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.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.api.FeatureColourI;
26 import jalview.bin.Cache;
27 import jalview.datamodel.GraphLine;
28 import jalview.datamodel.features.FeatureAttributes;
29 import jalview.datamodel.features.FeatureAttributes.Datatype;
30 import jalview.datamodel.features.FeatureMatcher;
31 import jalview.datamodel.features.FeatureMatcherI;
32 import jalview.datamodel.features.FeatureMatcherSet;
33 import jalview.datamodel.features.FeatureMatcherSetI;
34 import jalview.gui.JalviewColourChooser.ColourChooserListener;
35 import jalview.schemes.FeatureColour;
36 import jalview.util.ColorUtils;
37 import jalview.util.MessageManager;
38 import jalview.util.matcher.Condition;
40 import java.awt.BorderLayout;
41 import java.awt.Color;
42 import java.awt.Dimension;
43 import java.awt.FlowLayout;
44 import java.awt.GridLayout;
45 import java.awt.event.ActionEvent;
46 import java.awt.event.ActionListener;
47 import java.awt.event.FocusAdapter;
48 import java.awt.event.FocusEvent;
49 import java.awt.event.ItemEvent;
50 import java.awt.event.ItemListener;
51 import java.awt.event.MouseAdapter;
52 import java.awt.event.MouseEvent;
53 import java.math.BigDecimal;
54 import java.math.MathContext;
55 import java.text.DecimalFormat;
56 import java.util.ArrayList;
57 import java.util.List;
59 import javax.swing.BorderFactory;
60 import javax.swing.BoxLayout;
61 import javax.swing.ButtonGroup;
62 import javax.swing.JButton;
63 import javax.swing.JCheckBox;
64 import javax.swing.JComboBox;
65 import javax.swing.JLabel;
66 import javax.swing.JPanel;
67 import javax.swing.JRadioButton;
68 import javax.swing.JTextField;
69 import javax.swing.border.EmptyBorder;
70 import javax.swing.border.LineBorder;
71 import javax.swing.event.ChangeEvent;
72 import javax.swing.event.ChangeListener;
75 * A dialog where the user can configure colour scheme, and any filters, for one
78 * (Was FeatureColourChooser prior to Jalview 1.11, renamed with the addition of
81 public class FeatureTypeSettings extends JalviewDialog
83 private final static MathContext FOUR_SIG_FIG = new MathContext(4);
85 private final static String LABEL_18N = MessageManager
86 .getString("label.label");
88 private final static String SCORE_18N = MessageManager
89 .getString("label.score");
91 private static final int RADIO_WIDTH = 130;
93 private static final String COLON = ":";
95 private static final int MAX_TOOLTIP_LENGTH = 50;
97 private static final int NO_COLOUR_OPTION = 0;
99 private static final int MIN_COLOUR_OPTION = 1;
101 private static final int MAX_COLOUR_OPTION = 2;
103 private static final int ABOVE_THRESHOLD_OPTION = 1;
105 private static final int BELOW_THRESHOLD_OPTION = 2;
107 private static final DecimalFormat DECFMT_2_2 = new DecimalFormat(
111 * FeatureRenderer holds colour scheme and filters for feature types
113 private final FeatureRenderer fr; // todo refactor to allow interface type
117 * the view panel to update when settings change
119 final AlignmentViewPanel ap;
121 final String featureType;
124 * the colour and filters to reset to on Cancel
126 private final FeatureColourI originalColour;
128 private final FeatureMatcherSetI originalFilter;
131 * set flag to true when setting values programmatically,
132 * to avoid invocation of action handlers
134 boolean adjusting = false;
137 * minimum of the value range for graduated colour
138 * (may be for feature score or for a numeric attribute)
143 * maximum of the value range for graduated colour
148 * radio button group, to select what to colour by:
149 * simple colour, by category (text), or graduated
151 JRadioButton simpleColour = new JRadioButton();
153 JRadioButton byCategory = new JRadioButton();
155 JRadioButton graduatedColour = new JRadioButton();
161 JPanel singleColour = new JPanel();
163 JPanel minColour = new JPanel();
165 JPanel maxColour = new JPanel();
167 private JComboBox<Object> threshold = new JComboBox<>();
169 private Slider slider;
171 JTextField thresholdValue = new JTextField(20);
173 private JCheckBox thresholdIsMin = new JCheckBox();
175 private GraphLine threshline;
177 private ActionListener featureSettings = null;
179 private ActionListener changeColourAction;
182 * choice of option for 'colour for no value'
184 private JComboBox<Object> noValueCombo;
187 * choice of what to colour by text (Label or attribute)
189 private JComboBox<Object> colourByTextCombo;
192 * choice of what to colour by range (Score or attribute)
194 private JComboBox<Object> colourByRangeCombo;
196 private JRadioButton andFilters;
198 private JRadioButton orFilters;
201 * filters for the currently selected feature type
203 List<FeatureMatcherI> filters;
205 private JPanel chooseFiltersPanel;
213 public FeatureTypeSettings(FeatureRenderer frender, String theType)
216 this.featureType = theType;
218 originalFilter = fr.getFeatureFilter(theType);
219 originalColour = fr.getFeatureColours().get(theType);
226 } catch (Exception ex)
228 ex.printStackTrace();
232 updateColoursPanel();
234 updateFiltersPanel();
238 colourChanged(false);
240 String title = MessageManager
241 .formatMessage("label.display_settings_for", new String[]
243 initDialogFrame(this, true, false, title, 580, 500);
248 * Configures the widgets on the Colours panel according to the current feature
251 private void updateColoursPanel()
253 FeatureColourI fc = fr.getFeatureColours().get(featureType);
256 * suppress action handling while updating values programmatically
264 if (fc.isSimpleColour())
266 singleColour.setBackground(fc.getColour());
267 singleColour.setForeground(fc.getColour());
268 simpleColour.setSelected(true);
272 * colour by text (Label or attribute text)
274 if (fc.isColourByLabel())
276 byCategory.setSelected(true);
277 colourByTextCombo.setEnabled(colourByTextCombo.getItemCount() > 1);
278 if (fc.isColourByAttribute())
280 String[] attributeName = fc.getAttributeName();
281 colourByTextCombo.setSelectedItem(
282 FeatureMatcher.toAttributeDisplayName(attributeName));
286 colourByTextCombo.setSelectedItem(LABEL_18N);
291 colourByTextCombo.setEnabled(false);
294 if (!fc.isGraduatedColour())
296 colourByRangeCombo.setEnabled(false);
297 minColour.setEnabled(false);
298 maxColour.setEnabled(false);
299 noValueCombo.setEnabled(false);
300 threshold.setEnabled(false);
301 slider.setEnabled(false);
302 thresholdValue.setEnabled(false);
303 thresholdIsMin.setEnabled(false);
308 * Graduated colour, by score or attribute value range
310 graduatedColour.setSelected(true);
311 updateColourMinMax(); // ensure min, max are set
312 colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
313 minColour.setEnabled(true);
314 maxColour.setEnabled(true);
315 noValueCombo.setEnabled(true);
316 threshold.setEnabled(true);
317 minColour.setBackground(fc.getMinColour());
318 maxColour.setBackground(fc.getMaxColour());
320 if (fc.isColourByAttribute())
322 String[] attributeName = fc.getAttributeName();
323 colourByRangeCombo.setSelectedItem(
324 FeatureMatcher.toAttributeDisplayName(attributeName));
328 colourByRangeCombo.setSelectedItem(SCORE_18N);
330 Color noColour = fc.getNoColour();
331 if (noColour == null)
333 noValueCombo.setSelectedIndex(NO_COLOUR_OPTION);
335 else if (noColour.equals(fc.getMinColour()))
337 noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION);
339 else if (noColour.equals(fc.getMaxColour()))
341 noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION);
345 * update min-max scaling if there is a range to work with,
346 * else disable the widgets (this shouldn't happen if only
347 * valid options are offered in the combo box)
348 * offset slider to have only non-negative values if necessary (JAL-2983)
350 slider.setSliderModel(min, max, min);
351 slider.setMajorTickSpacing(
352 (int) ((slider.getMaximum() - slider.getMinimum()) / 10f));
354 threshline = new GraphLine((max - min) / 2f, "Threshold",
356 threshline.value = fc.getThreshold();
358 if (fc.hasThreshold())
360 threshold.setSelectedIndex(
361 fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
362 : BELOW_THRESHOLD_OPTION);
363 slider.setEnabled(true);
364 slider.setSliderValue(fc.getThreshold());
365 setThresholdValueText(fc.getThreshold());
366 thresholdValue.setEnabled(true);
367 thresholdIsMin.setEnabled(true);
371 slider.setEnabled(false);
372 thresholdValue.setEnabled(false);
373 thresholdIsMin.setEnabled(false);
375 thresholdIsMin.setSelected(!fc.isAutoScaled());
383 * Configures the initial layout
385 private void initialise()
387 this.setLayout(new BorderLayout());
390 * an ActionListener that applies colour changes
392 changeColourAction = new ActionListener()
395 public void actionPerformed(ActionEvent e)
402 * first panel: colour options
404 JPanel coloursPanel = initialiseColoursPanel();
405 this.add(coloursPanel, BorderLayout.NORTH);
408 * second panel: filter options
410 JPanel filtersPanel = initialiseFiltersPanel();
411 this.add(filtersPanel, BorderLayout.CENTER);
413 JPanel okCancelPanel = initialiseOkCancelPanel();
415 this.add(okCancelPanel, BorderLayout.SOUTH);
419 * Updates the min-max range if Colour By selected item is Score, or an
420 * attribute, with a min-max range
422 protected void updateColourMinMax()
424 if (!graduatedColour.isSelected())
429 String colourBy = (String) colourByRangeCombo.getSelectedItem();
430 float[] minMax = getMinMax(colourBy);
440 * Retrieves the min-max range:
442 * <li>of feature score, if colour or filter is by Score</li>
443 * <li>else of the selected attribute</li>
449 private float[] getMinMax(String attName)
451 float[] minMax = null;
452 if (SCORE_18N.equals(attName))
454 minMax = fr.getMinMax().get(featureType)[0];
458 // colour by attribute range
459 minMax = FeatureAttributes.getInstance().getMinMax(featureType,
460 FeatureMatcher.fromAttributeDisplayName(attName));
466 * Lay out fields for graduated colour (by score or attribute value)
470 private JPanel initialiseGraduatedColourPanel()
472 JPanel graduatedColourPanel = new JPanel();
473 graduatedColourPanel.setLayout(
474 new BoxLayout(graduatedColourPanel, BoxLayout.Y_AXIS));
475 JvSwingUtils.createTitledBorder(graduatedColourPanel,
476 MessageManager.getString("label.graduated_colour"), true);
477 graduatedColourPanel.setBackground(Color.white);
480 * first row: graduated colour radio button, score/attribute drop-down
482 JPanel graduatedChoicePanel = new JPanel(
483 new FlowLayout(FlowLayout.LEFT));
484 graduatedChoicePanel.setBackground(Color.white);
485 graduatedColour = new JRadioButton(
486 MessageManager.getString("label.by_range_of") + COLON);
487 graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
488 graduatedColour.setOpaque(false);
489 graduatedColour.addItemListener(new ItemListener()
492 public void itemStateChanged(ItemEvent e)
494 if (graduatedColour.isSelected())
500 graduatedChoicePanel.add(graduatedColour);
502 List<String[]> attNames = FeatureAttributes.getInstance()
503 .getAttributes(featureType);
504 colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
505 colourByRangeCombo.addItemListener(new ItemListener()
508 public void itemStateChanged(ItemEvent e)
515 * disable graduated colour option if no range found
517 graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
519 graduatedChoicePanel.add(colourByRangeCombo);
520 graduatedColourPanel.add(graduatedChoicePanel);
523 * second row - min/max/no colours
525 JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
526 colourRangePanel.setBackground(Color.white);
527 graduatedColourPanel.add(colourRangePanel);
529 minColour.setFont(JvSwingUtils.getLabelFont());
530 minColour.setBorder(BorderFactory.createLineBorder(Color.black));
531 minColour.setPreferredSize(new Dimension(40, 20));
532 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
533 minColour.addMouseListener(new MouseAdapter()
536 public void mousePressed(MouseEvent e)
538 if (minColour.isEnabled())
540 String ttl = MessageManager.getString("label.select_colour_minimum_value");
541 showColourChooser(minColour, ttl);
546 maxColour.setFont(JvSwingUtils.getLabelFont());
547 maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
548 maxColour.setPreferredSize(new Dimension(40, 20));
549 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
550 maxColour.addMouseListener(new MouseAdapter()
553 public void mousePressed(MouseEvent e)
555 if (maxColour.isEnabled())
557 String ttl = MessageManager.getString("label.select_colour_maximum_value");
558 showColourChooser(maxColour, ttl);
562 maxColour.setBorder(new LineBorder(Color.black));
565 * if not set, default max colour to last plain colour,
566 * and make min colour a pale version of max colour
568 Color max = originalColour.getMaxColour();
571 max = originalColour.getColour();
572 minColour.setBackground(ColorUtils.bleachColour(max, 0.9f));
576 maxColour.setBackground(max);
577 minColour.setBackground(originalColour.getMinColour());
580 noValueCombo = new JComboBox<>();
581 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
582 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
583 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
584 noValueCombo.addItemListener(new ItemListener()
587 public void itemStateChanged(ItemEvent e)
593 JLabel minText = new JLabel(
594 MessageManager.getString("label.min_value") + COLON);
595 minText.setFont(JvSwingUtils.getLabelFont());
596 JLabel maxText = new JLabel(
597 MessageManager.getString("label.max_value") + COLON);
598 maxText.setFont(JvSwingUtils.getLabelFont());
599 JLabel noText = new JLabel(
600 MessageManager.getString("label.no_value") + COLON);
601 noText.setFont(JvSwingUtils.getLabelFont());
603 colourRangePanel.add(minText);
604 colourRangePanel.add(minColour);
605 colourRangePanel.add(maxText);
606 colourRangePanel.add(maxColour);
607 colourRangePanel.add(noText);
608 colourRangePanel.add(noValueCombo);
611 * third row - threshold options and value
613 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
614 thresholdPanel.setBackground(Color.white);
615 graduatedColourPanel.add(thresholdPanel);
617 threshold.addActionListener(changeColourAction);
618 threshold.setToolTipText(MessageManager
619 .getString("label.threshold_feature_display_by_score"));
620 threshold.addItem(MessageManager
621 .getString("label.threshold_feature_no_threshold")); // index 0
622 threshold.addItem(MessageManager
623 .getString("label.threshold_feature_above_threshold")); // index 1
624 threshold.addItem(MessageManager
625 .getString("label.threshold_feature_below_threshold")); // index 2
627 thresholdValue.addActionListener(new ActionListener()
630 public void actionPerformed(ActionEvent e)
632 thresholdValue_actionPerformed();
635 thresholdValue.addFocusListener(new FocusAdapter()
638 public void focusLost(FocusEvent e)
640 thresholdValue_actionPerformed();
643 slider = new Slider(0f, 100f, 50f);
644 slider.setPaintLabels(false);
645 slider.setPaintTicks(true);
646 slider.setBackground(Color.white);
647 slider.setEnabled(false);
648 slider.setOpaque(false);
649 slider.setPreferredSize(new Dimension(100, 32));
650 slider.setToolTipText(
651 MessageManager.getString("label.adjust_threshold"));
653 slider.addChangeListener(new ChangeListener()
656 public void stateChanged(ChangeEvent evt)
660 setThresholdValueText(slider.getSliderValue());
661 thresholdValue.setBackground(Color.white); // to reset red for invalid
662 sliderValueChanged();
666 slider.addMouseListener(new MouseAdapter()
669 public void mouseReleased(MouseEvent evt)
672 * only update Overview and/or structure colouring
673 * when threshold slider drag ends (mouse up)
677 refreshDisplay(true);
682 thresholdValue.setEnabled(false);
683 thresholdValue.setColumns(7);
685 thresholdPanel.add(threshold);
686 thresholdPanel.add(slider);
687 thresholdPanel.add(thresholdValue);
689 thresholdIsMin.setBackground(Color.white);
691 .setText(MessageManager.getString("label.threshold_minmax"));
692 thresholdIsMin.setToolTipText(MessageManager
693 .getString("label.toggle_absolute_relative_display_threshold"));
694 thresholdIsMin.addActionListener(changeColourAction);
695 thresholdPanel.add(thresholdIsMin);
697 return graduatedColourPanel;
701 * Lay out OK and Cancel buttons
705 private JPanel initialiseOkCancelPanel()
707 JPanel okCancelPanel = new JPanel();
708 // okCancelPanel.setBackground(Color.white);
709 okCancelPanel.add(ok);
710 okCancelPanel.add(cancel);
711 return okCancelPanel;
715 * Lay out Colour options panel, containing
717 * <li>plain colour, with colour picker</li>
718 * <li>colour by text, with choice of Label or other attribute</li>
719 * <li>colour by range, of score or other attribute, when available</li>
724 private JPanel initialiseColoursPanel()
726 JPanel colourByPanel = new JPanel();
727 colourByPanel.setBackground(Color.white);
728 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
729 JvSwingUtils.createTitledBorder(colourByPanel,
730 MessageManager.getString("action.colour"), true);
733 * simple colour radio button and colour picker
735 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
736 simpleColourPanel.setBackground(Color.white);
737 colourByPanel.add(simpleColourPanel);
739 simpleColour = new JRadioButton(
740 MessageManager.getString("label.simple_colour"));
741 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
742 simpleColour.setOpaque(false);
743 simpleColour.addItemListener(new ItemListener()
746 public void itemStateChanged(ItemEvent e)
748 if (simpleColour.isSelected() && !adjusting)
755 singleColour.setFont(JvSwingUtils.getLabelFont());
756 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
757 singleColour.setPreferredSize(new Dimension(40, 20));
758 // if (originalColour.isGraduatedColour())
760 // singleColour.setBackground(originalColour.getMaxColour());
761 // singleColour.setForeground(originalColour.getMaxColour());
765 singleColour.setBackground(originalColour.getColour());
766 singleColour.setForeground(originalColour.getColour());
768 singleColour.addMouseListener(new MouseAdapter()
771 public void mousePressed(MouseEvent e)
773 if (simpleColour.isSelected())
775 String ttl = MessageManager.formatMessage("label.select_colour_for", featureType);
776 showColourChooser(singleColour, ttl);
780 simpleColourPanel.add(simpleColour); // radio button
781 simpleColourPanel.add(singleColour); // colour picker button
784 * colour by text (category) radio button and drop-down choice list
786 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
787 byTextPanel.setBackground(Color.white);
788 JvSwingUtils.createTitledBorder(byTextPanel,
789 MessageManager.getString("label.colour_by_text"), true);
790 colourByPanel.add(byTextPanel);
791 byCategory = new JRadioButton(
792 MessageManager.getString("label.by_text_of") + COLON);
793 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
794 byCategory.setOpaque(false);
795 byCategory.addItemListener(new ItemListener()
798 public void itemStateChanged(ItemEvent e)
800 if (byCategory.isSelected())
806 byTextPanel.add(byCategory);
808 List<String[]> attNames = FeatureAttributes.getInstance()
809 .getAttributes(featureType);
810 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
811 colourByTextCombo.addItemListener(new ItemListener()
814 public void itemStateChanged(ItemEvent e)
819 byTextPanel.add(colourByTextCombo);
822 * graduated colour panel
824 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
825 colourByPanel.add(graduatedColourPanel);
828 * 3 radio buttons select between simple colour,
829 * by category (text), or graduated
831 ButtonGroup bg = new ButtonGroup();
832 bg.add(simpleColour);
834 bg.add(graduatedColour);
836 return colourByPanel;
840 * Shows a colour chooser dialog, and if a selection is made, updates the
841 * colour of the given panel
844 * the panel whose background colour is being picked
847 void showColourChooser(JPanel colourPanel, String title)
849 ColourChooserListener listener = new ColourChooserListener()
852 public void colourSelected(Color col)
854 colourPanel.setBackground(col);
855 colourPanel.setForeground(col);
856 colourPanel.repaint();
860 JalviewColourChooser.showColourChooser(this, title,
861 colourPanel.getBackground(), listener);
865 * Constructs and sets the selected colour options as the colour for the
866 * feature type, and repaints the alignment, and optionally the Overview
867 * and/or structure viewer if open
869 * @param updateStructsAndOverview
871 void colourChanged(boolean updateStructsAndOverview)
876 * ignore action handlers while setting values programmatically
882 * ensure min-max range is for the latest choice of
883 * 'graduated colour by'
885 updateColourMinMax();
887 FeatureColourI acg = makeColourFromInputs();
890 * save the colour, and repaint stuff
892 fr.setColour(featureType, acg);
893 refreshDisplay(updateStructsAndOverview);
895 updateColoursPanel();
899 * Converts the input values into an instance of FeatureColour
903 private FeatureColourI makeColourFromInputs()
906 * min-max range is to (or from) threshold value if
907 * 'threshold is min/max' is selected
913 thresh = Float.valueOf(thresholdValue.getText());
914 } catch (NumberFormatException e)
916 // invalid inputs are already handled on entry
918 float minValue = min;
919 float maxValue = max;
920 int thresholdOption = threshold.getSelectedIndex();
921 if (thresholdIsMin.isSelected()
922 && thresholdOption == ABOVE_THRESHOLD_OPTION)
926 if (thresholdIsMin.isSelected()
927 && thresholdOption == BELOW_THRESHOLD_OPTION)
931 Color noColour = null;
932 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
934 noColour = minColour.getBackground();
936 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
938 noColour = maxColour.getBackground();
942 * construct a colour that 'remembers' all the options, including
943 * those not currently selected
945 FeatureColourI fc = new FeatureColour(singleColour.getBackground(),
946 minColour.getBackground(), maxColour.getBackground(), noColour,
950 * easiest case - a single colour
952 if (simpleColour.isSelected())
954 ((FeatureColour) fc).setGraduatedColour(false);
959 * next easiest case - colour by Label, or attribute text
961 if (byCategory.isSelected())
963 fc.setColourByLabel(true);
964 String byWhat = (String) colourByTextCombo.getSelectedItem();
965 if (!LABEL_18N.equals(byWhat))
968 FeatureMatcher.fromAttributeDisplayName(byWhat));
974 * remaining case - graduated colour by score, or attribute value;
975 * set attribute to colour by if selected
977 String byWhat = (String) colourByRangeCombo.getSelectedItem();
978 if (!SCORE_18N.equals(byWhat))
980 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
984 * set threshold options and 'autoscaled' which is
985 * false if 'threshold is min/max' is selected
986 * else true (colour range is on actual range of values)
988 fc.setThreshold(thresh);
989 fc.setAutoScaled(!thresholdIsMin.isSelected());
990 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
991 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
993 if (threshline == null)
996 * todo not yet implemented: visual indication of feature threshold
998 threshline = new GraphLine((max - min) / 2f, "Threshold",
1006 protected void raiseClosed()
1008 if (this.featureSettings != null)
1010 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
1015 * Action on OK is just to dismiss the dialog - any changes have already been
1019 public void okPressed()
1024 * Action on Cancel is to restore colour scheme and filters as they were when
1025 * the dialog was opened
1028 public void cancelPressed()
1030 fr.setColour(featureType, originalColour);
1031 fr.setFeatureFilter(featureType, originalFilter);
1032 refreshDisplay(true);
1036 * Action on text entry of a threshold value
1038 protected void thresholdValue_actionPerformed()
1043 * set 'adjusting' flag while moving the slider, so it
1044 * doesn't then in turn change the value (with rounding)
1047 float f = Float.parseFloat(thresholdValue.getText());
1048 f = Float.max(f, this.min);
1049 f = Float.min(f, this.max);
1050 setThresholdValueText(f);
1051 slider.setSliderValue(f);
1052 threshline.value = f;
1053 thresholdValue.setBackground(Color.white); // ok
1055 colourChanged(true);
1056 } catch (NumberFormatException ex)
1058 thresholdValue.setBackground(Color.red); // not ok
1064 * Sets the text field for threshold value, rounded to four significant figures
1068 void setThresholdValueText(float f)
1070 BigDecimal formatted = new BigDecimal(f).round(FOUR_SIG_FIG)
1071 .stripTrailingZeros();
1072 thresholdValue.setText(formatted.toPlainString());
1076 * Action on change of threshold slider value. This may be done interactively
1077 * (by moving the slider), or programmatically (to update the slider after
1078 * manual input of a threshold value).
1080 protected void sliderValueChanged()
1082 threshline.value = slider.getSliderValue();
1085 * repaint alignment, but not Overview or structure,
1086 * to avoid overload while dragging the slider
1088 colourChanged(false);
1091 void addActionListener(ActionListener listener)
1093 if (featureSettings != null)
1096 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1098 featureSettings = listener;
1102 * A helper method to build the drop-down choice of attributes for a feature.
1103 * If 'withRange' is true, then Score, and any attributes with a min-max
1104 * range, are added. If 'withText' is true, Label and any known attributes are
1105 * added. This allows 'categorical numerical' attributes e.g. codon position
1106 * to be coloured by text.
1108 * Where metadata is available with a description for an attribute, that is
1109 * added as a tooltip.
1111 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1112 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1114 * This method does not add any ActionListener to the JComboBox.
1120 protected JComboBox<Object> populateAttributesDropdown(
1121 List<String[]> attNames, boolean withRange, boolean withText)
1123 List<String> displayAtts = new ArrayList<>();
1124 List<String> tooltips = new ArrayList<>();
1128 displayAtts.add(LABEL_18N);
1129 tooltips.add(MessageManager.getString("label.description"));
1133 float[][] minMax = fr.getMinMax().get(featureType);
1134 if (minMax != null && minMax[0][0] != minMax[0][1])
1136 displayAtts.add(SCORE_18N);
1137 tooltips.add(SCORE_18N);
1141 FeatureAttributes fa = FeatureAttributes.getInstance();
1142 for (String[] attName : attNames)
1144 float[] minMax = fa.getMinMax(featureType, attName);
1145 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1146 if (!withText && !hasRange)
1150 displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
1151 String desc = fa.getDescription(featureType, attName);
1152 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1154 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1156 tooltips.add(desc == null ? "" : desc);
1159 // now convert String List to Object List for buildComboWithTooltips
1160 List<Object> displayAttsObjects = new ArrayList<>(displayAtts);
1161 JComboBox<Object> attCombo = JvSwingUtils
1162 .buildComboWithTooltips(displayAttsObjects, tooltips);
1168 * Populates initial layout of the feature attribute filters panel
1170 private JPanel initialiseFiltersPanel()
1172 filters = new ArrayList<>();
1174 JPanel filtersPanel = new JPanel();
1175 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1176 filtersPanel.setBackground(Color.white);
1177 JvSwingUtils.createTitledBorder(filtersPanel,
1178 MessageManager.getString("label.filters"), true);
1180 JPanel andOrPanel = initialiseAndOrPanel();
1181 filtersPanel.add(andOrPanel);
1184 * panel with filters - populated by refreshFiltersDisplay,
1185 * which also sets the layout manager
1187 chooseFiltersPanel = new JPanel();
1188 chooseFiltersPanel.setBackground(Color.white);
1189 filtersPanel.add(chooseFiltersPanel);
1191 return filtersPanel;
1195 * Lays out the panel with radio buttons to AND or OR filter conditions
1199 private JPanel initialiseAndOrPanel()
1201 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1202 andOrPanel.setBackground(Color.white);
1203 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1204 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1205 andFilters.setOpaque(false);
1206 orFilters.setOpaque(false);
1207 ActionListener actionListener = new ActionListener()
1210 public void actionPerformed(ActionEvent e)
1215 andFilters.addActionListener(actionListener);
1216 orFilters.addActionListener(actionListener);
1217 ButtonGroup andOr = new ButtonGroup();
1218 andOr.add(andFilters);
1219 andOr.add(orFilters);
1220 andFilters.setSelected(true);
1222 new JLabel(MessageManager.getString("label.join_conditions")));
1223 andOrPanel.add(andFilters);
1224 andOrPanel.add(orFilters);
1229 * Refreshes the display to show any filters currently configured for the
1230 * selected feature type (editable, with 'remove' option), plus one extra row
1231 * for adding a condition. This should be called after a filter has been
1232 * removed, added or amended.
1234 private void updateFiltersPanel()
1237 * clear the panel and list of filter conditions
1239 chooseFiltersPanel.removeAll();
1243 * look up attributes known for feature type
1245 List<String[]> attNames = FeatureAttributes.getInstance()
1246 .getAttributes(featureType);
1249 * if this feature type has filters set, load them first
1251 FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
1252 if (featureFilters != null)
1254 if (!featureFilters.isAnded())
1256 orFilters.setSelected(true);
1258 // avoid use of lambda expression to keep SwingJS happy
1259 // featureFilters.getMatchers().forEach(item -> filters.add(item));
1260 for (FeatureMatcherI matcher : featureFilters.getMatchers())
1262 filters.add(matcher);
1267 * and an empty filter for the user to populate (add)
1269 filters.add(FeatureMatcher.NULL_MATCHER);
1272 * use GridLayout to 'justify' rows to the top of the panel, until
1273 * there are too many to fit in, then fall back on BoxLayout
1275 if (filters.size() <= 5)
1277 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1281 chooseFiltersPanel.setLayout(
1282 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1286 * render the conditions in rows, each in its own JPanel
1288 int filterIndex = 0;
1289 for (FeatureMatcherI filter : filters)
1291 JPanel row = addFilter(filter, attNames, filterIndex);
1292 chooseFiltersPanel.add(row);
1301 * A helper method that constructs a row (panel) with one filter condition:
1303 * <li>a drop-down list of Label, Score and attribute names to choose
1305 * <li>a drop-down list of conditions to choose from</li>
1306 * <li>a text field for input of a match pattern</li>
1307 * <li>optionally, a 'remove' button</li>
1309 * The filter values are set as defaults for the input fields. The 'remove'
1310 * button is added unless the pattern is empty (incomplete filter condition).
1312 * Action handlers on these fields provide for
1314 * <li>validate pattern field - should be numeric if condition is numeric</li>
1315 * <li>save filters and refresh display on any (valid) change</li>
1316 * <li>remove filter and refresh on 'Remove'</li>
1317 * <li>update conditions list on change of Label/Score/Attribute</li>
1318 * <li>refresh value field tooltip with min-max range on change of
1324 * @param filterIndex
1327 protected JPanel addFilter(FeatureMatcherI filter,
1328 List<String[]> attNames, int filterIndex)
1330 String[] attName = filter.getAttribute();
1331 Condition cond = filter.getMatcher().getCondition();
1332 String pattern = filter.getMatcher().getPattern();
1334 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1335 filterRow.setBackground(Color.white);
1338 * drop-down choice of attribute, with description as a tooltip
1339 * if we can obtain it
1341 final JComboBox<Object> attCombo = populateAttributesDropdown(attNames,
1343 String filterBy = setSelectedAttribute(attCombo, filter);
1345 JComboBox<Condition> condCombo = new JComboBox<>();
1347 JTextField patternField = new JTextField(8);
1348 patternField.setText(pattern);
1351 * action handlers that validate and (if valid) apply changes
1353 ActionListener actionListener = new ActionListener()
1356 public void actionPerformed(ActionEvent e)
1358 if (validateFilter(patternField, condCombo))
1360 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1367 ItemListener itemListener = new ItemListener()
1370 public void itemStateChanged(ItemEvent e)
1372 actionListener.actionPerformed(null);
1376 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1378 attCombo.setSelectedIndex(0);
1382 attCombo.setSelectedItem(
1383 FeatureMatcher.toAttributeDisplayName(attName));
1385 attCombo.addItemListener(new ItemListener()
1388 public void itemStateChanged(ItemEvent e)
1391 * on change of attribute, refresh the conditions list to
1392 * ensure it is appropriate for the attribute datatype
1394 populateConditions((String) attCombo.getSelectedItem(),
1395 (Condition) condCombo.getSelectedItem(), condCombo,
1397 actionListener.actionPerformed(null);
1401 filterRow.add(attCombo);
1404 * drop-down choice of test condition
1406 populateConditions(filterBy, cond, condCombo, patternField);
1407 condCombo.setPreferredSize(new Dimension(150, 20));
1408 condCombo.addItemListener(itemListener);
1409 filterRow.add(condCombo);
1412 * pattern to match against
1414 patternField.addActionListener(actionListener);
1415 patternField.addFocusListener(new FocusAdapter()
1418 public void focusLost(FocusEvent e)
1420 actionListener.actionPerformed(null);
1423 filterRow.add(patternField);
1426 * disable pattern field for condition 'Present / NotPresent'
1428 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1429 patternField.setEnabled(selectedCondition.needsAPattern());
1432 * if a numeric condition is selected, show the value range
1433 * as a tooltip on the value input field
1435 setNumericHints(filterBy, selectedCondition, patternField);
1438 * add remove button if filter is populated (non-empty pattern)
1440 if (!patternField.isEnabled()
1441 || (pattern != null && pattern.trim().length() > 0))
1443 JButton removeCondition = new JButton("\u2717");
1444 // Dingbats cursive x
1445 removeCondition.setBorder(new EmptyBorder(0, 0, 0, 0));
1446 removeCondition.setBackground(Color.WHITE);
1447 removeCondition.setPreferredSize(new Dimension(23, 17));
1448 removeCondition.setToolTipText(
1449 MessageManager.getString("label.delete_condition"));
1450 removeCondition.addActionListener(new ActionListener()
1453 public void actionPerformed(ActionEvent e)
1455 filters.remove(filterIndex);
1459 filterRow.add(removeCondition);
1466 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1472 private String setSelectedAttribute(JComboBox<Object> attCombo,
1473 FeatureMatcherI filter)
1476 if (filter.isByScore())
1480 else if (filter.isByLabel())
1486 item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
1488 attCombo.setSelectedItem(item);
1493 * If a numeric comparison condition is selected, retrieves the min-max range
1494 * for the value (score or attribute), and sets it as a tooltip on the value
1495 * field. If the field is currently empty, then pre-populates it with
1497 * <li>the minimum value, if condition is > or >=</li>
1498 * <li>the maximum value, if condition is < or <=</li>
1502 * @param selectedCondition
1503 * @param patternField
1505 private void setNumericHints(String attName, Condition selectedCondition,
1506 JTextField patternField)
1508 patternField.setToolTipText("");
1510 if (selectedCondition.isNumeric())
1512 float[] minMax = getMinMax(attName);
1515 String minFormatted = DECFMT_2_2.format(minMax[0]);
1516 String maxFormatted = DECFMT_2_2.format(minMax[1]);
1517 String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
1518 patternField.setToolTipText(tip);
1519 if (patternField.getText().isEmpty())
1521 if (selectedCondition == Condition.GE
1522 || selectedCondition == Condition.GT)
1524 patternField.setText(minFormatted);
1528 if (selectedCondition == Condition.LE
1529 || selectedCondition == Condition.LT)
1531 patternField.setText(maxFormatted);
1540 * Populates the drop-down list of comparison conditions for the given
1541 * attribute name. The conditions added depend on the datatype of the
1542 * attribute values. The supplied condition is set as the selected item in the
1543 * list, provided it is in the list. If the pattern is now invalid
1544 * (non-numeric pattern for a numeric condition), it is cleared.
1549 * @param patternField
1551 void populateConditions(String attName, Condition cond,
1552 JComboBox<Condition> condCombo, JTextField patternField)
1554 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1555 FeatureMatcher.fromAttributeDisplayName(attName));
1556 if (LABEL_18N.equals(attName))
1558 type = Datatype.Character;
1560 else if (SCORE_18N.equals(attName))
1562 type = Datatype.Number;
1566 * remove itemListener before starting
1568 ItemListener listener = condCombo.getItemListeners()[0];
1569 condCombo.removeItemListener(listener);
1570 boolean condIsValid = false;
1572 condCombo.removeAllItems();
1573 for (Condition c : Condition.values())
1575 if ((c.isNumeric() && type == Datatype.Number)
1576 || (!c.isNumeric() && type != Datatype.Number))
1578 condCombo.addItem(c);
1587 * set the selected condition (does nothing if not in the list)
1591 condCombo.setSelectedItem(cond);
1595 condCombo.setSelectedIndex(0);
1599 * clear pattern if it is now invalid for condition
1601 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1605 String pattern = patternField.getText().trim();
1606 if (pattern.length() > 0)
1608 Float.valueOf(pattern);
1610 } catch (NumberFormatException e)
1612 patternField.setText("");
1617 * restore the listener
1619 condCombo.addItemListener(listener);
1623 * Answers true unless a numeric condition has been selected with a
1624 * non-numeric value. Sets the value field to RED with a tooltip if in error.
1626 * If the pattern is expected but is empty, this method returns false, but
1627 * does not mark the field as invalid. This supports selecting an attribute
1628 * for a new condition before a match pattern has been entered.
1633 protected boolean validateFilter(JTextField value,
1634 JComboBox<Condition> condCombo)
1636 if (value == null || condCombo == null)
1638 return true; // fields not populated
1641 Condition cond = (Condition) condCombo.getSelectedItem();
1642 if (!cond.needsAPattern())
1647 value.setBackground(Color.white);
1648 value.setToolTipText("");
1649 String v1 = value.getText().trim();
1650 if (v1.length() == 0)
1655 if (cond.isNumeric() && v1.length() > 0)
1660 } catch (NumberFormatException e)
1662 value.setBackground(Color.red);
1663 value.setToolTipText(
1664 MessageManager.getString("label.numeric_required"));
1673 * Constructs a filter condition from the given input fields, and replaces the
1674 * condition at filterIndex with the new one. Does nothing if the pattern
1675 * field is blank (unless the match condition is one that doesn't require a
1676 * pattern, e.g. 'Is present'). Answers true if the filter was updated, else
1679 * This method may update the tooltip on the filter value field to show the
1680 * value range, if a numeric condition is selected. This ensures the tooltip
1681 * is updated when a numeric valued attribute is chosen on the last 'add a
1687 * @param filterIndex
1689 protected boolean updateFilter(JComboBox<Object> attCombo,
1690 JComboBox<Condition> condCombo, JTextField valueField,
1696 attName = (String) attCombo.getSelectedItem();
1697 } catch (Exception e)
1699 Cache.log.error("Problem casting Combo box entry to String");
1700 attName = attCombo.getSelectedItem().toString();
1702 Condition cond = (Condition) condCombo.getSelectedItem();
1703 String pattern = valueField.getText().trim();
1705 setNumericHints(attName, cond, valueField);
1707 if (pattern.length() == 0 && cond.needsAPattern())
1709 valueField.setEnabled(true); // ensure pattern field is enabled!
1714 * Construct a matcher that operates on Label, Score,
1715 * or named attribute
1717 FeatureMatcherI km = null;
1718 if (LABEL_18N.equals(attName))
1720 km = FeatureMatcher.byLabel(cond, pattern);
1722 else if (SCORE_18N.equals(attName))
1724 km = FeatureMatcher.byScore(cond, pattern);
1728 km = FeatureMatcher.byAttribute(cond, pattern,
1729 FeatureMatcher.fromAttributeDisplayName(attName));
1732 filters.set(filterIndex, km);
1738 * Action on any change to feature filtering, namely
1740 * <li>change of selected attribute</li>
1741 * <li>change of selected condition</li>
1742 * <li>change of match pattern</li>
1743 * <li>removal of a condition</li>
1745 * The inputs are parsed into a combined filter and this is set for the
1746 * feature type, and the alignment redrawn.
1748 protected void filtersChanged()
1751 * update the filter conditions for the feature type
1753 boolean anded = andFilters.isSelected();
1754 FeatureMatcherSetI combined = new FeatureMatcherSet();
1756 for (FeatureMatcherI filter : filters)
1758 String pattern = filter.getMatcher().getPattern();
1759 Condition condition = filter.getMatcher().getCondition();
1760 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1764 combined.and(filter);
1768 combined.or(filter);
1774 * save the filter conditions in the FeatureRenderer
1775 * (note this might now be an empty filter with no conditions)
1777 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1778 refreshDisplay(true);
1780 updateFiltersPanel();
1784 * Repaints alignment, structure and overview (if shown). If there is a
1785 * complementary view which is showing this view's features, then also
1788 * @param updateStructsAndOverview
1790 void refreshDisplay(boolean updateStructsAndOverview)
1792 ap.paintAlignment(true, updateStructsAndOverview);
1793 AlignViewportI complement = ap.getAlignViewport().getCodingComplement();
1794 if (complement != null && complement.isShowComplementFeatures())
1796 AlignFrame af2 = Desktop.getAlignFrameFor(complement);
1797 af2.alignPanel.paintAlignment(true, updateStructsAndOverview);