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.JTextField;
66 import javax.swing.SwingConstants;
67 import javax.swing.border.LineBorder;
68 import javax.swing.event.ChangeEvent;
69 import javax.swing.event.ChangeListener;
70 import javax.swing.plaf.basic.BasicArrowButton;
73 * A dialog where the user can configure colour scheme, and any filters, for one
76 * (Was FeatureColourChooser prior to Jalview 1.11, renamed with the addition of
79 public class FeatureTypeSettings extends JalviewDialog
81 private final static String LABEL_18N = MessageManager
82 .getString("label.label");
84 private final static String SCORE_18N = MessageManager
85 .getString("label.score");
87 private static final int RADIO_WIDTH = 130;
89 private static final String COLON = ":";
91 private static final int MAX_TOOLTIP_LENGTH = 50;
93 private static final int NO_COLOUR_OPTION = 0;
95 private static final int MIN_COLOUR_OPTION = 1;
97 private static final int MAX_COLOUR_OPTION = 2;
99 private static final int ABOVE_THRESHOLD_OPTION = 1;
101 private static final int BELOW_THRESHOLD_OPTION = 2;
103 private static final DecimalFormat DECFMT_2_2 = new DecimalFormat(
107 * FeatureRenderer holds colour scheme and filters for feature types
109 private final FeatureRenderer fr; // todo refactor to allow interface type
113 * the view panel to update when settings change
115 private final AlignmentViewPanel ap;
117 private final String featureType;
120 * the colour and filters to reset to on Cancel
122 private final FeatureColourI originalColour;
124 private final FeatureMatcherSetI originalFilter;
127 * set flag to true when setting values programmatically,
128 * to avoid invocation of action handlers
130 private boolean adjusting = false;
133 * minimum of the value range for graduated colour
134 * (may be for feature score or for a numeric attribute)
139 * maximum of the value range for graduated colour
144 * scale factor for conversion between absolute min-max and slider
146 private float scaleFactor;
149 * radio button group, to select what to colour by:
150 * simple colour, by category (text), or graduated
152 private JRadioButton simpleColour = new JRadioButton();
154 private JRadioButton byCategory = new JRadioButton();
156 private JRadioButton graduatedColour = new JRadioButton();
159 * colours and filters are shown in tabbed view or single content pane
161 JPanel coloursPanel, filtersPanel;
163 JPanel singleColour = new JPanel();
165 private JPanel minColour = new JPanel();
167 private JPanel maxColour = new JPanel();
169 private JComboBox<String> threshold = new JComboBox<>();
171 private JSlider slider = new JSlider();
173 private JTextField thresholdValue = new JTextField(20);
175 private JCheckBox thresholdIsMin = new JCheckBox();
177 private GraphLine threshline;
179 private ActionListener featureSettings = null;
181 private ActionListener changeColourAction;
184 * choice of option for 'colour for no value'
186 private JComboBox<String> noValueCombo;
189 * choice of what to colour by text (Label or attribute)
191 private JComboBox<String> colourByTextCombo;
194 * choice of what to colour by range (Score or attribute)
196 private JComboBox<String> colourByRangeCombo;
198 private JRadioButton andFilters;
200 private JRadioButton orFilters;
203 * filters for the currently selected feature type
205 private List<FeatureMatcherI> filters;
207 private JPanel chooseFiltersPanel;
215 public FeatureTypeSettings(FeatureRenderer frender, String theType)
218 this.featureType = theType;
220 originalFilter = fr.getFeatureFilter(theType);
221 originalColour = fr.getFeatureColours().get(theType);
228 } catch (Exception ex)
230 ex.printStackTrace();
240 colourChanged(false);
242 String title = MessageManager
243 .formatMessage("label.display_settings_for", new String[]
245 initDialogFrame(this, true, false, title, 500, 500);
251 * Configures the widgets on the Colours tab according to the current feature
254 private void updateColoursTab()
256 FeatureColourI fc = fr.getFeatureColours().get(featureType);
259 * suppress action handling while updating values programmatically
267 if (fc.isSimpleColour())
269 singleColour.setBackground(fc.getColour());
270 singleColour.setForeground(fc.getColour());
271 simpleColour.setSelected(true);
275 * colour by text (Label or attribute text)
277 if (fc.isColourByLabel())
279 byCategory.setSelected(true);
280 colourByTextCombo.setEnabled(colourByTextCombo.getItemCount() > 1);
281 if (fc.isColourByAttribute())
283 String[] attributeName = fc.getAttributeName();
284 colourByTextCombo.setSelectedItem(
285 FeatureMatcher.toAttributeDisplayName(attributeName));
289 colourByTextCombo.setSelectedItem(LABEL_18N);
294 colourByTextCombo.setEnabled(false);
297 if (!fc.isGraduatedColour())
299 colourByRangeCombo.setEnabled(false);
300 minColour.setEnabled(false);
301 maxColour.setEnabled(false);
302 noValueCombo.setEnabled(false);
303 threshold.setEnabled(false);
304 slider.setEnabled(false);
305 thresholdValue.setEnabled(false);
306 thresholdIsMin.setEnabled(false);
311 * Graduated colour, by score or attribute value range
313 graduatedColour.setSelected(true);
314 updateColourMinMax(); // ensure min, max are set
315 colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
316 minColour.setEnabled(true);
317 maxColour.setEnabled(true);
318 noValueCombo.setEnabled(true);
319 threshold.setEnabled(true);
320 minColour.setBackground(fc.getMinColour());
321 maxColour.setBackground(fc.getMaxColour());
323 if (fc.isColourByAttribute())
325 String[] attributeName = fc.getAttributeName();
326 colourByRangeCombo.setSelectedItem(
327 FeatureMatcher.toAttributeDisplayName(attributeName));
331 colourByRangeCombo.setSelectedItem(SCORE_18N);
333 Color noColour = fc.getNoColour();
334 if (noColour == null)
336 noValueCombo.setSelectedIndex(NO_COLOUR_OPTION);
338 else if (noColour.equals(fc.getMinColour()))
340 noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION);
342 else if (noColour.equals(fc.getMaxColour()))
344 noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION);
348 * update min-max scaling if there is a range to work with,
349 * else disable the widgets (this shouldn't happen if only
350 * valid options are offered in the combo box)
352 scaleFactor = (max == min) ? 1f : 100f / (max - min);
353 float range = (max - min) * scaleFactor;
354 slider.setMinimum((int) (min * scaleFactor));
355 slider.setMaximum((int) (max * scaleFactor));
356 slider.setMajorTickSpacing((int) (range / 10f));
358 threshline = new GraphLine((max - min) / 2f, "Threshold",
360 threshline.value = fc.getThreshold();
362 if (fc.hasThreshold())
364 threshold.setSelectedIndex(
365 fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
366 : BELOW_THRESHOLD_OPTION);
367 slider.setEnabled(true);
368 slider.setValue((int) (fc.getThreshold() * scaleFactor));
369 thresholdValue.setText(String.valueOf(fc.getThreshold()));
370 thresholdValue.setEnabled(true);
371 thresholdIsMin.setEnabled(true);
375 slider.setEnabled(false);
376 thresholdValue.setEnabled(false);
377 thresholdIsMin.setEnabled(false);
379 thresholdIsMin.setSelected(!fc.isAutoScaled());
387 * Configures the initial layout
389 private void initialise()
391 this.setLayout(new BorderLayout());
394 * an ActionListener that applies colour changes
396 changeColourAction = new ActionListener()
399 public void actionPerformed(ActionEvent e)
406 * first panel/tab: colour options
408 JPanel coloursPanel = initialiseColoursPanel();
409 this.add(coloursPanel, BorderLayout.NORTH);
412 * second panel/tab: filter options
414 JPanel filtersPanel = initialiseFiltersPanel();
415 this.add(filtersPanel, BorderLayout.CENTER);
417 JPanel okCancelPanel = initialiseOkCancelPanel();
419 this.add(okCancelPanel, BorderLayout.SOUTH);
423 * Updates the min-max range if Colour By selected item is Score, or an
424 * attribute, with a min-max range
426 protected void updateColourMinMax()
428 if (!graduatedColour.isSelected())
433 String colourBy = (String) colourByRangeCombo.getSelectedItem();
434 float[] minMax = getMinMax(colourBy);
444 * Retrieves the min-max range:
446 * <li>of feature score, if colour or filter is by Score</li>
447 * <li>else of the selected attribute</li>
453 private float[] getMinMax(String attName)
455 float[] minMax = null;
456 if (SCORE_18N.equals(attName))
458 minMax = fr.getMinMax().get(featureType)[0];
462 // colour by attribute range
463 minMax = FeatureAttributes.getInstance().getMinMax(featureType,
464 FeatureMatcher.fromAttributeDisplayName(attName));
470 * Lay out fields for graduated colour (by score or attribute value)
474 private JPanel initialiseGraduatedColourPanel()
476 JPanel graduatedColourPanel = new JPanel();
477 graduatedColourPanel.setLayout(
478 new BoxLayout(graduatedColourPanel, BoxLayout.Y_AXIS));
479 JvSwingUtils.createTitledBorder(graduatedColourPanel,
480 MessageManager.getString("label.graduated_colour"), true);
481 graduatedColourPanel.setBackground(Color.white);
484 * first row: graduated colour radio button, score/attribute drop-down
486 JPanel graduatedChoicePanel = new JPanel(
487 new FlowLayout(FlowLayout.LEFT));
488 graduatedChoicePanel.setBackground(Color.white);
489 graduatedColour = new JRadioButton(
490 MessageManager.getString("label.by_range_of") + COLON);
491 graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
492 graduatedColour.addItemListener(new ItemListener()
495 public void itemStateChanged(ItemEvent e)
497 if (graduatedColour.isSelected())
503 graduatedChoicePanel.add(graduatedColour);
505 List<String[]> attNames = FeatureAttributes.getInstance()
506 .getAttributes(featureType);
507 colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
508 colourByRangeCombo.addItemListener(new ItemListener()
511 public void itemStateChanged(ItemEvent e)
518 * disable graduated colour option if no range found
520 graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
522 graduatedChoicePanel.add(colourByRangeCombo);
523 graduatedColourPanel.add(graduatedChoicePanel);
526 * second row - min/max/no colours
528 JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
529 colourRangePanel.setBackground(Color.white);
530 graduatedColourPanel.add(colourRangePanel);
532 minColour.setFont(JvSwingUtils.getLabelFont());
533 minColour.setBorder(BorderFactory.createLineBorder(Color.black));
534 minColour.setPreferredSize(new Dimension(40, 20));
535 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
536 minColour.addMouseListener(new MouseAdapter()
539 public void mousePressed(MouseEvent e)
541 if (minColour.isEnabled())
543 showColourChooser(minColour, "label.select_colour_minimum_value");
548 maxColour.setFont(JvSwingUtils.getLabelFont());
549 maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
550 maxColour.setPreferredSize(new Dimension(40, 20));
551 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
552 maxColour.addMouseListener(new MouseAdapter()
555 public void mousePressed(MouseEvent e)
557 if (maxColour.isEnabled())
559 showColourChooser(maxColour, "label.select_colour_maximum_value");
563 maxColour.setBorder(new LineBorder(Color.black));
566 * default max colour to last plain colour;
567 * make min colour a pale version of max colour
569 FeatureColourI fc = fr.getFeatureColours().get(featureType);
570 Color bg = fc.getColour() == null ? Color.BLACK : fc.getColour();
571 maxColour.setBackground(bg);
572 minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
574 noValueCombo = new JComboBox<>();
575 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
576 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
577 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
578 noValueCombo.addItemListener(new ItemListener()
581 public void itemStateChanged(ItemEvent e)
587 JLabel minText = new JLabel(
588 MessageManager.getString("label.min_value") + COLON);
589 minText.setFont(JvSwingUtils.getLabelFont());
590 JLabel maxText = new JLabel(
591 MessageManager.getString("label.max_value") + COLON);
592 maxText.setFont(JvSwingUtils.getLabelFont());
593 JLabel noText = new JLabel(
594 MessageManager.getString("label.no_value") + COLON);
595 noText.setFont(JvSwingUtils.getLabelFont());
597 colourRangePanel.add(minText);
598 colourRangePanel.add(minColour);
599 colourRangePanel.add(maxText);
600 colourRangePanel.add(maxColour);
601 colourRangePanel.add(noText);
602 colourRangePanel.add(noValueCombo);
605 * third row - threshold options and value
607 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
608 thresholdPanel.setBackground(Color.white);
609 graduatedColourPanel.add(thresholdPanel);
611 threshold.addActionListener(changeColourAction);
612 threshold.setToolTipText(MessageManager
613 .getString("label.threshold_feature_display_by_score"));
614 threshold.addItem(MessageManager
615 .getString("label.threshold_feature_no_threshold")); // index 0
616 threshold.addItem(MessageManager
617 .getString("label.threshold_feature_above_threshold")); // index 1
618 threshold.addItem(MessageManager
619 .getString("label.threshold_feature_below_threshold")); // index 2
621 thresholdValue.addActionListener(new ActionListener()
624 public void actionPerformed(ActionEvent e)
626 thresholdValue_actionPerformed();
629 thresholdValue.addFocusListener(new FocusAdapter()
632 public void focusLost(FocusEvent e)
634 thresholdValue_actionPerformed();
637 slider.setPaintLabels(false);
638 slider.setPaintTicks(true);
639 slider.setBackground(Color.white);
640 slider.setEnabled(false);
641 slider.setOpaque(false);
642 slider.setPreferredSize(new Dimension(100, 32));
643 slider.setToolTipText(
644 MessageManager.getString("label.adjust_threshold"));
646 slider.addChangeListener(new ChangeListener()
649 public void stateChanged(ChangeEvent evt)
654 .setText(String.valueOf(slider.getValue() / scaleFactor));
655 sliderValueChanged();
659 slider.addMouseListener(new MouseAdapter()
662 public void mouseReleased(MouseEvent evt)
665 * only update Overview and/or structure colouring
666 * when threshold slider drag ends (mouse up)
670 ap.paintAlignment(true, true);
675 thresholdValue.setEnabled(false);
676 thresholdValue.setColumns(7);
678 thresholdPanel.add(threshold);
679 thresholdPanel.add(slider);
680 thresholdPanel.add(thresholdValue);
682 thresholdIsMin.setBackground(Color.white);
684 .setText(MessageManager.getString("label.threshold_minmax"));
685 thresholdIsMin.setToolTipText(MessageManager
686 .getString("label.toggle_absolute_relative_display_threshold"));
687 thresholdIsMin.addActionListener(changeColourAction);
688 thresholdPanel.add(thresholdIsMin);
690 return graduatedColourPanel;
694 * Lay out OK and Cancel buttons
698 private JPanel initialiseOkCancelPanel()
700 JPanel okCancelPanel = new JPanel();
701 // okCancelPanel.setBackground(Color.white);
702 okCancelPanel.add(ok);
703 okCancelPanel.add(cancel);
704 return okCancelPanel;
708 * Lay out Colour options panel, containing
710 * <li>plain colour, with colour picker</li>
711 * <li>colour by text, with choice of Label or other attribute</li>
712 * <li>colour by range, of score or other attribute, when available</li>
717 private JPanel initialiseColoursPanel()
719 JPanel colourByPanel = new JPanel();
720 colourByPanel.setBackground(Color.white);
721 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
722 JvSwingUtils.createTitledBorder(colourByPanel,
723 MessageManager.getString("action.colour"), true);
726 * simple colour radio button and colour picker
728 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
729 simpleColourPanel.setBackground(Color.white);
730 colourByPanel.add(simpleColourPanel);
732 simpleColour = new JRadioButton(
733 MessageManager.getString("label.simple_colour"));
734 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
735 simpleColour.addItemListener(new ItemListener()
738 public void itemStateChanged(ItemEvent e)
740 if (simpleColour.isSelected() && !adjusting)
747 singleColour.setFont(JvSwingUtils.getLabelFont());
748 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
749 singleColour.setPreferredSize(new Dimension(40, 20));
750 if (originalColour.isGraduatedColour())
752 singleColour.setBackground(originalColour.getMaxColour());
753 singleColour.setForeground(originalColour.getMaxColour());
757 singleColour.setBackground(originalColour.getColour());
758 singleColour.setForeground(originalColour.getColour());
760 singleColour.addMouseListener(new MouseAdapter()
763 public void mousePressed(MouseEvent e)
765 if (simpleColour.isSelected())
767 showColourChooser(singleColour, "label.select_colour");
771 simpleColourPanel.add(simpleColour); // radio button
772 simpleColourPanel.add(singleColour); // colour picker button
775 * colour by text (category) radio button and drop-down choice list
777 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
778 byTextPanel.setBackground(Color.white);
779 JvSwingUtils.createTitledBorder(byTextPanel,
780 MessageManager.getString("label.colour_by_text"), true);
781 colourByPanel.add(byTextPanel);
782 byCategory = new JRadioButton(
783 MessageManager.getString("label.by_text_of") + COLON);
784 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
785 byCategory.addItemListener(new ItemListener()
788 public void itemStateChanged(ItemEvent e)
790 if (byCategory.isSelected())
796 byTextPanel.add(byCategory);
798 List<String[]> attNames = FeatureAttributes.getInstance()
799 .getAttributes(featureType);
800 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
801 colourByTextCombo.addItemListener(new ItemListener()
804 public void itemStateChanged(ItemEvent e)
809 byTextPanel.add(colourByTextCombo);
812 * graduated colour panel
814 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
815 colourByPanel.add(graduatedColourPanel);
818 * 3 radio buttons select between simple colour,
819 * by category (text), or graduated
821 ButtonGroup bg = new ButtonGroup();
822 bg.add(simpleColour);
824 bg.add(graduatedColour);
826 return colourByPanel;
829 private void showColourChooser(JPanel colourPanel, String key)
831 Color col = JColorChooser.showDialog(this,
832 MessageManager.getString(key), colourPanel.getBackground());
835 colourPanel.setBackground(col);
836 colourPanel.setForeground(col);
838 colourPanel.repaint();
843 * Constructs and sets the selected colour options as the colour for the
844 * feature type, and repaints the alignment, and optionally the Overview
845 * and/or structure viewer if open
847 * @param updateStructsAndOverview
849 void colourChanged(boolean updateStructsAndOverview)
854 * ignore action handlers while setting values programmatically
860 * ensure min-max range is for the latest choice of
861 * 'graduated colour by'
863 updateColourMinMax();
865 FeatureColourI acg = makeColourFromInputs();
868 * save the colour, and repaint stuff
870 fr.setColour(featureType, acg);
871 ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
877 * Converts the input values into an instance of FeatureColour
881 private FeatureColourI makeColourFromInputs()
884 * easiest case - a single colour
886 if (simpleColour.isSelected())
888 return new FeatureColour(singleColour.getBackground());
892 * next easiest case - colour by Label, or attribute text
894 if (byCategory.isSelected())
896 Color c = singleColour.getBackground();
897 FeatureColourI fc = new FeatureColour(c);
898 fc.setColourByLabel(true);
899 String byWhat = (String) colourByTextCombo.getSelectedItem();
900 if (!LABEL_18N.equals(byWhat))
903 FeatureMatcher.fromAttributeDisplayName(byWhat));
909 * remaining case - graduated colour by score, or attribute value
911 Color noColour = null;
912 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
914 noColour = minColour.getBackground();
916 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
918 noColour = maxColour.getBackground();
924 thresh = Float.valueOf(thresholdValue.getText());
925 } catch (NumberFormatException e)
927 // invalid inputs are already handled on entry
931 * min-max range is to (or from) threshold value if
932 * 'threshold is min/max' is selected
934 float minValue = min;
935 float maxValue = max;
936 final int thresholdOption = threshold.getSelectedIndex();
937 if (thresholdIsMin.isSelected()
938 && thresholdOption == ABOVE_THRESHOLD_OPTION)
942 if (thresholdIsMin.isSelected()
943 && thresholdOption == BELOW_THRESHOLD_OPTION)
949 * make the graduated colour
951 FeatureColourI fc = new FeatureColour(minColour.getBackground(),
952 maxColour.getBackground(), noColour, minValue, maxValue);
955 * set attribute to colour by if selected
957 String byWhat = (String) colourByRangeCombo.getSelectedItem();
958 if (!SCORE_18N.equals(byWhat))
960 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
964 * set threshold options and 'autoscaled' which is
965 * false if 'threshold is min/max' is selected
966 * else true (colour range is on actual range of values)
968 fc.setThreshold(thresh);
969 fc.setAutoScaled(!thresholdIsMin.isSelected());
970 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
971 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
973 if (threshline == null)
976 * todo not yet implemented: visual indication of feature threshold
978 threshline = new GraphLine((max - min) / 2f, "Threshold",
986 protected void raiseClosed()
988 if (this.featureSettings != null)
990 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
995 * Action on OK is just to dismiss the dialog - any changes have already been
999 public void okPressed()
1004 * Action on Cancel is to restore colour scheme and filters as they were when
1005 * the dialog was opened
1008 public void cancelPressed()
1010 fr.setColour(featureType, originalColour);
1011 fr.setFeatureFilter(featureType, originalFilter);
1012 ap.paintAlignment(true, true);
1016 * Action on text entry of a threshold value
1018 protected void thresholdValue_actionPerformed()
1023 * set 'adjusting' flag while moving the slider, so it
1024 * doesn't then in turn change the value (with rounding)
1027 float f = Float.parseFloat(thresholdValue.getText());
1028 f = Float.max(f, this.min);
1029 f = Float.min(f, this.max);
1030 thresholdValue.setText(String.valueOf(f));
1031 slider.setValue((int) (f * scaleFactor));
1032 threshline.value = f;
1033 thresholdValue.setBackground(Color.white); // ok
1035 colourChanged(true);
1036 } catch (NumberFormatException ex)
1038 thresholdValue.setBackground(Color.red); // not ok
1044 * Action on change of threshold slider value. This may be done interactively
1045 * (by moving the slider), or programmatically (to update the slider after
1046 * manual input of a threshold value).
1048 protected void sliderValueChanged()
1050 threshline.value = getRoundedSliderValue();
1053 * repaint alignment, but not Overview or structure,
1054 * to avoid overload while dragging the slider
1056 colourChanged(false);
1060 * Converts the slider value to its absolute value by dividing by the
1061 * scaleFactor. Rounding errors are squashed by forcing min/max of slider
1062 * range to the actual min/max of feature score range
1066 private float getRoundedSliderValue()
1068 int value = slider.getValue();
1069 float f = value == slider.getMaximum() ? max
1070 : (value == slider.getMinimum() ? min : value / scaleFactor);
1074 void addActionListener(ActionListener listener)
1076 if (featureSettings != null)
1079 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1081 featureSettings = listener;
1085 * A helper method to build the drop-down choice of attributes for a feature.
1086 * If 'withRange' is true, then Score, and any attributes with a min-max
1087 * range, are added. If 'withText' is true, Label and any known attributes are
1088 * added. This allows 'categorical numerical' attributes e.g. codon position
1089 * to be coloured by text.
1091 * Where metadata is available with a description for an attribute, that is
1092 * added as a tooltip.
1094 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1095 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1097 * This method does not add any ActionListener to the JComboBox.
1103 protected JComboBox<String> populateAttributesDropdown(
1104 List<String[]> attNames, boolean withRange, boolean withText)
1106 List<String> displayAtts = new ArrayList<>();
1107 List<String> tooltips = new ArrayList<>();
1111 displayAtts.add(LABEL_18N);
1112 tooltips.add(MessageManager.getString("label.description"));
1116 float[][] minMax = fr.getMinMax().get(featureType);
1117 if (minMax != null && minMax[0][0] != minMax[0][1])
1119 displayAtts.add(SCORE_18N);
1120 tooltips.add(SCORE_18N);
1124 FeatureAttributes fa = FeatureAttributes.getInstance();
1125 for (String[] attName : attNames)
1127 float[] minMax = fa.getMinMax(featureType, attName);
1128 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1129 if (!withText && !hasRange)
1133 displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
1134 String desc = fa.getDescription(featureType, attName);
1135 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1137 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1139 tooltips.add(desc == null ? "" : desc);
1142 JComboBox<String> attCombo = JvSwingUtils
1143 .buildComboWithTooltips(displayAtts, tooltips);
1149 * Populates initial layout of the feature attribute filters panel
1151 private JPanel initialiseFiltersPanel()
1153 filters = new ArrayList<>();
1155 JPanel filtersPanel = new JPanel();
1156 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1157 filtersPanel.setBackground(Color.white);
1158 JvSwingUtils.createTitledBorder(filtersPanel,
1159 MessageManager.getString("label.filters"), true);
1161 JPanel andOrPanel = initialiseAndOrPanel();
1162 filtersPanel.add(andOrPanel);
1165 * panel with filters - populated by refreshFiltersDisplay,
1166 * which also sets the layout manager
1168 chooseFiltersPanel = new JPanel();
1169 chooseFiltersPanel.setBackground(Color.white);
1170 filtersPanel.add(chooseFiltersPanel);
1172 return filtersPanel;
1176 * Lays out the panel with radio buttons to AND or OR filter conditions
1180 private JPanel initialiseAndOrPanel()
1182 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1183 andOrPanel.setBackground(Color.white);
1184 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1185 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1186 ActionListener actionListener = new ActionListener()
1189 public void actionPerformed(ActionEvent e)
1194 andFilters.addActionListener(actionListener);
1195 orFilters.addActionListener(actionListener);
1196 ButtonGroup andOr = new ButtonGroup();
1197 andOr.add(andFilters);
1198 andOr.add(orFilters);
1199 andFilters.setSelected(true);
1201 new JLabel(MessageManager.getString("label.join_conditions")));
1202 andOrPanel.add(andFilters);
1203 andOrPanel.add(orFilters);
1208 * Refreshes the display to show any filters currently configured for the
1209 * selected feature type (editable, with 'remove' option), plus one extra row
1210 * for adding a condition. This should be called after a filter has been
1211 * removed, added or amended.
1213 private void updateFiltersTab()
1216 * clear the panel and list of filter conditions
1218 chooseFiltersPanel.removeAll();
1222 * look up attributes known for feature type
1224 List<String[]> attNames = FeatureAttributes.getInstance()
1225 .getAttributes(featureType);
1228 * if this feature type has filters set, load them first
1230 FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
1231 if (featureFilters != null)
1233 if (!featureFilters.isAnded())
1235 orFilters.setSelected(true);
1237 featureFilters.getMatchers().forEach(matcher -> filters.add(matcher));
1241 * and an empty filter for the user to populate (add)
1243 filters.add(FeatureMatcher.NULL_MATCHER);
1246 * use GridLayout to 'justify' rows to the top of the panel, until
1247 * there are too many to fit in, then fall back on BoxLayout
1249 if (filters.size() <= 5)
1251 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1255 chooseFiltersPanel.setLayout(
1256 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1260 * render the conditions in rows, each in its own JPanel
1262 int filterIndex = 0;
1263 for (FeatureMatcherI filter : filters)
1265 JPanel row = addFilter(filter, attNames, filterIndex);
1266 chooseFiltersPanel.add(row);
1275 * A helper method that constructs a row (panel) with one filter condition:
1277 * <li>a drop-down list of Label, Score and attribute names to choose
1279 * <li>a drop-down list of conditions to choose from</li>
1280 * <li>a text field for input of a match pattern</li>
1281 * <li>optionally, a 'remove' button</li>
1283 * The filter values are set as defaults for the input fields. The 'remove'
1284 * button is added unless the pattern is empty (incomplete filter condition).
1286 * Action handlers on these fields provide for
1288 * <li>validate pattern field - should be numeric if condition is numeric</li>
1289 * <li>save filters and refresh display on any (valid) change</li>
1290 * <li>remove filter and refresh on 'Remove'</li>
1291 * <li>update conditions list on change of Label/Score/Attribute</li>
1292 * <li>refresh value field tooltip with min-max range on change of
1298 * @param filterIndex
1301 protected JPanel addFilter(FeatureMatcherI filter,
1302 List<String[]> attNames, int filterIndex)
1304 String[] attName = filter.getAttribute();
1305 Condition cond = filter.getMatcher().getCondition();
1306 String pattern = filter.getMatcher().getPattern();
1308 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1309 filterRow.setBackground(Color.white);
1312 * drop-down choice of attribute, with description as a tooltip
1313 * if we can obtain it
1315 final JComboBox<String> attCombo = populateAttributesDropdown(attNames,
1317 String filterBy = setSelectedAttribute(attCombo, filter);
1319 JComboBox<Condition> condCombo = new JComboBox<>();
1321 JTextField patternField = new JTextField(8);
1322 patternField.setText(pattern);
1325 * action handlers that validate and (if valid) apply changes
1327 ActionListener actionListener = new ActionListener()
1330 public void actionPerformed(ActionEvent e)
1332 if (validateFilter(patternField, condCombo))
1334 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1341 ItemListener itemListener = new ItemListener()
1344 public void itemStateChanged(ItemEvent e)
1346 actionListener.actionPerformed(null);
1350 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1352 attCombo.setSelectedIndex(0);
1356 attCombo.setSelectedItem(
1357 FeatureMatcher.toAttributeDisplayName(attName));
1359 attCombo.addItemListener(new ItemListener()
1362 public void itemStateChanged(ItemEvent e)
1365 * on change of attribute, refresh the conditions list to
1366 * ensure it is appropriate for the attribute datatype
1368 populateConditions((String) attCombo.getSelectedItem(),
1369 (Condition) condCombo.getSelectedItem(), condCombo,
1371 actionListener.actionPerformed(null);
1375 filterRow.add(attCombo);
1378 * drop-down choice of test condition
1380 populateConditions(filterBy, cond, condCombo, patternField);
1381 condCombo.setPreferredSize(new Dimension(150, 20));
1382 condCombo.addItemListener(itemListener);
1383 filterRow.add(condCombo);
1386 * pattern to match against
1388 patternField.addActionListener(actionListener);
1389 patternField.addFocusListener(new FocusAdapter()
1392 public void focusLost(FocusEvent e)
1394 actionListener.actionPerformed(null);
1397 filterRow.add(patternField);
1400 * disable pattern field for condition 'Present / NotPresent'
1402 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1403 patternField.setEnabled(selectedCondition.needsAPattern());
1406 * if a numeric condition is selected, show the value range
1407 * as a tooltip on the value input field
1409 setNumericHints(filterBy, selectedCondition, patternField);
1412 * add remove button if filter is populated (non-empty pattern)
1414 if (!patternField.isEnabled()
1415 || (pattern != null && pattern.trim().length() > 0))
1417 // todo: gif for button drawing '-' or 'x'
1418 JButton removeCondition = new BasicArrowButton(SwingConstants.WEST);
1420 .setToolTipText(MessageManager.getString("label.delete_row"));
1421 removeCondition.addActionListener(new ActionListener()
1424 public void actionPerformed(ActionEvent e)
1426 filters.remove(filterIndex);
1430 filterRow.add(removeCondition);
1437 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1443 private String setSelectedAttribute(JComboBox<String> attCombo,
1444 FeatureMatcherI filter)
1447 if (filter.isByScore())
1451 else if (filter.isByLabel())
1457 item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
1459 attCombo.setSelectedItem(item);
1464 * If a numeric comparison condition is selected, retrieves the min-max range
1465 * for the value (score or attribute), and sets it as a tooltip on the value
1466 * field. If the field is currently empty, then pre-populates it with
1468 * <li>the minimum value, if condition is > or >=</li>
1469 * <li>the maximum value, if condition is < or <=</li>
1473 * @param selectedCondition
1474 * @param patternField
1476 private void setNumericHints(String attName, Condition selectedCondition,
1477 JTextField patternField)
1479 patternField.setToolTipText("");
1481 if (selectedCondition.isNumeric())
1483 float[] minMax = getMinMax(attName);
1486 String minFormatted = DECFMT_2_2.format(minMax[0]);
1487 String maxFormatted = DECFMT_2_2.format(minMax[1]);
1488 String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
1489 patternField.setToolTipText(tip);
1490 if (patternField.getText().isEmpty())
1492 if (selectedCondition == Condition.GE
1493 || selectedCondition == Condition.GT)
1495 patternField.setText(minFormatted);
1499 if (selectedCondition == Condition.LE
1500 || selectedCondition == Condition.LT)
1502 patternField.setText(maxFormatted);
1511 * Populates the drop-down list of comparison conditions for the given
1512 * attribute name. The conditions added depend on the datatype of the
1513 * attribute values. The supplied condition is set as the selected item in the
1514 * list, provided it is in the list. If the pattern is now invalid
1515 * (non-numeric pattern for a numeric condition), it is cleared.
1520 * @param patternField
1522 private void populateConditions(String attName, Condition cond,
1523 JComboBox<Condition> condCombo, JTextField patternField)
1525 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1526 FeatureMatcher.fromAttributeDisplayName(attName));
1527 if (LABEL_18N.equals(attName))
1529 type = Datatype.Character;
1531 else if (SCORE_18N.equals(attName))
1533 type = Datatype.Number;
1537 * remove itemListener before starting
1539 ItemListener listener = condCombo.getItemListeners()[0];
1540 condCombo.removeItemListener(listener);
1541 boolean condIsValid = false;
1543 condCombo.removeAllItems();
1544 for (Condition c : Condition.values())
1546 if ((c.isNumeric() && type == Datatype.Number)
1547 || (!c.isNumeric() && type != Datatype.Number))
1549 condCombo.addItem(c);
1558 * set the selected condition (does nothing if not in the list)
1562 condCombo.setSelectedItem(cond);
1566 condCombo.setSelectedIndex(0);
1570 * clear pattern if it is now invalid for condition
1572 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1576 String pattern = patternField.getText().trim();
1577 if (pattern.length() > 0)
1579 Float.valueOf(pattern);
1581 } catch (NumberFormatException e)
1583 patternField.setText("");
1588 * restore the listener
1590 condCombo.addItemListener(listener);
1594 * Answers true unless a numeric condition has been selected with a
1595 * non-numeric value. Sets the value field to RED with a tooltip if in error.
1597 * If the pattern is expected but is empty, this method returns false, but
1598 * does not mark the field as invalid. This supports selecting an attribute
1599 * for a new condition before a match pattern has been entered.
1604 protected boolean validateFilter(JTextField value,
1605 JComboBox<Condition> condCombo)
1607 if (value == null || condCombo == null)
1609 return true; // fields not populated
1612 Condition cond = (Condition) condCombo.getSelectedItem();
1613 if (!cond.needsAPattern())
1618 value.setBackground(Color.white);
1619 value.setToolTipText("");
1620 String v1 = value.getText().trim();
1621 if (v1.length() == 0)
1626 if (cond.isNumeric() && v1.length() > 0)
1631 } catch (NumberFormatException e)
1633 value.setBackground(Color.red);
1634 value.setToolTipText(
1635 MessageManager.getString("label.numeric_required"));
1644 * Constructs a filter condition from the given input fields, and replaces the
1645 * condition at filterIndex with the new one. Does nothing if the pattern
1646 * field is blank (unless the match condition is one that doesn't require a
1647 * pattern, e.g. 'Is present'). Answers true if the filter was updated, else
1650 * This method may update the tooltip on the filter value field to show the
1651 * value range, if a numeric condition is selected. This ensures the tooltip
1652 * is updated when a numeric valued attribute is chosen on the last 'add a
1658 * @param filterIndex
1660 protected boolean updateFilter(JComboBox<String> attCombo,
1661 JComboBox<Condition> condCombo, JTextField valueField,
1664 String attName = (String) attCombo.getSelectedItem();
1665 Condition cond = (Condition) condCombo.getSelectedItem();
1666 String pattern = valueField.getText().trim();
1668 setNumericHints(attName, cond, valueField);
1670 if (pattern.length() == 0 && cond.needsAPattern())
1672 valueField.setEnabled(true); // ensure pattern field is enabled!
1677 * Construct a matcher that operates on Label, Score,
1678 * or named attribute
1680 FeatureMatcherI km = null;
1681 if (LABEL_18N.equals(attName))
1683 km = FeatureMatcher.byLabel(cond, pattern);
1685 else if (SCORE_18N.equals(attName))
1687 km = FeatureMatcher.byScore(cond, pattern);
1691 km = FeatureMatcher.byAttribute(cond, pattern,
1692 FeatureMatcher.fromAttributeDisplayName(attName));
1695 filters.set(filterIndex, km);
1701 * Action on any change to feature filtering, namely
1703 * <li>change of selected attribute</li>
1704 * <li>change of selected condition</li>
1705 * <li>change of match pattern</li>
1706 * <li>removal of a condition</li>
1708 * The inputs are parsed into a combined filter and this is set for the
1709 * feature type, and the alignment redrawn.
1711 protected void filtersChanged()
1714 * update the filter conditions for the feature type
1716 boolean anded = andFilters.isSelected();
1717 FeatureMatcherSetI combined = new FeatureMatcherSet();
1719 for (FeatureMatcherI filter : filters)
1721 String pattern = filter.getMatcher().getPattern();
1722 Condition condition = filter.getMatcher().getCondition();
1723 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1727 combined.and(filter);
1731 combined.or(filter);
1737 * save the filter conditions in the FeatureRenderer
1738 * (note this might now be an empty filter with no conditions)
1740 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1741 ap.paintAlignment(true, true);