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.
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.FeatureColourI;
25 import jalview.datamodel.GraphLine;
26 import jalview.datamodel.features.FeatureAttributes;
27 import jalview.datamodel.features.FeatureAttributes.Datatype;
28 import jalview.datamodel.features.FeatureMatcher;
29 import jalview.datamodel.features.FeatureMatcherI;
30 import jalview.datamodel.features.FeatureMatcherSet;
31 import jalview.datamodel.features.FeatureMatcherSetI;
32 import jalview.schemes.FeatureColour;
33 import jalview.util.ColorUtils;
34 import jalview.util.MessageManager;
35 import jalview.util.matcher.Condition;
37 import java.awt.BorderLayout;
38 import java.awt.Color;
39 import java.awt.Dimension;
40 import java.awt.FlowLayout;
41 import java.awt.GridLayout;
42 import java.awt.event.ActionEvent;
43 import java.awt.event.ActionListener;
44 import java.awt.event.FocusAdapter;
45 import java.awt.event.FocusEvent;
46 import java.awt.event.ItemEvent;
47 import java.awt.event.ItemListener;
48 import java.awt.event.MouseAdapter;
49 import java.awt.event.MouseEvent;
50 import java.text.DecimalFormat;
51 import java.util.ArrayList;
52 import java.util.List;
54 import javax.swing.BorderFactory;
55 import javax.swing.BoxLayout;
56 import javax.swing.ButtonGroup;
57 import javax.swing.JButton;
58 import javax.swing.JCheckBox;
59 import javax.swing.JColorChooser;
60 import javax.swing.JComboBox;
61 import javax.swing.JLabel;
62 import javax.swing.JPanel;
63 import javax.swing.JRadioButton;
64 import javax.swing.JSlider;
65 import javax.swing.JTabbedPane;
66 import javax.swing.JTextField;
67 import javax.swing.border.LineBorder;
68 import javax.swing.event.ChangeEvent;
69 import javax.swing.event.ChangeListener;
72 * A dialog where the user can configure colour scheme, and any filters, for one
75 * (Was FeatureColourChooser prior to Jalview 1.11, renamed with the addition of
78 public class FeatureTypeSettings extends JalviewDialog
80 private final static String LABEL_18N = MessageManager
81 .getString("label.label");
83 private final static String SCORE_18N = MessageManager
84 .getString("label.score");
86 private static final int RADIO_WIDTH = 130;
88 private static final String COLON = ":";
90 private static final int MAX_TOOLTIP_LENGTH = 50;
92 private static final int NO_COLOUR_OPTION = 0;
94 private static final int MIN_COLOUR_OPTION = 1;
96 private static final int MAX_COLOUR_OPTION = 2;
98 private static final int ABOVE_THRESHOLD_OPTION = 1;
100 private static final int BELOW_THRESHOLD_OPTION = 2;
102 private static final DecimalFormat DECFMT_2_2 = new DecimalFormat(
106 * FeatureRenderer holds colour scheme and filters for feature types
108 private final FeatureRenderer fr; // todo refactor to allow interface type here
111 * the view panel to update when settings change
113 private final AlignmentViewPanel ap;
115 private final String featureType;
118 * the colour and filters to reset to on Cancel
120 private final FeatureColourI originalColour;
122 private final FeatureMatcherSetI originalFilter;
125 * set flag to true when setting values programmatically,
126 * to avoid invocation of action handlers
128 private boolean adjusting = false;
131 * minimum of the value range for graduated colour
132 * (may be for feature score or for a numeric attribute)
137 * maximum of the value range for graduated colour
142 * scale factor for conversion between absolute min-max and slider
144 private float scaleFactor;
147 * radio button group, to select what to colour by:
148 * simple colour, by category (text), or graduated
150 private JRadioButton simpleColour = new JRadioButton();
152 private JRadioButton byCategory = new JRadioButton();
154 private JRadioButton graduatedColour = new JRadioButton();
156 private JPanel singleColour = new JPanel();
158 private JPanel minColour = new JPanel();
160 private JPanel maxColour = new JPanel();
162 private JComboBox<String> threshold = new JComboBox<>();
164 private JSlider slider = new JSlider();
166 private JTextField thresholdValue = new JTextField(20);
168 private JCheckBox thresholdIsMin = new JCheckBox();
170 private GraphLine threshline;
172 private ActionListener featureSettings = null;
174 private ActionListener changeColourAction;
177 * choice of option for 'colour for no value'
179 private JComboBox<String> noValueCombo;
182 * choice of what to colour by text (Label or attribute)
184 private JComboBox<String> colourByTextCombo;
187 * choice of what to colour by range (Score or attribute)
189 private JComboBox<String> colourByRangeCombo;
191 private JRadioButton andFilters;
193 private JRadioButton orFilters;
196 * filters for the currently selected feature type
198 private List<FeatureMatcherI> filters;
200 // set white normally, black to debug layout
201 private Color debugBorderColour = Color.white;
203 private JPanel chooseFiltersPanel;
205 private JTabbedPane tabbedPane;
213 public FeatureTypeSettings(FeatureRenderer frender, String theType)
215 this(frender, false, theType);
219 * Constructor, with option to make a blocking dialog (has to complete in the
220 * AWT event queue thread). Currently this option is always set to false.
226 FeatureTypeSettings(FeatureRenderer frender, boolean blocking,
230 this.featureType = theType;
232 originalFilter = fr.getFeatureFilter(theType);
233 originalColour = fr.getFeatureColours().get(theType);
240 } catch (Exception ex)
242 ex.printStackTrace();
252 colourChanged(false);
254 String title = MessageManager
255 .formatMessage("label.display_settings_for", new String[]
257 initDialogFrame(this, true, blocking, title, 600, 360);
263 * Configures the widgets on the Colours tab according to the current feature
266 private void updateColoursTab()
268 FeatureColourI fc = fr.getFeatureColours().get(featureType);
271 * suppress action handling while updating values programmatically
279 if (fc.isSimpleColour())
281 simpleColour.setSelected(true);
282 singleColour.setBackground(fc.getColour());
283 singleColour.setForeground(fc.getColour());
287 * colour by text (Label or attribute text)
289 if (fc.isColourByLabel())
291 byCategory.setSelected(true);
292 colourByTextCombo.setEnabled(colourByTextCombo.getItemCount() > 1);
293 if (fc.isColourByAttribute())
295 String[] attributeName = fc.getAttributeName();
296 colourByTextCombo.setSelectedItem(
297 FeatureMatcher.toAttributeDisplayName(attributeName));
301 colourByTextCombo.setSelectedItem(LABEL_18N);
306 colourByTextCombo.setEnabled(false);
309 if (!fc.isGraduatedColour())
311 colourByRangeCombo.setEnabled(false);
312 minColour.setEnabled(false);
313 maxColour.setEnabled(false);
314 noValueCombo.setEnabled(false);
315 threshold.setEnabled(false);
316 slider.setEnabled(false);
317 thresholdValue.setEnabled(false);
318 thresholdIsMin.setEnabled(false);
323 * Graduated colour, by score or attribute value range
325 graduatedColour.setSelected(true);
326 updateColourMinMax(); // ensure min, max are set
327 colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
328 minColour.setEnabled(true);
329 maxColour.setEnabled(true);
330 noValueCombo.setEnabled(true);
331 threshold.setEnabled(true);
332 minColour.setBackground(fc.getMinColour());
333 maxColour.setBackground(fc.getMaxColour());
335 if (fc.isColourByAttribute())
337 String[] attributeName = fc.getAttributeName();
338 colourByRangeCombo.setSelectedItem(
339 FeatureMatcher.toAttributeDisplayName(attributeName));
343 colourByRangeCombo.setSelectedItem(SCORE_18N);
345 Color noColour = fc.getNoColour();
346 if (noColour == null)
348 noValueCombo.setSelectedIndex(NO_COLOUR_OPTION);
350 else if (noColour.equals(fc.getMinColour()))
352 noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION);
354 else if (noColour.equals(fc.getMaxColour()))
356 noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION);
360 * update min-max scaling if there is a range to work with,
361 * else disable the widgets (this shouldn't happen if only
362 * valid options are offered in the combo box)
364 scaleFactor = (max == min) ? 1f : 100f / (max - min);
365 float range = (max - min) * scaleFactor;
366 slider.setMinimum((int) (min * scaleFactor));
367 slider.setMaximum((int) (max * scaleFactor));
368 slider.setMajorTickSpacing((int) (range / 10f));
370 threshline = new GraphLine((max - min) / 2f, "Threshold",
372 threshline.value = fc.getThreshold();
374 if (fc.hasThreshold())
376 threshold.setSelectedIndex(
377 fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
378 : BELOW_THRESHOLD_OPTION);
379 slider.setEnabled(true);
380 slider.setValue((int) (fc.getThreshold() * scaleFactor));
381 thresholdValue.setText(String.valueOf(getRoundedSliderValue()));
382 thresholdValue.setEnabled(true);
383 thresholdIsMin.setEnabled(true);
387 slider.setEnabled(false);
388 thresholdValue.setEnabled(false);
389 thresholdIsMin.setEnabled(false);
391 thresholdIsMin.setSelected(!fc.isAutoScaled());
399 * Configures the initial layout
401 private void initialise()
403 this.setLayout(new BorderLayout());
404 tabbedPane = new JTabbedPane();
405 this.add(tabbedPane, BorderLayout.CENTER);
408 * an ActionListener that applies colour changes
410 changeColourAction = new ActionListener()
413 public void actionPerformed(ActionEvent e)
420 * first tab: colour options
422 JPanel coloursPanel = initialiseColoursPanel();
423 tabbedPane.addTab(MessageManager.getString("action.colour"),
427 * second tab: filter options
429 JPanel filtersPanel = initialiseFiltersPanel();
430 tabbedPane.addTab(MessageManager.getString("label.filters"),
433 JPanel okCancelPanel = initialiseOkCancelPanel();
435 this.add(okCancelPanel, BorderLayout.SOUTH);
439 * Updates the min-max range if Colour By selected item is Score, or an
440 * attribute, with a min-max range
442 protected void updateColourMinMax()
444 if (!graduatedColour.isSelected())
449 String colourBy = (String) colourByRangeCombo.getSelectedItem();
450 float[] minMax = getMinMax(colourBy);
460 * Retrieves the min-max range:
462 * <li>of feature score, if colour or filter is by Score</li>
463 * <li>else of the selected attribute</li>
469 private float[] getMinMax(String attName)
471 float[] minMax = null;
472 if (SCORE_18N.equals(attName))
474 minMax = fr.getMinMax().get(featureType)[0];
478 // colour by attribute range
479 minMax = FeatureAttributes.getInstance().getMinMax(featureType,
480 FeatureMatcher.fromAttributeDisplayName(attName));
486 * Lay out fields for graduated colour (by score or attribute value)
490 private JPanel initialiseGraduatedColourPanel()
492 JPanel graduatedColourPanel = new JPanel();
493 graduatedColourPanel.setLayout(
494 new BoxLayout(graduatedColourPanel, BoxLayout.Y_AXIS));
495 JvSwingUtils.createTitledBorder(graduatedColourPanel,
496 MessageManager.getString("label.graduated_colour"), true);
497 graduatedColourPanel.setBackground(Color.white);
500 * first row: graduated colour radio button, score/attribute drop-down
502 JPanel graduatedChoicePanel = new JPanel(
503 new FlowLayout(FlowLayout.LEFT));
504 graduatedChoicePanel.setBackground(Color.white);
505 graduatedColour = new JRadioButton(
506 MessageManager.getString("label.by_range_of") + COLON);
507 graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
508 graduatedColour.addItemListener(new ItemListener()
511 public void itemStateChanged(ItemEvent e)
513 if (graduatedColour.isSelected())
519 graduatedChoicePanel.add(graduatedColour);
521 List<String[]> attNames = FeatureAttributes.getInstance()
522 .getAttributes(featureType);
523 colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
524 colourByRangeCombo.addItemListener(new ItemListener()
527 public void itemStateChanged(ItemEvent e)
534 * disable graduated colour option if no range found
536 graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
538 graduatedChoicePanel.add(colourByRangeCombo);
539 graduatedColourPanel.add(graduatedChoicePanel);
542 * second row - min/max/no colours
544 JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
545 colourRangePanel.setBackground(Color.white);
546 graduatedColourPanel.add(colourRangePanel);
548 minColour.setFont(JvSwingUtils.getLabelFont());
549 minColour.setBorder(BorderFactory.createLineBorder(Color.black));
550 minColour.setPreferredSize(new Dimension(40, 20));
551 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
552 minColour.addMouseListener(new MouseAdapter()
555 public void mousePressed(MouseEvent e)
557 if (minColour.isEnabled())
559 showColourChooser(minColour, "label.select_colour_minimum_value");
564 maxColour.setFont(JvSwingUtils.getLabelFont());
565 maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
566 maxColour.setPreferredSize(new Dimension(40, 20));
567 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
568 maxColour.addMouseListener(new MouseAdapter()
571 public void mousePressed(MouseEvent e)
573 if (maxColour.isEnabled())
575 showColourChooser(maxColour, "label.select_colour_maximum_value");
579 maxColour.setBorder(new LineBorder(Color.black));
582 * default max colour to current colour (if a plain colour),
583 * or to Black if colour by label; make min colour a pale
584 * version of max colour
586 FeatureColourI fc = fr.getFeatureColours().get(featureType);
587 Color bg = fc.isSimpleColour() ? fc.getColour() : Color.BLACK;
588 maxColour.setBackground(bg);
589 minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
591 noValueCombo = new JComboBox<>();
592 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
593 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
594 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
595 noValueCombo.addItemListener(new ItemListener()
598 public void itemStateChanged(ItemEvent e)
604 JLabel minText = new JLabel(
605 MessageManager.getString("label.min_value") + COLON);
606 minText.setFont(JvSwingUtils.getLabelFont());
607 JLabel maxText = new JLabel(
608 MessageManager.getString("label.max_value") + COLON);
609 maxText.setFont(JvSwingUtils.getLabelFont());
610 JLabel noText = new JLabel(
611 MessageManager.getString("label.no_value") + COLON);
612 noText.setFont(JvSwingUtils.getLabelFont());
614 colourRangePanel.add(minText);
615 colourRangePanel.add(minColour);
616 colourRangePanel.add(maxText);
617 colourRangePanel.add(maxColour);
618 colourRangePanel.add(noText);
619 colourRangePanel.add(noValueCombo);
622 * third row - threshold options and value
624 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
625 thresholdPanel.setBackground(Color.white);
626 graduatedColourPanel.add(thresholdPanel);
628 threshold.addActionListener(changeColourAction);
629 threshold.setToolTipText(MessageManager
630 .getString("label.threshold_feature_display_by_score"));
631 threshold.addItem(MessageManager
632 .getString("label.threshold_feature_no_threshold")); // index 0
633 threshold.addItem(MessageManager
634 .getString("label.threshold_feature_above_threshold")); // index 1
635 threshold.addItem(MessageManager
636 .getString("label.threshold_feature_below_threshold")); // index 2
638 thresholdValue.addActionListener(new ActionListener()
641 public void actionPerformed(ActionEvent e)
643 thresholdValue_actionPerformed();
646 thresholdValue.addFocusListener(new FocusAdapter()
649 public void focusLost(FocusEvent e)
651 thresholdValue_actionPerformed();
654 slider.setPaintLabels(false);
655 slider.setPaintTicks(true);
656 slider.setBackground(Color.white);
657 slider.setEnabled(false);
658 slider.setOpaque(false);
659 slider.setPreferredSize(new Dimension(100, 32));
660 slider.setToolTipText(
661 MessageManager.getString("label.adjust_threshold"));
663 slider.addChangeListener(new ChangeListener()
666 public void stateChanged(ChangeEvent evt)
671 .setText(String.valueOf(slider.getValue() / scaleFactor));
672 sliderValueChanged();
676 slider.addMouseListener(new MouseAdapter()
679 public void mouseReleased(MouseEvent evt)
682 * only update Overview and/or structure colouring
683 * when threshold slider drag ends (mouse up)
687 ap.paintAlignment(true, true);
692 thresholdValue.setEnabled(false);
693 thresholdValue.setColumns(7);
695 thresholdPanel.add(threshold);
696 thresholdPanel.add(slider);
697 thresholdPanel.add(thresholdValue);
699 thresholdIsMin.setBackground(Color.white);
701 .setText(MessageManager.getString("label.threshold_minmax"));
702 thresholdIsMin.setToolTipText(MessageManager
703 .getString("label.toggle_absolute_relative_display_threshold"));
704 thresholdIsMin.addActionListener(changeColourAction);
705 thresholdPanel.add(thresholdIsMin);
707 return graduatedColourPanel;
711 * Lay out OK and Cancel buttons
715 private JPanel initialiseOkCancelPanel()
717 JPanel okCancelPanel = new JPanel();
718 // okCancelPanel.setBackground(Color.white);
719 okCancelPanel.add(ok);
720 okCancelPanel.add(cancel);
721 return okCancelPanel;
725 * Lay out Colour options panel, containing
727 * <li>plain colour, with colour picker</li>
728 * <li>colour by text, with choice of Label or other attribute</li>
729 * <li>colour by range, of score or other attribute, when available</li>
734 private JPanel initialiseColoursPanel()
736 JPanel colourByPanel = new JPanel();
737 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
740 * simple colour radio button and colour picker
742 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
743 simpleColourPanel.setBackground(Color.white);
744 JvSwingUtils.createTitledBorder(simpleColourPanel,
745 MessageManager.getString("label.simple"), true);
746 colourByPanel.add(simpleColourPanel);
748 simpleColour = new JRadioButton(
749 MessageManager.getString("label.simple_colour"));
750 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
751 simpleColour.addItemListener(new ItemListener()
754 public void itemStateChanged(ItemEvent e)
756 if (simpleColour.isSelected() && !adjusting)
758 showColourChooser(singleColour, "label.select_colour");
764 singleColour.setFont(JvSwingUtils.getLabelFont());
765 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
766 singleColour.setPreferredSize(new Dimension(40, 20));
767 singleColour.addMouseListener(new MouseAdapter()
770 public void mousePressed(MouseEvent e)
772 if (simpleColour.isSelected())
774 showColourChooser(singleColour, "label.select_colour");
778 simpleColourPanel.add(simpleColour); // radio button
779 simpleColourPanel.add(singleColour); // colour picker button
782 * colour by text (category) radio button and drop-down choice list
784 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
785 byTextPanel.setBackground(Color.white);
786 JvSwingUtils.createTitledBorder(byTextPanel,
787 MessageManager.getString("label.colour_by_text"), true);
788 colourByPanel.add(byTextPanel);
789 byCategory = new JRadioButton(
790 MessageManager.getString("label.by_text_of") + COLON);
791 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
792 byCategory.addItemListener(new ItemListener()
795 public void itemStateChanged(ItemEvent e)
797 if (byCategory.isSelected())
803 byTextPanel.add(byCategory);
805 List<String[]> attNames = FeatureAttributes.getInstance()
806 .getAttributes(featureType);
807 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
808 colourByTextCombo.addItemListener(new ItemListener()
811 public void itemStateChanged(ItemEvent e)
816 byTextPanel.add(colourByTextCombo);
819 * graduated colour panel
821 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
822 colourByPanel.add(graduatedColourPanel);
825 * 3 radio buttons select between simple colour,
826 * by category (text), or graduated
828 ButtonGroup bg = new ButtonGroup();
829 bg.add(simpleColour);
831 bg.add(graduatedColour);
833 return colourByPanel;
836 private void showColourChooser(JPanel colourPanel, String key)
838 Color col = JColorChooser.showDialog(this,
839 MessageManager.getString(key), colourPanel.getBackground());
842 colourPanel.setBackground(col);
843 colourPanel.setForeground(col);
845 colourPanel.repaint();
850 * Constructs and sets the selected colour options as the colour for the feature
851 * type, and repaints the alignment, and optionally the Overview and/or
852 * structure viewer if open
854 * @param updateStructsAndOverview
856 void colourChanged(boolean updateStructsAndOverview)
861 * ignore action handlers while setting values programmatically
867 * ensure min-max range is for the latest choice of
868 * 'graduated colour by'
870 updateColourMinMax();
872 FeatureColourI acg = makeColourFromInputs();
875 * save the colour, and repaint stuff
877 fr.setColour(featureType, acg);
878 ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
884 * Converts the input values into an instance of FeatureColour
888 private FeatureColourI makeColourFromInputs()
891 * easiest case - a single colour
893 if (simpleColour.isSelected())
895 return new FeatureColour(singleColour.getBackground());
899 * next easiest case - colour by Label, or attribute text
901 if (byCategory.isSelected())
903 Color c = this.getBackground();
904 FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f);
905 fc.setColourByLabel(true);
906 String byWhat = (String) colourByTextCombo.getSelectedItem();
907 if (!LABEL_18N.equals(byWhat))
910 FeatureMatcher.fromAttributeDisplayName(byWhat));
916 * remaining case - graduated colour by score, or attribute value
918 Color noColour = null;
919 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
921 noColour = minColour.getBackground();
923 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
925 noColour = maxColour.getBackground();
931 thresh = Float.valueOf(thresholdValue.getText());
932 } catch (NumberFormatException e)
934 // invalid inputs are already handled on entry
938 * min-max range is to (or from) threshold value if
939 * 'threshold is min/max' is selected
941 float minValue = min;
942 float maxValue = max;
943 final int thresholdOption = threshold.getSelectedIndex();
944 if (thresholdIsMin.isSelected()
945 && thresholdOption == ABOVE_THRESHOLD_OPTION)
949 if (thresholdIsMin.isSelected()
950 && thresholdOption == BELOW_THRESHOLD_OPTION)
956 * make the graduated colour
958 FeatureColourI fc = new FeatureColour(minColour.getBackground(),
959 maxColour.getBackground(), noColour, minValue, maxValue);
962 * set attribute to colour by if selected
964 String byWhat = (String) colourByRangeCombo.getSelectedItem();
965 if (!SCORE_18N.equals(byWhat))
967 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
971 * set threshold options and 'autoscaled' which is
972 * false if 'threshold is min/max' is selected
973 * else true (colour range is on actual range of values)
975 fc.setThreshold(thresh);
976 fc.setAutoScaled(!thresholdIsMin.isSelected());
977 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
978 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
980 if (threshline == null)
983 * todo not yet implemented: visual indication of feature threshold
985 threshline = new GraphLine((max - min) / 2f, "Threshold",
993 protected void raiseClosed()
995 if (this.featureSettings != null)
997 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
1002 * Action on OK is just to dismiss the dialog - any changes have already been
1006 public void okPressed()
1011 * Action on Cancel is to restore colour scheme and filters as they were when
1012 * the dialog was opened
1015 public void cancelPressed()
1017 fr.setColour(featureType, originalColour);
1018 fr.setFeatureFilter(featureType, originalFilter);
1019 ap.paintAlignment(true, true);
1023 * Action on text entry of a threshold value
1025 protected void thresholdValue_actionPerformed()
1030 float f = Float.parseFloat(thresholdValue.getText());
1031 slider.setValue((int) (f * scaleFactor));
1032 threshline.value = f;
1033 thresholdValue.setBackground(Color.white); // ok
1036 * force repaint of any Overview window or structure
1038 ap.paintAlignment(true, true);
1039 } catch (NumberFormatException ex)
1041 thresholdValue.setBackground(Color.red); // not ok
1049 * Action on change of threshold slider value. This may be done interactively
1050 * (by moving the slider), or programmatically (to update the slider after
1051 * manual input of a threshold value).
1053 protected void sliderValueChanged()
1055 threshline.value = getRoundedSliderValue();
1058 * repaint alignment, but not Overview or structure,
1059 * to avoid overload while dragging the slider
1061 colourChanged(false);
1065 * Converts the slider value to its absolute value by dividing by the
1066 * scaleFactor. Rounding errors are squashed by forcing min/max of slider range
1067 * to the actual min/max of feature score range
1071 private float getRoundedSliderValue()
1073 int value = slider.getValue();
1074 float f = value == slider.getMaximum() ? max
1075 : (value == slider.getMinimum() ? min : value / scaleFactor);
1079 void addActionListener(ActionListener listener)
1081 if (featureSettings != null)
1084 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1086 featureSettings = listener;
1090 * A helper method to build the drop-down choice of attributes for a feature. If
1091 * 'withRange' is true, then Score, and any attributes with a min-max range, are
1092 * added. If 'withText' is true, Label and any known attributes are added. This
1093 * allows 'categorical numerical' attributes e.g. codon position to be coloured
1096 * Where metadata is available with a description for an attribute, that is
1097 * added as a tooltip.
1099 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1100 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1102 * This method does not add any ActionListener to the JComboBox.
1108 protected JComboBox<String> populateAttributesDropdown(
1109 List<String[]> attNames, boolean withRange, boolean withText)
1111 List<String> displayAtts = new ArrayList<>();
1112 List<String> tooltips = new ArrayList<>();
1116 displayAtts.add(LABEL_18N);
1117 tooltips.add(MessageManager.getString("label.description"));
1121 float[][] minMax = fr.getMinMax().get(featureType);
1122 if (minMax != null && minMax[0][0] != minMax[0][1])
1124 displayAtts.add(SCORE_18N);
1125 tooltips.add(SCORE_18N);
1129 FeatureAttributes fa = FeatureAttributes.getInstance();
1130 for (String[] attName : attNames)
1132 float[] minMax = fa.getMinMax(featureType, attName);
1133 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1134 if (!withText && !hasRange)
1138 displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
1139 String desc = fa.getDescription(featureType, attName);
1140 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1142 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1144 tooltips.add(desc == null ? "" : desc);
1147 JComboBox<String> attCombo = JvSwingUtils
1148 .buildComboWithTooltips(displayAtts, tooltips);
1154 * Populates initial layout of the feature attribute filters panel
1156 private JPanel initialiseFiltersPanel()
1158 filters = new ArrayList<>();
1160 JPanel filtersPanel = new JPanel();
1161 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1162 filtersPanel.setBackground(Color.white);
1163 JvSwingUtils.createTitledBorder(filtersPanel,
1164 MessageManager.getString("label.filters"), true);
1166 JPanel andOrPanel = initialiseAndOrPanel();
1167 filtersPanel.add(andOrPanel);
1170 * panel with filters - populated by refreshFiltersDisplay,
1171 * which also sets the layout manager
1173 chooseFiltersPanel = new JPanel();
1174 chooseFiltersPanel.setBackground(Color.white);
1175 filtersPanel.add(chooseFiltersPanel);
1177 return filtersPanel;
1181 * Lays out the panel with radio buttons to AND or OR filter conditions
1185 private JPanel initialiseAndOrPanel()
1187 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1188 andOrPanel.setBackground(Color.white);
1189 andOrPanel.setBorder(BorderFactory.createLineBorder(debugBorderColour));
1190 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1191 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1192 ActionListener actionListener = new ActionListener()
1195 public void actionPerformed(ActionEvent e)
1200 andFilters.addActionListener(actionListener);
1201 orFilters.addActionListener(actionListener);
1202 ButtonGroup andOr = new ButtonGroup();
1203 andOr.add(andFilters);
1204 andOr.add(orFilters);
1205 andFilters.setSelected(true);
1207 new JLabel(MessageManager.getString("label.join_conditions")));
1208 andOrPanel.add(andFilters);
1209 andOrPanel.add(orFilters);
1214 * Refreshes the display to show any filters currently configured for the
1215 * selected feature type (editable, with 'remove' option), plus one extra row
1216 * for adding a condition. This should be called after a filter has been
1217 * removed, added or amended.
1219 private void updateFiltersTab()
1222 * clear the panel and list of filter conditions
1224 chooseFiltersPanel.removeAll();
1228 * look up attributes known for feature type
1230 List<String[]> attNames = FeatureAttributes.getInstance()
1231 .getAttributes(featureType);
1234 * if this feature type has filters set, load them first
1236 FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
1237 if (featureFilters != null)
1239 if (!featureFilters.isAnded())
1241 orFilters.setSelected(true);
1243 // avoid use of lambda expression to keep SwingJS happy
1244 // featureFilters.getMatchers().forEach(item -> filters.add(item));
1245 for (FeatureMatcherI matcher : featureFilters.getMatchers())
1247 filters.add(matcher);
1252 * and an empty filter for the user to populate (add)
1254 filters.add(FeatureMatcher.NULL_MATCHER);
1257 * use GridLayout to 'justify' rows to the top of the panel, until
1258 * there are too many to fit in, then fall back on BoxLayout
1260 if (filters.size() <= 5)
1262 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1266 chooseFiltersPanel.setLayout(
1267 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1271 * render the conditions in rows, each in its own JPanel
1273 int filterIndex = 0;
1274 for (FeatureMatcherI filter : filters)
1276 JPanel row = addFilter(filter, attNames, filterIndex);
1277 row.setBorder(BorderFactory.createLineBorder(debugBorderColour));
1278 chooseFiltersPanel.add(row);
1287 * A helper method that constructs a row (panel) with one filter condition:
1289 * <li>a drop-down list of Label, Score and attribute names to choose from</li>
1290 * <li>a drop-down list of conditions to choose from</li>
1291 * <li>a text field for input of a match pattern</li>
1292 * <li>optionally, a 'remove' button</li>
1294 * The filter values are set as defaults for the input fields. The 'remove'
1295 * button is added unless the pattern is empty (incomplete filter condition).
1297 * Action handlers on these fields provide for
1299 * <li>validate pattern field - should be numeric if condition is numeric</li>
1300 * <li>save filters and refresh display on any (valid) change</li>
1301 * <li>remove filter and refresh on 'Remove'</li>
1302 * <li>update conditions list on change of Label/Score/Attribute</li>
1303 * <li>refresh value field tooltip with min-max range on change of
1309 * @param filterIndex
1312 protected JPanel addFilter(FeatureMatcherI filter,
1313 List<String[]> attNames, int filterIndex)
1315 String[] attName = filter.getAttribute();
1316 Condition cond = filter.getMatcher().getCondition();
1317 String pattern = filter.getMatcher().getPattern();
1319 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1320 filterRow.setBackground(Color.white);
1323 * drop-down choice of attribute, with description as a tooltip
1324 * if we can obtain it
1326 final JComboBox<String> attCombo = populateAttributesDropdown(attNames,
1328 String filterBy = setSelectedAttribute(attCombo, filter);
1330 JComboBox<Condition> condCombo = new JComboBox<>();
1332 JTextField patternField = new JTextField(8);
1333 patternField.setText(pattern);
1336 * action handlers that validate and (if valid) apply changes
1338 ActionListener actionListener = new ActionListener()
1341 public void actionPerformed(ActionEvent e)
1343 if (validateFilter(patternField, condCombo))
1345 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1352 ItemListener itemListener = new ItemListener()
1355 public void itemStateChanged(ItemEvent e)
1357 actionListener.actionPerformed(null);
1361 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1363 attCombo.setSelectedIndex(0);
1367 attCombo.setSelectedItem(
1368 FeatureMatcher.toAttributeDisplayName(attName));
1370 attCombo.addItemListener(new ItemListener()
1373 public void itemStateChanged(ItemEvent e)
1376 * on change of attribute, refresh the conditions list to
1377 * ensure it is appropriate for the attribute datatype
1379 populateConditions((String) attCombo.getSelectedItem(),
1380 (Condition) condCombo.getSelectedItem(), condCombo,
1382 actionListener.actionPerformed(null);
1386 filterRow.add(attCombo);
1389 * drop-down choice of test condition
1391 populateConditions(filterBy, cond, condCombo, patternField);
1392 condCombo.setPreferredSize(new Dimension(150, 20));
1393 condCombo.addItemListener(itemListener);
1394 filterRow.add(condCombo);
1397 * pattern to match against
1399 patternField.addActionListener(actionListener);
1400 patternField.addFocusListener(new FocusAdapter()
1403 public void focusLost(FocusEvent e)
1405 actionListener.actionPerformed(null);
1408 filterRow.add(patternField);
1411 * disable pattern field for condition 'Present / NotPresent'
1413 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1414 patternField.setEnabled(selectedCondition.needsAPattern());
1417 * if a numeric condition is selected, show the value range
1418 * as a tooltip on the value input field
1420 setNumericHints(filterBy, selectedCondition, patternField);
1423 * add remove button if filter is populated (non-empty pattern)
1425 if (!patternField.isEnabled()
1426 || (pattern != null && pattern.trim().length() > 0))
1428 JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x
1429 removeCondition.setPreferredSize(new Dimension(23, 17));
1431 .setToolTipText(MessageManager.getString("label.delete_row"));
1432 removeCondition.addActionListener(new ActionListener()
1435 public void actionPerformed(ActionEvent e)
1437 filters.remove(filterIndex);
1441 filterRow.add(removeCondition);
1448 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1454 private String setSelectedAttribute(JComboBox<String> attCombo,
1455 FeatureMatcherI filter)
1458 if (filter.isByScore())
1462 else if (filter.isByLabel())
1468 item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
1470 attCombo.setSelectedItem(item);
1475 * If a numeric comparison condition is selected, retrieves the min-max range
1476 * for the value (score or attribute), and sets it as a tooltip on the value
1477 * field. If the field is currently empty, then pre-populates it with
1479 * <li>the minimum value, if condition is > or >=</li>
1480 * <li>the maximum value, if condition is < or <=</li>
1484 * @param selectedCondition
1485 * @param patternField
1487 private void setNumericHints(String attName,
1488 Condition selectedCondition, JTextField patternField)
1490 patternField.setToolTipText("");
1492 if (selectedCondition.isNumeric())
1494 float[] minMax = getMinMax(attName);
1497 String minFormatted = DECFMT_2_2.format(minMax[0]);
1498 String maxFormatted = DECFMT_2_2.format(minMax[1]);
1499 String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
1500 patternField.setToolTipText(tip);
1501 if (patternField.getText().isEmpty())
1503 if (selectedCondition == Condition.GE
1504 || selectedCondition == Condition.GT)
1506 patternField.setText(minFormatted);
1510 if (selectedCondition == Condition.LE
1511 || selectedCondition == Condition.LT)
1513 patternField.setText(maxFormatted);
1522 * Populates the drop-down list of comparison conditions for the given attribute
1523 * name. The conditions added depend on the datatype of the attribute values.
1524 * The supplied condition is set as the selected item in the list, provided it
1525 * is in the list. If the pattern is now invalid (non-numeric pattern for a
1526 * numeric condition), it is cleared.
1531 * @param patternField
1533 private void populateConditions(String attName, Condition cond,
1534 JComboBox<Condition> condCombo, JTextField patternField)
1536 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1537 FeatureMatcher.fromAttributeDisplayName(attName));
1538 if (LABEL_18N.equals(attName))
1540 type = Datatype.Character;
1542 else if (SCORE_18N.equals(attName))
1544 type = Datatype.Number;
1548 * remove itemListener before starting
1550 ItemListener listener = condCombo.getItemListeners()[0];
1551 condCombo.removeItemListener(listener);
1552 boolean condIsValid = false;
1554 condCombo.removeAllItems();
1555 for (Condition c : Condition.values())
1557 if ((c.isNumeric() && type == Datatype.Number)
1558 || (!c.isNumeric() && type != Datatype.Number))
1560 condCombo.addItem(c);
1569 * set the selected condition (does nothing if not in the list)
1573 condCombo.setSelectedItem(cond);
1577 condCombo.setSelectedIndex(0);
1581 * clear pattern if it is now invalid for condition
1583 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1587 String pattern = patternField.getText().trim();
1588 if (pattern.length() > 0)
1590 Float.valueOf(pattern);
1592 } catch (NumberFormatException e)
1594 patternField.setText("");
1599 * restore the listener
1601 condCombo.addItemListener(listener);
1605 * Answers true unless a numeric condition has been selected with a non-numeric
1606 * value. Sets the value field to RED with a tooltip if in error.
1608 * If the pattern is expected but is empty, this method returns false, but does
1609 * not mark the field as invalid. This supports selecting an attribute for a new
1610 * condition before a match pattern has been entered.
1615 protected boolean validateFilter(JTextField value,
1616 JComboBox<Condition> condCombo)
1618 if (value == null || condCombo == null)
1620 return true; // fields not populated
1623 Condition cond = (Condition) condCombo.getSelectedItem();
1624 if (!cond.needsAPattern())
1629 value.setBackground(Color.white);
1630 value.setToolTipText("");
1631 String v1 = value.getText().trim();
1632 if (v1.length() == 0)
1637 if (cond.isNumeric() && v1.length() > 0)
1642 } catch (NumberFormatException e)
1644 value.setBackground(Color.red);
1645 value.setToolTipText(
1646 MessageManager.getString("label.numeric_required"));
1655 * Constructs a filter condition from the given input fields, and replaces the
1656 * condition at filterIndex with the new one. Does nothing if the pattern field
1657 * is blank (unless the match condition is one that doesn't require a pattern,
1658 * e.g. 'Is present'). Answers true if the filter was updated, else false.
1660 * This method may update the tooltip on the filter value field to show the
1661 * value range, if a numeric condition is selected. This ensures the tooltip is
1662 * updated when a numeric valued attribute is chosen on the last 'add a filter'
1668 * @param filterIndex
1670 protected boolean updateFilter(JComboBox<String> attCombo,
1671 JComboBox<Condition> condCombo, JTextField valueField,
1674 String attName = (String) attCombo.getSelectedItem();
1675 Condition cond = (Condition) condCombo.getSelectedItem();
1676 String pattern = valueField.getText().trim();
1678 setNumericHints(attName, cond, valueField);
1680 if (pattern.length() == 0 && cond.needsAPattern())
1682 valueField.setEnabled(true); // ensure pattern field is enabled!
1687 * Construct a matcher that operates on Label, Score,
1688 * or named attribute
1690 FeatureMatcherI km = null;
1691 if (LABEL_18N.equals(attName))
1693 km = FeatureMatcher.byLabel(cond, pattern);
1695 else if (SCORE_18N.equals(attName))
1697 km = FeatureMatcher.byScore(cond, pattern);
1701 km = FeatureMatcher.byAttribute(cond, pattern,
1702 FeatureMatcher.fromAttributeDisplayName(attName));
1705 filters.set(filterIndex, km);
1711 * Makes the dialog visible, at the Feature Colour tab or at the Filters tab
1715 public void showTab(boolean coloursTab)
1718 tabbedPane.setSelectedIndex(coloursTab ? 0 : 1);
1722 * Action on any change to feature filtering, namely
1724 * <li>change of selected attribute</li>
1725 * <li>change of selected condition</li>
1726 * <li>change of match pattern</li>
1727 * <li>removal of a condition</li>
1729 * The inputs are parsed into a combined filter and this is set for the feature
1730 * type, and the alignment redrawn.
1732 protected void filtersChanged()
1735 * update the filter conditions for the feature type
1737 boolean anded = andFilters.isSelected();
1738 FeatureMatcherSetI combined = new FeatureMatcherSet();
1740 for (FeatureMatcherI filter : filters)
1742 String pattern = filter.getMatcher().getPattern();
1743 Condition condition = filter.getMatcher().getCondition();
1744 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1748 combined.and(filter);
1752 combined.or(filter);
1758 * save the filter conditions in the FeatureRenderer
1759 * (note this might now be an empty filter with no conditions)
1761 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1762 ap.paintAlignment(true, true);