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.
21 package jalview.appletgui;
23 import jalview.datamodel.AlignmentAnnotation;
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.Checkbox;
32 import java.awt.Choice;
33 import java.awt.Color;
34 import java.awt.Dimension;
35 import java.awt.Frame;
36 import java.awt.Panel;
37 import java.awt.TextField;
38 import java.awt.event.ActionEvent;
39 import java.awt.event.ActionListener;
40 import java.awt.event.AdjustmentEvent;
41 import java.awt.event.AdjustmentListener;
42 import java.awt.event.ItemEvent;
43 import java.awt.event.ItemListener;
44 import java.awt.event.MouseAdapter;
45 import java.awt.event.MouseEvent;
46 import java.awt.event.MouseListener;
47 import java.awt.event.TextEvent;
48 import java.awt.event.TextListener;
49 import java.util.ArrayList;
50 import java.util.Vector;
52 //import javax.swing.JPanel;
54 //import net.miginfocom.swing.MigLayout;
56 public class AnnotationColumnChooser extends AnnotationRowFilter implements
57 ActionListener, AdjustmentListener, ItemListener, MouseListener
60 private Choice annotations = new Choice();
62 private Panel actionPanel = new Panel();
64 private TitledPanel thresholdPanel = new TitledPanel();
66 private Panel switchableViewsPanel = new Panel(new CardLayout());
68 private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
71 private Panel noGraphFilterView = new Panel();
73 private Panel graphFilterView = new Panel();
75 private Panel annotationComboBoxPanel = new Panel();
77 private BorderLayout borderLayout1 = new BorderLayout();
79 private BorderLayout gBorderLayout = new BorderLayout();
81 private BorderLayout ngBorderLayout = new BorderLayout();
83 private Choice threshold = new Choice();
85 private StructureFilterPanel gStructureFilterPanel;
87 private StructureFilterPanel ngStructureFilterPanel;
89 private StructureFilterPanel currentStructureFilterPanel;
91 private SearchPanel currentSearchPanel;
93 private SearchPanel gSearchPanel;
95 private SearchPanel ngSearchPanel;
97 private FurtherActionPanel currentFurtherActionPanel;
99 private FurtherActionPanel gFurtherActionPanel;
101 private FurtherActionPanel ngFurtherActionPanel;
103 public static final int ACTION_OPTION_SELECT = 1;
105 public static int ACTION_OPTION_HIDE = 2;
107 public static String NO_GRAPH_VIEW = "0";
109 public static String GRAPH_VIEW = "1";
111 private int actionOption = ACTION_OPTION_SELECT;
113 private HiddenColumns oldHiddenColumns;
115 public AnnotationColumnChooser()
120 } catch (Exception ex)
122 ex.printStackTrace();
126 public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
131 jalview.bin.JalviewLite.addFrame(frame,
132 MessageManager.getString("label.select_by_annotation"), 520,
135 slider.addAdjustmentListener(this);
136 slider.addMouseListener(this);
138 AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
143 setOldHiddenColumns(av.getAlignment().getHiddenColumns());
145 Vector<String> list = new Vector<>();
147 for (int i = 0; i < anns.length; i++)
149 String label = anns[i].label;
150 if (anns[i].sequenceRef != null)
152 label = label + "_" + anns[i].sequenceRef.getName();
154 if (!list.contains(label))
156 list.addElement(label);
160 list.addElement(label + "_" + (index++));
164 for (int i = 0; i < list.size(); i++)
166 annotations.addItem(list.elementAt(i).toString());
169 populateThresholdComboBox(threshold);
170 AnnotationColumnChooser lastChooser = av
171 .getAnnotationColumnSelectionState();
172 // restore Object state from the previous session if one exists
173 if (lastChooser != null)
175 currentSearchPanel = lastChooser.getCurrentSearchPanel();
176 currentStructureFilterPanel = lastChooser
177 .getCurrentStructureFilterPanel();
178 annotations.select(lastChooser.getAnnotations().getSelectedIndex());
179 threshold.select(lastChooser.getThreshold().getSelectedIndex());
180 actionOption = lastChooser.getActionOption();
181 percentThreshold.setState(lastChooser.percentThreshold.getState());
187 } catch (Exception ex)
197 private void jbInit() throws Exception
199 ok.setLabel(MessageManager.getString("action.ok"));
201 cancel.setLabel(MessageManager.getString("action.cancel"));
203 thresholdValue.setEnabled(false);
204 thresholdValue.setColumns(7);
205 thresholdValue.setCaretPosition(0);
207 ok.addActionListener(this);
208 cancel.addActionListener(this);
209 annotations.addItemListener(this);
210 thresholdValue.addActionListener(this);
211 threshold.addItemListener(this);
213 slider.setBackground(Color.white);
214 slider.setEnabled(false);
215 slider.setPreferredSize(new Dimension(100, 32));
217 thresholdPanel.setBackground(Color.white);
218 // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
219 // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
221 percentThreshold.setLabel("As percentage");
222 percentThreshold.addItemListener(this);
224 actionPanel.setBackground(Color.white);
225 // actionPanel.setFont(JvSwingUtils.getLabelFont());
227 graphFilterView.setLayout(gBorderLayout);
228 graphFilterView.setBackground(Color.white);
230 noGraphFilterView.setLayout(ngBorderLayout);
231 noGraphFilterView.setBackground(Color.white);
233 annotationComboBoxPanel.setBackground(Color.white);
234 // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
236 gSearchPanel = new SearchPanel(this);
237 ngSearchPanel = new SearchPanel(this);
238 gFurtherActionPanel = new FurtherActionPanel(this);
239 ngFurtherActionPanel = new FurtherActionPanel(this);
240 gStructureFilterPanel = new StructureFilterPanel(this);
241 ngStructureFilterPanel = new StructureFilterPanel(this);
243 thresholdPanel.setTitle("Threshold Filter");
244 thresholdPanel.add(getThreshold());
245 thresholdPanel.add(slider);
246 thresholdPanel.add(thresholdValue);
247 thresholdPanel.add(percentThreshold);
250 actionPanel.add(cancel);
252 Panel staticPanel = new Panel();
253 staticPanel.setLayout(new BorderLayout());
254 staticPanel.setBackground(Color.white);
256 staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
257 staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
259 graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
260 graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
261 graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
263 noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
264 noGraphFilterView.add(ngStructureFilterPanel,
265 java.awt.BorderLayout.CENTER);
266 noGraphFilterView.add(ngFurtherActionPanel,
267 java.awt.BorderLayout.CENTER);
269 annotationComboBoxPanel.add(getAnnotations());
270 switchableViewsPanel.add(noGraphFilterView,
271 AnnotationColumnChooser.NO_GRAPH_VIEW);
272 switchableViewsPanel.add(graphFilterView,
273 AnnotationColumnChooser.GRAPH_VIEW);
275 this.setLayout(borderLayout1);
276 this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
277 this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
278 this.add(actionPanel, java.awt.BorderLayout.SOUTH);
280 selectedAnnotationChanged();
285 @SuppressWarnings("unchecked")
288 if (this.getOldHiddenColumns() != null)
290 av.getColumnSelection().clear();
292 if (av.getAnnotationColumnSelectionState() != null)
294 HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
295 .getOldHiddenColumns();
296 if (oldHidden != null)
298 ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
299 for (int[] positions : regions)
301 av.hideColumns(positions[0], positions[1]);
304 // TODO not clear why we need to hide all the columns (above) if we are
305 // going to copy the hidden columns over wholesale anyway
306 av.getAlignment().setHiddenColumns(oldHidden);
309 ap.paintAlignment(true);
315 public void adjustmentValueChanged(AdjustmentEvent evt)
319 setThresholdValueText();
320 valueChanged(!sliderDragging);
324 protected void addSliderMouseListeners()
327 slider.addMouseListener(new MouseAdapter()
330 public void mousePressed(MouseEvent e)
332 sliderDragging = true;
333 super.mousePressed(e);
337 public void mouseDragged(MouseEvent e)
339 sliderDragging = true;
340 super.mouseDragged(e);
344 public void mouseReleased(MouseEvent evt)
348 sliderDragging = false;
351 ap.paintAlignment(true);
357 public void valueChanged(boolean updateAllAnnotation)
359 if (slider.isEnabled())
361 getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
363 ap.paintAlignment(false);
367 public Choice getThreshold()
372 public void setThreshold(Choice threshold)
374 this.threshold = threshold;
377 public Choice getAnnotations()
382 public void setAnnotations(Choice annotations)
384 this.annotations = annotations;
388 public void updateView()
390 // Check if combobox is still adjusting
396 AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
397 setCurrentAnnotation(av.getAlignment()
398 .getAlignmentAnnotation()[getAnnotations().getSelectedIndex()]);
400 int selectedThresholdItem = getSelectedThresholdItem(
401 getThreshold().getSelectedIndex());
403 slider.setEnabled(true);
404 thresholdValue.setEnabled(true);
405 percentThreshold.setEnabled(true);
407 if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
409 slider.setEnabled(false);
410 thresholdValue.setEnabled(false);
411 thresholdValue.setText("");
412 percentThreshold.setEnabled(false);
413 // build filter params
415 else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
417 if (getCurrentAnnotation().threshold == null)
419 getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
420 (getCurrentAnnotation().graphMax
421 - getCurrentAnnotation().graphMin) / 2f,
422 "Threshold", Color.black));
426 // float range = getCurrentAnnotation().graphMax * 1000
427 // - getCurrentAnnotation().graphMin * 1000;
429 slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
430 slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
432 (int) (getCurrentAnnotation().threshold.value * 1000));
433 setThresholdValueText();
434 // slider.setMajorTickSpacing((int) (range / 10f));
435 slider.setEnabled(true);
436 thresholdValue.setEnabled(true);
437 percentThreshold.setEnabled(true);
440 // build filter params
441 filterParams.setThresholdType(
442 AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
443 if (getCurrentAnnotation().isQuantitative())
446 .setThresholdValue(getCurrentAnnotation().threshold.value);
448 if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
450 filterParams.setThresholdType(
451 AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
453 else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
455 filterParams.setThresholdType(
456 AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
461 if (currentStructureFilterPanel != null)
463 if (currentStructureFilterPanel.alphaHelix.getState())
465 filterParams.setFilterAlphaHelix(true);
467 if (currentStructureFilterPanel.betaStrand.getState())
469 filterParams.setFilterBetaSheet(true);
471 if (currentStructureFilterPanel.turn.getState())
473 filterParams.setFilterTurn(true);
477 if (currentSearchPanel != null)
480 if (!currentSearchPanel.searchBox.getText().isEmpty())
482 currentSearchPanel.description.setEnabled(true);
483 currentSearchPanel.displayName.setEnabled(true);
484 filterParams.setRegexString(currentSearchPanel.searchBox.getText());
485 if (currentSearchPanel.displayName.getState())
487 filterParams.addRegexSearchField(
488 AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
490 if (currentSearchPanel.description.getState())
492 filterParams.addRegexSearchField(
493 AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
498 currentSearchPanel.description.setEnabled(false);
499 currentSearchPanel.displayName.setEnabled(false);
503 // show hidden columns here, before changing the column selection in
504 // filterAnnotations, because showing hidden columns has the side effect of
505 // adding them to the selection
506 av.showAllHiddenColumns();
507 av.getColumnSelection().filterAnnotations(
508 getCurrentAnnotation().annotations, filterParams);
510 if (getActionOption() == ACTION_OPTION_HIDE)
512 av.hideSelectedColumns();
516 av.setAnnotationColumnSelectionState(this);
518 ap.paintAlignment(true);
521 public HiddenColumns getOldHiddenColumns()
523 return oldHiddenColumns;
526 public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
528 if (currentHiddenColumns != null)
530 this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
534 public FurtherActionPanel getCurrentFutherActionPanel()
536 return currentFurtherActionPanel;
539 public void setCurrentFutherActionPanel(
540 FurtherActionPanel currentFutherActionPanel)
542 this.currentFurtherActionPanel = currentFutherActionPanel;
545 public SearchPanel getCurrentSearchPanel()
547 return currentSearchPanel;
550 public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
552 this.currentSearchPanel = currentSearchPanel;
555 public int getActionOption()
560 public void setActionOption(int actionOption)
562 this.actionOption = actionOption;
565 public StructureFilterPanel getCurrentStructureFilterPanel()
567 return currentStructureFilterPanel;
570 public void setCurrentStructureFilterPanel(
571 StructureFilterPanel currentStructureFilterPanel)
573 this.currentStructureFilterPanel = currentStructureFilterPanel;
577 public void itemStateChanged(ItemEvent e)
579 if (e.getSource() == annotations)
581 selectedAnnotationChanged();
583 else if (e.getSource() == threshold)
585 threshold_actionPerformed(null);
587 else if (e.getSource() == percentThreshold)
591 percentageValue_actionPerformed();
597 public void selectedAnnotationChanged()
599 String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
600 if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
601 .getSelectedIndex()].isQuantitative())
603 currentView = AnnotationColumnChooser.GRAPH_VIEW;
606 gSearchPanel.syncState();
607 gFurtherActionPanel.syncState();
608 gStructureFilterPanel.syncState();
610 ngSearchPanel.syncState();
611 ngFurtherActionPanel.syncState();
612 ngStructureFilterPanel.syncState();
614 switchableViewsLayout.show(switchableViewsPanel, currentView);
618 public class FurtherActionPanel extends Panel implements ItemListener
620 private AnnotationColumnChooser aColChooser;
622 private Choice furtherAction = new Choice();
624 public FurtherActionPanel(AnnotationColumnChooser aColChooser)
626 this.aColChooser = aColChooser;
627 furtherAction.addItem("Select");
628 furtherAction.addItem("Hide");
629 furtherAction.addItemListener(this);
632 // this.setTitle("Filter Actions");
633 // this.setFont(JvSwingUtils.getLabelFont());
635 this.add(furtherAction);
638 public void syncState()
641 .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
643 furtherAction.select("Hide");
647 furtherAction.select("Select");
652 public void itemStateChanged(ItemEvent e)
654 aColChooser.setCurrentFutherActionPanel(this);
655 if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
657 setActionOption(ACTION_OPTION_SELECT);
662 setActionOption(ACTION_OPTION_HIDE);
669 public class StructureFilterPanel extends TitledPanel
670 implements ItemListener
672 private AnnotationColumnChooser aColChooser;
674 private Checkbox alphaHelix = new Checkbox();
676 private Checkbox betaStrand = new Checkbox();
678 private Checkbox turn = new Checkbox();
680 private Checkbox all = new Checkbox();
682 public StructureFilterPanel(AnnotationColumnChooser aColChooser)
684 this.aColChooser = aColChooser;
686 alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
687 alphaHelix.setBackground(Color.white);
689 alphaHelix.addItemListener(this);
691 betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
692 betaStrand.setBackground(Color.white);
693 betaStrand.addItemListener(this);
695 turn.setLabel(MessageManager.getString("label.turn"));
696 turn.setBackground(Color.white);
697 turn.addItemListener(this);
699 all.setLabel(MessageManager.getString("label.select_all"));
700 all.setBackground(Color.white);
701 all.addItemListener(this);
703 this.setBackground(Color.white);
704 this.setTitle("Structure Filter");
705 // this.setFont(JvSwingUtils.getLabelFont());
708 this.add(alphaHelix);
709 this.add(betaStrand);
713 public void alphaHelix_actionPerformed()
715 updateSelectAllState();
716 aColChooser.setCurrentStructureFilterPanel(this);
717 aColChooser.updateView();
720 public void betaStrand_actionPerformed()
722 updateSelectAllState();
723 aColChooser.setCurrentStructureFilterPanel(this);
724 aColChooser.updateView();
727 public void turn_actionPerformed()
729 updateSelectAllState();
730 aColChooser.setCurrentStructureFilterPanel(this);
731 aColChooser.updateView();
734 public void all_actionPerformed()
738 alphaHelix.setState(true);
739 betaStrand.setState(true);
744 alphaHelix.setState(false);
745 betaStrand.setState(false);
746 turn.setState(false);
748 aColChooser.setCurrentStructureFilterPanel(this);
749 aColChooser.updateView();
752 public void updateSelectAllState()
754 if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
764 public void syncState()
766 StructureFilterPanel sfp = aColChooser
767 .getCurrentStructureFilterPanel();
770 alphaHelix.setState(sfp.alphaHelix.getState());
771 betaStrand.setState(sfp.betaStrand.getState());
772 turn.setState(sfp.turn.getState());
773 if (sfp.all.getState())
776 alphaHelix.setState(true);
777 betaStrand.setState(true);
785 public void itemStateChanged(ItemEvent e)
787 if (e.getSource() == alphaHelix)
789 alphaHelix_actionPerformed();
791 else if (e.getSource() == betaStrand)
793 betaStrand_actionPerformed();
795 else if (e.getSource() == turn)
797 turn_actionPerformed();
799 else if (e.getSource() == all)
801 all_actionPerformed();
806 public class SearchPanel extends TitledPanel implements ItemListener
808 private AnnotationColumnChooser aColChooser;
810 private Checkbox displayName = new Checkbox();
812 private Checkbox description = new Checkbox();
814 private TextField searchBox = new TextField(10);
816 public SearchPanel(AnnotationColumnChooser aColChooser)
819 this.aColChooser = aColChooser;
820 searchBox.addTextListener(new TextListener()
824 public void textValueChanged(TextEvent e)
826 searchStringAction();
832 displayName.setLabel(MessageManager.getString("label.label"));
833 displayName.setEnabled(false);
834 displayName.addItemListener(this);
836 description.setLabel(MessageManager.getString("label.description"));
837 description.setEnabled(false);
838 description.addItemListener(this);
839 this.setTitle("Search Filter");
840 // this.setFont(JvSwingUtils.getLabelFont());
844 this.add(displayName);
845 this.add(description);
848 public void displayNameCheckboxAction()
850 aColChooser.setCurrentSearchPanel(this);
851 aColChooser.updateView();
854 public void discriptionCheckboxAction()
856 aColChooser.setCurrentSearchPanel(this);
857 aColChooser.updateView();
860 public void searchStringAction()
862 aColChooser.setCurrentSearchPanel(this);
863 aColChooser.updateView();
866 public void syncState()
868 SearchPanel sp = aColChooser.getCurrentSearchPanel();
871 description.setEnabled(sp.description.isEnabled());
872 description.setState(sp.description.getState());
874 displayName.setEnabled(sp.displayName.isEnabled());
875 displayName.setState(sp.displayName.getState());
877 searchBox.setText(sp.searchBox.getText());
882 public void itemStateChanged(ItemEvent e)
884 if (e.getSource() == displayName)
886 displayNameCheckboxAction();
888 else if (e.getSource() == description)
890 discriptionCheckboxAction();
897 public void actionPerformed(ActionEvent evt)
900 if (evt.getSource() == ok)
902 ok_actionPerformed(null);
904 else if (evt.getSource() == cancel)
906 cancel_actionPerformed(null);
908 else if (evt.getSource() == thresholdValue)
910 thresholdValue_actionPerformed(null);
919 public void mouseClicked(MouseEvent e)
921 // TODO Auto-generated method stub
926 public void mousePressed(MouseEvent e)
928 if (e.getSource() == slider)
936 public void mouseReleased(MouseEvent e)
938 if (e.getSource() == slider)
945 public void mouseEntered(MouseEvent e)
947 if (e.getSource() == slider)
954 public void mouseExited(MouseEvent e)
956 if (e.getSource() == slider)