColumns();
391 av.getColumnSelection().filterAnnotations(
392 getCurrentAnnotation().annotations, filterParams);
394 if (getActionOption() == ACTION_OPTION_HIDE)
396 av.hideSelectedColumns();
400 av.setAnnotationColumnSelectionState(this);
401 ap.paintAlignment(true);
404 public HiddenColumns getOldHiddenColumns()
406 return oldHiddenColumns;
409 public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
411 if (currentHiddenColumns != null)
413 this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
417 public FurtherActionPanel getCurrentFutherActionPanel()
419 return currentFurtherActionPanel;
422 public void setCurrentFutherActionPanel(
423 FurtherActionPanel currentFutherActionPanel)
425 this.currentFurtherActionPanel = currentFutherActionPanel;
428 public SearchPanel getCurrentSearchPanel()
430 return currentSearchPanel;
433 public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
435 this.currentSearchPanel = currentSearchPanel;
438 public int getActionOption()
443 public void setActionOption(int actionOption)
445 this.actionOption = actionOption;
448 public StructureFilterPanel getCurrentStructureFilterPanel()
450 return currentStructureFilterPanel;
453 public void setCurrentStructureFilterPanel(
454 StructureFilterPanel currentStructureFilterPanel)
456 this.currentStructureFilterPanel = currentStructureFilterPanel;
459 public void select_action(ActionEvent actionEvent)
461 JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
462 if (radioButton.isSelected())
464 setActionOption(ACTION_OPTION_SELECT);
469 public void hide_action(ActionEvent actionEvent)
471 JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
472 if (radioButton.isSelected())
474 setActionOption(ACTION_OPTION_HIDE);
480 public void itemStateChanged(ItemEvent e)
482 selectedAnnotationChanged();
486 public void selectedAnnotationChanged()
488 String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
489 if (av.getAlignment()
490 .getAlignmentAnnotation()[annmap[getAnnotations()
491 .getSelectedIndex()]].isQuantitative())
493 currentView = AnnotationColumnChooser.GRAPH_VIEW;
496 gSearchPanel.syncState();
497 gFurtherActionPanel.syncState();
498 gStructureFilterPanel.syncState();
500 ngSearchPanel.syncState();
501 ngFurtherActionPanel.syncState();
502 ngStructureFilterPanel.syncState();
504 CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
506 switchableViewsLayout.show(switchableViewsPanel, currentView);
510 public class FurtherActionPanel extends JPanel
512 private AnnotationColumnChooser aColChooser;
514 private JRadioButton hideOption = new JRadioButton();
516 private JRadioButton selectOption = new JRadioButton();
518 private ButtonGroup optionsGroup = new ButtonGroup();
520 public FurtherActionPanel(AnnotationColumnChooser aColChooser)
522 this.aColChooser = aColChooser;
523 JvSwingUtils.jvInitComponent(selectOption, "action.select");
524 selectOption.addActionListener(new ActionListener()
527 public void actionPerformed(ActionEvent actionEvent)
529 selectRadioAction(actionEvent);
533 JvSwingUtils.jvInitComponent(hideOption, "action.hide");
534 hideOption.addActionListener(new ActionListener()
537 public void actionPerformed(ActionEvent actionEvent)
539 hideRadioAction(actionEvent);
543 optionsGroup.add(selectOption);
544 optionsGroup.add(hideOption);
545 optionsGroup.setSelected(selectOption.getModel(), true);
547 JvSwingUtils.jvInitComponent(this);
550 this.add(selectOption);
551 this.add(hideOption);
554 public void selectRadioAction(ActionEvent actionEvent)
556 aColChooser.setCurrentFutherActionPanel(this);
557 aColChooser.select_action(actionEvent);
560 public void hideRadioAction(ActionEvent actionEvent)
562 aColChooser.setCurrentFutherActionPanel(this);
563 aColChooser.hide_action(actionEvent);
566 public void syncState()
568 if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
570 this.optionsGroup.setSelected(this.hideOption.getModel(), true);
574 this.optionsGroup.setSelected(this.selectOption.getModel(), true);
579 public class StructureFilterPanel extends JPanel
581 private AnnotationColumnChooser aColChooser;
583 private JCheckBox alphaHelix = new JCheckBox();
585 private JCheckBox betaStrand = new JCheckBox();
587 private JCheckBox turn = new JCheckBox();
589 private JCheckBox all = new JCheckBox();
591 public StructureFilterPanel(AnnotationColumnChooser aColChooser)
593 this.aColChooser = aColChooser;
595 JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
596 alphaHelix.addActionListener(new ActionListener()
599 public void actionPerformed(ActionEvent actionEvent)
601 alphaHelix_actionPerformed();
605 JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
606 betaStrand.addActionListener(new ActionListener()
609 public void actionPerformed(ActionEvent actionEvent)
611 betaStrand_actionPerformed();
615 JvSwingUtils.jvInitComponent(turn, "label.turn");
616 turn.addActionListener(new ActionListener()
619 public void actionPerformed(ActionEvent actionEvent)
621 turn_actionPerformed();
625 JvSwingUtils.jvInitComponent(all, "label.select_all");
626 all.addActionListener(new ActionListener()
629 public void actionPerformed(ActionEvent actionEvent)
631 all_actionPerformed();
635 this.setBorder(new TitledBorder(MessageManager
636 .getString("label.structures_filter")));
637 JvSwingUtils.jvInitComponent(this);
640 this.add(alphaHelix);
641 this.add(betaStrand);
645 public void alphaHelix_actionPerformed()
647 updateSelectAllState();
648 aColChooser.setCurrentStructureFilterPanel(this);
649 aColChooser.updateView();
652 public void betaStrand_actionPerformed()
654 updateSelectAllState();
655 aColChooser.setCurrentStructureFilterPanel(this);
656 aColChooser.updateView();
659 public void turn_actionPerformed()
661 updateSelectAllState();
662 aColChooser.setCurrentStructureFilterPanel(this);
663 aColChooser.updateView();
666 public void all_actionPerformed()
668 if (all.isSelected())
670 alphaHelix.setSelected(true);
671 betaStrand.setSelected(true);
672 turn.setSelected(true);
676 alphaHelix.setSelected(false);
677 betaStrand.setSelected(false);
678 turn.setSelected(false);
680 aColChooser.setCurrentStructureFilterPanel(this);
681 aColChooser.updateView();
684 public void updateSelectAllState()
686 if (alphaHelix.isSelected() && betaStrand.isSelected()
687 && turn.isSelected())
689 all.setSelected(true);
693 all.setSelected(false);
697 public void syncState()
699 StructureFilterPanel sfp = aColChooser
700 .getCurrentStructureFilterPanel();
703 alphaHelix.setSelected(sfp.alphaHelix.isSelected());
704 betaStrand.setSelected(sfp.betaStrand.isSelected());
705 turn.setSelected(sfp.turn.isSelected());
706 if (sfp.all.isSelected())
708 all.setSelected(true);
709 alphaHelix.setSelected(true);
710 betaStrand.setSelected(true);
711 turn.setSelected(true);
718 public class SearchPanel extends JPanel
720 private AnnotationColumnChooser aColChooser;
722 private JCheckBox displayName = new JCheckBox();
724 private JCheckBox description = new JCheckBox();
726 private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
728 public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
729 FILTER_BY_ANN_CACHE_KEY);
731 public SearchPanel(AnnotationColumnChooser aColChooser)
734 this.aColChooser = aColChooser;
735 JvSwingUtils.jvInitComponent(this);
736 this.setBorder(new TitledBorder(MessageManager
737 .getString("label.search_filter")));
739 searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
740 searchBox.setToolTipText(MessageManager
741 .getString("info.enter_search_text_here"));
742 searchBox.getEditor().getEditorComponent()
743 .addKeyListener(new java.awt.event.KeyAdapter()
746 public void keyPressed(KeyEvent e)
748 if (e.getKeyCode() == KeyEvent.VK_ENTER)
751 searchStringAction();
758 JvSwingUtils.jvInitComponent(displayName, "label.label");
759 displayName.addActionListener(new ActionListener()
762 public void actionPerformed(ActionEvent actionEvent)
764 displayNameCheckboxAction();
768 JvSwingUtils.jvInitComponent(description, "label.description");
769 description.addActionListener(new ActionListener()
772 public void actionPerformed(ActionEvent actionEvent)
774 discriptionCheckboxAction();
780 this.add(displayName);
781 this.add(description);
784 public void displayNameCheckboxAction()
786 aColChooser.setCurrentSearchPanel(this);
787 aColChooser.updateView();
790 public void discriptionCheckboxAction()
792 aColChooser.setCurrentSearchPanel(this);
793 aColChooser.updateView();
796 public void searchStringAction()
798 aColChooser.setCurrentSearchPanel(this);
799 aColChooser.updateView();
800 updateSearchPanelToolTips();
801 searchBox.updateCache();
804 public void syncState()
806 SearchPanel sp = aColChooser.getCurrentSearchPanel();
809 description.setEnabled(sp.description.isEnabled());
810 description.setSelected(sp.description.isSelected());
812 displayName.setEnabled(sp.displayName.isEnabled());
813 displayName.setSelected(sp.displayName.isSelected());
815 searchBox.setSelectedItem(sp.searchBox.getUserInput());
817 updateSearchPanelToolTips();
820 public void updateSearchPanelToolTips()
822 String defaultTtip = MessageManager
823 .getString("info.enter_search_text_to_enable");
824 String labelTtip = MessageManager.formatMessage(
825 "info.search_in_annotation_label", annotations
826 .getSelectedItem().toString());
827 String descTtip = MessageManager.formatMessage(
828 "info.search_in_annotation_description", annotations
829 .getSelectedItem().toString());
830 displayName.setToolTipText(displayName.isEnabled() ? labelTtip
832 description.setToolTipText(description.isEnabled() ? descTtip
838 public void ok_actionPerformed()
841 super.ok_actionPerformed();
845 public void cancel_actionPerformed()
848 super.cancel_actionPerformed();
851 private void saveCache()
853 gSearchPanel.searchBox.persistCache();
854 ngSearchPanel.searchBox.persistCache();
855 gSearchPanel.searchBox.updateCache();
856 ngSearchPanel.searchBox.updateCache();