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.gui.JalviewColourChooser.ColourChooserListener;
33 import jalview.schemes.FeatureColour;
34 import jalview.util.ColorUtils;
35 import jalview.util.MessageManager;
36 import jalview.util.matcher.Condition;
38 import java.awt.BorderLayout;
39 import java.awt.Color;
40 import java.awt.Dimension;
41 import java.awt.FlowLayout;
42 import java.awt.GridLayout;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.awt.event.FocusAdapter;
46 import java.awt.event.FocusEvent;
47 import java.awt.event.ItemEvent;
48 import java.awt.event.ItemListener;
49 import java.awt.event.MouseAdapter;
50 import java.awt.event.MouseEvent;
51 import java.text.DecimalFormat;
52 import java.util.ArrayList;
53 import java.util.List;
55 import javax.swing.BorderFactory;
56 import javax.swing.BoxLayout;
57 import javax.swing.ButtonGroup;
58 import javax.swing.JButton;
59 import javax.swing.JCheckBox;
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.border.LineBorder;
67 import javax.swing.event.ChangeEvent;
68 import javax.swing.event.ChangeListener;
71 * A dialog where the user can configure colour scheme, and any filters, for one
74 * (Was FeatureColourChooser prior to Jalview 1.11, renamed with the addition of
77 public class FeatureTypeSettings extends JalviewDialog
79 private final static String LABEL_18N = MessageManager
80 .getString("label.label");
82 private final static String SCORE_18N = MessageManager
83 .getString("label.score");
85 private static final int RADIO_WIDTH = 130;
87 private static final String COLON = ":";
89 private static final int MAX_TOOLTIP_LENGTH = 50;
91 private static final int NO_COLOUR_OPTION = 0;
93 private static final int MIN_COLOUR_OPTION = 1;
95 private static final int MAX_COLOUR_OPTION = 2;
97 private static final int ABOVE_THRESHOLD_OPTION = 1;
99 private static final int BELOW_THRESHOLD_OPTION = 2;
101 private static final DecimalFormat DECFMT_2_2 = new DecimalFormat(
105 * FeatureRenderer holds colour scheme and filters for feature types
107 private final FeatureRenderer fr; // todo refactor to allow interface type
111 * the view panel to update when settings change
113 final AlignmentViewPanel ap;
115 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 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
147 * radio button group, to select what to colour by:
148 * simple colour, by category (text), or graduated
150 JRadioButton simpleColour = new JRadioButton();
152 JRadioButton byCategory = new JRadioButton();
154 JRadioButton graduatedColour = new JRadioButton();
160 JPanel singleColour = new JPanel();
162 JPanel minColour = new JPanel();
164 JPanel maxColour = new JPanel();
166 private JComboBox<String> threshold = new JComboBox<>();
168 JSlider slider = new JSlider();
170 JTextField thresholdValue = new JTextField(20);
172 private JCheckBox thresholdIsMin = new JCheckBox();
174 private GraphLine threshline;
176 private ActionListener featureSettings = null;
178 private ActionListener changeColourAction;
181 * choice of option for 'colour for no value'
183 private JComboBox<String> noValueCombo;
186 * choice of what to colour by text (Label or attribute)
188 private JComboBox<String> colourByTextCombo;
191 * choice of what to colour by range (Score or attribute)
193 private JComboBox<String> colourByRangeCombo;
195 private JRadioButton andFilters;
197 private JRadioButton orFilters;
200 * filters for the currently selected feature type
202 List<FeatureMatcherI> filters;
204 private JPanel chooseFiltersPanel;
212 public FeatureTypeSettings(FeatureRenderer frender, String theType)
215 this.featureType = theType;
217 originalFilter = fr.getFeatureFilter(theType);
218 originalColour = fr.getFeatureColours().get(theType);
225 } catch (Exception ex)
227 ex.printStackTrace();
231 updateColoursPanel();
233 updateFiltersPanel();
237 colourChanged(false);
239 String title = MessageManager
240 .formatMessage("label.display_settings_for", new String[]
242 initDialogFrame(this, true, false, title, 580, 500);
247 * Configures the widgets on the Colours panel according to the current feature
250 private void updateColoursPanel()
252 FeatureColourI fc = fr.getFeatureColours().get(featureType);
255 * suppress action handling while updating values programmatically
263 if (fc.isSimpleColour())
265 singleColour.setBackground(fc.getColour());
266 singleColour.setForeground(fc.getColour());
267 simpleColour.setSelected(true);
271 * colour by text (Label or attribute text)
273 if (fc.isColourByLabel())
275 byCategory.setSelected(true);
276 colourByTextCombo.setEnabled(colourByTextCombo.getItemCount() > 1);
277 if (fc.isColourByAttribute())
279 String[] attributeName = fc.getAttributeName();
280 colourByTextCombo.setSelectedItem(
281 FeatureMatcher.toAttributeDisplayName(attributeName));
285 colourByTextCombo.setSelectedItem(LABEL_18N);
290 colourByTextCombo.setEnabled(false);
293 if (!fc.isGraduatedColour())
295 colourByRangeCombo.setEnabled(false);
296 minColour.setEnabled(false);
297 maxColour.setEnabled(false);
298 noValueCombo.setEnabled(false);
299 threshold.setEnabled(false);
300 slider.setEnabled(false);
301 thresholdValue.setEnabled(false);
302 thresholdIsMin.setEnabled(false);
307 * Graduated colour, by score or attribute value range
309 graduatedColour.setSelected(true);
310 updateColourMinMax(); // ensure min, max are set
311 colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
312 minColour.setEnabled(true);
313 maxColour.setEnabled(true);
314 noValueCombo.setEnabled(true);
315 threshold.setEnabled(true);
316 minColour.setBackground(fc.getMinColour());
317 maxColour.setBackground(fc.getMaxColour());
319 if (fc.isColourByAttribute())
321 String[] attributeName = fc.getAttributeName();
322 colourByRangeCombo.setSelectedItem(
323 FeatureMatcher.toAttributeDisplayName(attributeName));
327 colourByRangeCombo.setSelectedItem(SCORE_18N);
329 Color noColour = fc.getNoColour();
330 if (noColour == null)
332 noValueCombo.setSelectedIndex(NO_COLOUR_OPTION);
334 else if (noColour.equals(fc.getMinColour()))
336 noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION);
338 else if (noColour.equals(fc.getMaxColour()))
340 noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION);
344 * update min-max scaling if there is a range to work with,
345 * else disable the widgets (this shouldn't happen if only
346 * valid options are offered in the combo box)
348 scaleFactor = (max == min) ? 1f : 100f / (max - min);
349 float range = (max - min) * scaleFactor;
350 slider.setMinimum((int) (min * scaleFactor));
351 slider.setMaximum((int) (max * scaleFactor));
352 slider.setMajorTickSpacing((int) (range / 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.setValue((int) (fc.getThreshold() * scaleFactor));
365 thresholdValue.setText(String.valueOf(getRoundedSliderValue()));
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 * default max colour to last plain colour;
566 * make min colour a pale version of max colour
568 FeatureColourI fc = fr.getFeatureColours().get(featureType);
569 Color bg = fc.getColour() == null ? Color.BLACK : fc.getColour();
570 maxColour.setBackground(bg);
571 minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
573 noValueCombo = new JComboBox<>();
574 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
575 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
576 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
577 noValueCombo.addItemListener(new ItemListener()
580 public void itemStateChanged(ItemEvent e)
586 JLabel minText = new JLabel(
587 MessageManager.getString("label.min_value") + COLON);
588 minText.setFont(JvSwingUtils.getLabelFont());
589 JLabel maxText = new JLabel(
590 MessageManager.getString("label.max_value") + COLON);
591 maxText.setFont(JvSwingUtils.getLabelFont());
592 JLabel noText = new JLabel(
593 MessageManager.getString("label.no_value") + COLON);
594 noText.setFont(JvSwingUtils.getLabelFont());
596 colourRangePanel.add(minText);
597 colourRangePanel.add(minColour);
598 colourRangePanel.add(maxText);
599 colourRangePanel.add(maxColour);
600 colourRangePanel.add(noText);
601 colourRangePanel.add(noValueCombo);
604 * third row - threshold options and value
606 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
607 thresholdPanel.setBackground(Color.white);
608 graduatedColourPanel.add(thresholdPanel);
610 threshold.addActionListener(changeColourAction);
611 threshold.setToolTipText(MessageManager
612 .getString("label.threshold_feature_display_by_score"));
613 threshold.addItem(MessageManager
614 .getString("label.threshold_feature_no_threshold")); // index 0
615 threshold.addItem(MessageManager
616 .getString("label.threshold_feature_above_threshold")); // index 1
617 threshold.addItem(MessageManager
618 .getString("label.threshold_feature_below_threshold")); // index 2
620 thresholdValue.addActionListener(new ActionListener()
623 public void actionPerformed(ActionEvent e)
625 thresholdValue_actionPerformed();
628 thresholdValue.addFocusListener(new FocusAdapter()
631 public void focusLost(FocusEvent e)
633 thresholdValue_actionPerformed();
636 slider.setPaintLabels(false);
637 slider.setPaintTicks(true);
638 slider.setBackground(Color.white);
639 slider.setEnabled(false);
640 slider.setOpaque(false);
641 slider.setPreferredSize(new Dimension(100, 32));
642 slider.setToolTipText(
643 MessageManager.getString("label.adjust_threshold"));
645 slider.addChangeListener(new ChangeListener()
648 public void stateChanged(ChangeEvent evt)
653 .setText(String.valueOf(slider.getValue() / scaleFactor));
654 sliderValueChanged();
658 slider.addMouseListener(new MouseAdapter()
661 public void mouseReleased(MouseEvent evt)
664 * only update Overview and/or structure colouring
665 * when threshold slider drag ends (mouse up)
669 ap.paintAlignment(true, true);
674 thresholdValue.setEnabled(false);
675 thresholdValue.setColumns(7);
677 thresholdPanel.add(threshold);
678 thresholdPanel.add(slider);
679 thresholdPanel.add(thresholdValue);
681 thresholdIsMin.setBackground(Color.white);
683 .setText(MessageManager.getString("label.threshold_minmax"));
684 thresholdIsMin.setToolTipText(MessageManager
685 .getString("label.toggle_absolute_relative_display_threshold"));
686 thresholdIsMin.addActionListener(changeColourAction);
687 thresholdPanel.add(thresholdIsMin);
689 return graduatedColourPanel;
693 * Lay out OK and Cancel buttons
697 private JPanel initialiseOkCancelPanel()
699 JPanel okCancelPanel = new JPanel();
700 // okCancelPanel.setBackground(Color.white);
701 okCancelPanel.add(ok);
702 okCancelPanel.add(cancel);
703 return okCancelPanel;
707 * Lay out Colour options panel, containing
709 * <li>plain colour, with colour picker</li>
710 * <li>colour by text, with choice of Label or other attribute</li>
711 * <li>colour by range, of score or other attribute, when available</li>
716 private JPanel initialiseColoursPanel()
718 JPanel colourByPanel = new JPanel();
719 colourByPanel.setBackground(Color.white);
720 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
721 JvSwingUtils.createTitledBorder(colourByPanel,
722 MessageManager.getString("action.colour"), true);
725 * simple colour radio button and colour picker
727 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
728 simpleColourPanel.setBackground(Color.white);
729 colourByPanel.add(simpleColourPanel);
731 simpleColour = new JRadioButton(
732 MessageManager.getString("label.simple_colour"));
733 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
734 simpleColour.setOpaque(false);
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 String ttl = MessageManager.formatMessage("label.select_colour_for", featureType);
768 showColourChooser(singleColour, ttl);
772 simpleColourPanel.add(simpleColour); // radio button
773 simpleColourPanel.add(singleColour); // colour picker button
776 * colour by text (category) radio button and drop-down choice list
778 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
779 byTextPanel.setBackground(Color.white);
780 JvSwingUtils.createTitledBorder(byTextPanel,
781 MessageManager.getString("label.colour_by_text"), true);
782 colourByPanel.add(byTextPanel);
783 byCategory = new JRadioButton(
784 MessageManager.getString("label.by_text_of") + COLON);
785 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
786 byCategory.setOpaque(false);
787 byCategory.addItemListener(new ItemListener()
790 public void itemStateChanged(ItemEvent e)
792 if (byCategory.isSelected())
798 byTextPanel.add(byCategory);
800 List<String[]> attNames = FeatureAttributes.getInstance()
801 .getAttributes(featureType);
802 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
803 colourByTextCombo.addItemListener(new ItemListener()
806 public void itemStateChanged(ItemEvent e)
811 byTextPanel.add(colourByTextCombo);
814 * graduated colour panel
816 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
817 colourByPanel.add(graduatedColourPanel);
820 * 3 radio buttons select between simple colour,
821 * by category (text), or graduated
823 ButtonGroup bg = new ButtonGroup();
824 bg.add(simpleColour);
826 bg.add(graduatedColour);
828 return colourByPanel;
832 * Shows a colour chooser dialog, and if a selection is made, updates the
833 * colour of the given panel
836 * the panel whose background colour is being picked
839 void showColourChooser(JPanel colourPanel, String title)
841 ColourChooserListener listener = new ColourChooserListener()
844 public void colourSelected(Color col)
846 colourPanel.setBackground(col);
847 colourPanel.setForeground(col);
848 colourPanel.repaint();
852 JalviewColourChooser.showColourChooser(this, title,
853 colourPanel.getBackground(), listener);
857 * Constructs and sets the selected colour options as the colour for the
858 * feature type, and repaints the alignment, and optionally the Overview
859 * and/or structure viewer if open
861 * @param updateStructsAndOverview
863 void colourChanged(boolean updateStructsAndOverview)
868 * ignore action handlers while setting values programmatically
874 * ensure min-max range is for the latest choice of
875 * 'graduated colour by'
877 updateColourMinMax();
879 FeatureColourI acg = makeColourFromInputs();
882 * save the colour, and repaint stuff
884 fr.setColour(featureType, acg);
885 ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
887 updateColoursPanel();
891 * Converts the input values into an instance of FeatureColour
895 private FeatureColourI makeColourFromInputs()
898 * easiest case - a single colour
900 if (simpleColour.isSelected())
902 return new FeatureColour(singleColour.getBackground());
906 * next easiest case - colour by Label, or attribute text
908 if (byCategory.isSelected())
910 Color c = singleColour.getBackground();
911 FeatureColourI fc = new FeatureColour(c);
912 fc.setColourByLabel(true);
913 String byWhat = (String) colourByTextCombo.getSelectedItem();
914 if (!LABEL_18N.equals(byWhat))
917 FeatureMatcher.fromAttributeDisplayName(byWhat));
923 * remaining case - graduated colour by score, or attribute value
925 Color noColour = null;
926 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
928 noColour = minColour.getBackground();
930 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
932 noColour = maxColour.getBackground();
938 thresh = Float.valueOf(thresholdValue.getText());
939 } catch (NumberFormatException e)
941 // invalid inputs are already handled on entry
945 * min-max range is to (or from) threshold value if
946 * 'threshold is min/max' is selected
948 float minValue = min;
949 float maxValue = max;
950 int thresholdOption = threshold.getSelectedIndex();
951 if (thresholdIsMin.isSelected()
952 && thresholdOption == ABOVE_THRESHOLD_OPTION)
956 if (thresholdIsMin.isSelected()
957 && thresholdOption == BELOW_THRESHOLD_OPTION)
963 * make the graduated colour
965 FeatureColourI fc = new FeatureColour(minColour.getBackground(),
966 maxColour.getBackground(), noColour, minValue, maxValue);
969 * set attribute to colour by if selected
971 String byWhat = (String) colourByRangeCombo.getSelectedItem();
972 if (!SCORE_18N.equals(byWhat))
974 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
978 * set threshold options and 'autoscaled' which is
979 * false if 'threshold is min/max' is selected
980 * else true (colour range is on actual range of values)
982 fc.setThreshold(thresh);
983 fc.setAutoScaled(!thresholdIsMin.isSelected());
984 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
985 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
987 if (threshline == null)
990 * todo not yet implemented: visual indication of feature threshold
992 threshline = new GraphLine((max - min) / 2f, "Threshold",
1000 protected void raiseClosed()
1002 if (this.featureSettings != null)
1004 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
1009 * Action on OK is just to dismiss the dialog - any changes have already been
1013 public void okPressed()
1018 * Action on Cancel is to restore colour scheme and filters as they were when
1019 * the dialog was opened
1022 public void cancelPressed()
1024 fr.setColour(featureType, originalColour);
1025 fr.setFeatureFilter(featureType, originalFilter);
1026 ap.paintAlignment(true, true);
1030 * Action on text entry of a threshold value
1032 protected void thresholdValue_actionPerformed()
1037 float f = Float.parseFloat(thresholdValue.getText());
1038 slider.setValue((int) (f * scaleFactor));
1039 threshline.value = f;
1040 thresholdValue.setBackground(Color.white); // ok
1043 * force repaint of any Overview window or structure
1045 ap.paintAlignment(true, true);
1046 } catch (NumberFormatException ex)
1048 thresholdValue.setBackground(Color.red); // not ok
1056 * Action on change of threshold slider value. This may be done interactively
1057 * (by moving the slider), or programmatically (to update the slider after
1058 * manual input of a threshold value).
1060 protected void sliderValueChanged()
1062 threshline.value = getRoundedSliderValue();
1065 * repaint alignment, but not Overview or structure,
1066 * to avoid overload while dragging the slider
1068 colourChanged(false);
1072 * Converts the slider value to its absolute value by dividing by the
1073 * scaleFactor. Rounding errors are squashed by forcing min/max of slider
1074 * range to the actual min/max of feature score range
1078 private float getRoundedSliderValue()
1080 int value = slider.getValue();
1081 float f = value == slider.getMaximum() ? max
1082 : (value == slider.getMinimum() ? min : value / scaleFactor);
1086 void addActionListener(ActionListener listener)
1088 if (featureSettings != null)
1091 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1093 featureSettings = listener;
1097 * A helper method to build the drop-down choice of attributes for a feature.
1098 * If 'withRange' is true, then Score, and any attributes with a min-max
1099 * range, are added. If 'withText' is true, Label and any known attributes are
1100 * added. This allows 'categorical numerical' attributes e.g. codon position
1101 * to be coloured by text.
1103 * Where metadata is available with a description for an attribute, that is
1104 * added as a tooltip.
1106 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1107 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1109 * This method does not add any ActionListener to the JComboBox.
1115 protected JComboBox<String> populateAttributesDropdown(
1116 List<String[]> attNames, boolean withRange, boolean withText)
1118 List<String> displayAtts = new ArrayList<>();
1119 List<String> tooltips = new ArrayList<>();
1123 displayAtts.add(LABEL_18N);
1124 tooltips.add(MessageManager.getString("label.description"));
1128 float[][] minMax = fr.getMinMax().get(featureType);
1129 if (minMax != null && minMax[0][0] != minMax[0][1])
1131 displayAtts.add(SCORE_18N);
1132 tooltips.add(SCORE_18N);
1136 FeatureAttributes fa = FeatureAttributes.getInstance();
1137 for (String[] attName : attNames)
1139 float[] minMax = fa.getMinMax(featureType, attName);
1140 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1141 if (!withText && !hasRange)
1145 displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
1146 String desc = fa.getDescription(featureType, attName);
1147 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1149 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1151 tooltips.add(desc == null ? "" : desc);
1154 JComboBox<String> attCombo = JvSwingUtils
1155 .buildComboWithTooltips(displayAtts, tooltips);
1161 * Populates initial layout of the feature attribute filters panel
1163 private JPanel initialiseFiltersPanel()
1165 filters = new ArrayList<>();
1167 JPanel filtersPanel = new JPanel();
1168 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1169 filtersPanel.setBackground(Color.white);
1170 JvSwingUtils.createTitledBorder(filtersPanel,
1171 MessageManager.getString("label.filters"), true);
1173 JPanel andOrPanel = initialiseAndOrPanel();
1174 filtersPanel.add(andOrPanel);
1177 * panel with filters - populated by refreshFiltersDisplay,
1178 * which also sets the layout manager
1180 chooseFiltersPanel = new JPanel();
1181 chooseFiltersPanel.setBackground(Color.white);
1182 filtersPanel.add(chooseFiltersPanel);
1184 return filtersPanel;
1188 * Lays out the panel with radio buttons to AND or OR filter conditions
1192 private JPanel initialiseAndOrPanel()
1194 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1195 andOrPanel.setBackground(Color.white);
1196 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1197 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1198 andFilters.setOpaque(false);
1199 orFilters.setOpaque(false);
1200 ActionListener actionListener = new ActionListener()
1203 public void actionPerformed(ActionEvent e)
1208 andFilters.addActionListener(actionListener);
1209 orFilters.addActionListener(actionListener);
1210 ButtonGroup andOr = new ButtonGroup();
1211 andOr.add(andFilters);
1212 andOr.add(orFilters);
1213 andFilters.setSelected(true);
1215 new JLabel(MessageManager.getString("label.join_conditions")));
1216 andOrPanel.add(andFilters);
1217 andOrPanel.add(orFilters);
1222 * Refreshes the display to show any filters currently configured for the
1223 * selected feature type (editable, with 'remove' option), plus one extra row
1224 * for adding a condition. This should be called after a filter has been
1225 * removed, added or amended.
1227 private void updateFiltersPanel()
1230 * clear the panel and list of filter conditions
1232 chooseFiltersPanel.removeAll();
1236 * look up attributes known for feature type
1238 List<String[]> attNames = FeatureAttributes.getInstance()
1239 .getAttributes(featureType);
1242 * if this feature type has filters set, load them first
1244 FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
1245 if (featureFilters != null)
1247 if (!featureFilters.isAnded())
1249 orFilters.setSelected(true);
1251 // avoid use of lambda expression to keep SwingJS happy
1252 // featureFilters.getMatchers().forEach(item -> filters.add(item));
1253 for (FeatureMatcherI matcher : featureFilters.getMatchers())
1255 filters.add(matcher);
1260 * and an empty filter for the user to populate (add)
1262 filters.add(FeatureMatcher.NULL_MATCHER);
1265 * use GridLayout to 'justify' rows to the top of the panel, until
1266 * there are too many to fit in, then fall back on BoxLayout
1268 if (filters.size() <= 5)
1270 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1274 chooseFiltersPanel.setLayout(
1275 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1279 * render the conditions in rows, each in its own JPanel
1281 int filterIndex = 0;
1282 for (FeatureMatcherI filter : filters)
1284 JPanel row = addFilter(filter, attNames, filterIndex);
1285 chooseFiltersPanel.add(row);
1294 * A helper method that constructs a row (panel) with one filter condition:
1296 * <li>a drop-down list of Label, Score and attribute names to choose
1298 * <li>a drop-down list of conditions to choose from</li>
1299 * <li>a text field for input of a match pattern</li>
1300 * <li>optionally, a 'remove' button</li>
1302 * The filter values are set as defaults for the input fields. The 'remove'
1303 * button is added unless the pattern is empty (incomplete filter condition).
1305 * Action handlers on these fields provide for
1307 * <li>validate pattern field - should be numeric if condition is numeric</li>
1308 * <li>save filters and refresh display on any (valid) change</li>
1309 * <li>remove filter and refresh on 'Remove'</li>
1310 * <li>update conditions list on change of Label/Score/Attribute</li>
1311 * <li>refresh value field tooltip with min-max range on change of
1317 * @param filterIndex
1320 protected JPanel addFilter(FeatureMatcherI filter,
1321 List<String[]> attNames, int filterIndex)
1323 String[] attName = filter.getAttribute();
1324 Condition cond = filter.getMatcher().getCondition();
1325 String pattern = filter.getMatcher().getPattern();
1327 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1328 filterRow.setBackground(Color.white);
1331 * drop-down choice of attribute, with description as a tooltip
1332 * if we can obtain it
1334 JComboBox<String> attCombo = populateAttributesDropdown(attNames, true,
1336 String filterBy = setSelectedAttribute(attCombo, filter);
1338 JComboBox<Condition> condCombo = new JComboBox<>();
1340 JTextField patternField = new JTextField(8);
1341 patternField.setText(pattern);
1344 * action handlers that validate and (if valid) apply changes
1346 ActionListener actionListener = new ActionListener()
1349 public void actionPerformed(ActionEvent e)
1351 if (validateFilter(patternField, condCombo))
1353 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1360 ItemListener itemListener = new ItemListener()
1363 public void itemStateChanged(ItemEvent e)
1365 actionListener.actionPerformed(null);
1369 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1371 attCombo.setSelectedIndex(0);
1375 attCombo.setSelectedItem(
1376 FeatureMatcher.toAttributeDisplayName(attName));
1378 attCombo.addItemListener(new ItemListener()
1381 public void itemStateChanged(ItemEvent e)
1384 * on change of attribute, refresh the conditions list to
1385 * ensure it is appropriate for the attribute datatype
1387 populateConditions((String) attCombo.getSelectedItem(),
1388 (Condition) condCombo.getSelectedItem(), condCombo,
1390 actionListener.actionPerformed(null);
1394 filterRow.add(attCombo);
1397 * drop-down choice of test condition
1399 populateConditions(filterBy, cond, condCombo, patternField);
1400 condCombo.setPreferredSize(new Dimension(150, 20));
1401 condCombo.addItemListener(itemListener);
1402 filterRow.add(condCombo);
1405 * pattern to match against
1407 patternField.addActionListener(actionListener);
1408 patternField.addFocusListener(new FocusAdapter()
1411 public void focusLost(FocusEvent e)
1413 actionListener.actionPerformed(null);
1416 filterRow.add(patternField);
1419 * disable pattern field for condition 'Present / NotPresent'
1421 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1422 patternField.setEnabled(selectedCondition.needsAPattern());
1425 * if a numeric condition is selected, show the value range
1426 * as a tooltip on the value input field
1428 setNumericHints(filterBy, selectedCondition, patternField);
1431 * add remove button if filter is populated (non-empty pattern)
1433 if (!patternField.isEnabled()
1434 || (pattern != null && pattern.trim().length() > 0))
1436 JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x
1437 removeCondition.setPreferredSize(new Dimension(23, 17));
1439 .setToolTipText(MessageManager.getString("label.delete_row"));
1440 removeCondition.addActionListener(new ActionListener()
1443 public void actionPerformed(ActionEvent e)
1445 filters.remove(filterIndex);
1449 filterRow.add(removeCondition);
1456 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1462 private String setSelectedAttribute(JComboBox<String> attCombo,
1463 FeatureMatcherI filter)
1466 if (filter.isByScore())
1470 else if (filter.isByLabel())
1476 item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
1478 attCombo.setSelectedItem(item);
1483 * If a numeric comparison condition is selected, retrieves the min-max range
1484 * for the value (score or attribute), and sets it as a tooltip on the value
1485 * field. If the field is currently empty, then pre-populates it with
1487 * <li>the minimum value, if condition is > or >=</li>
1488 * <li>the maximum value, if condition is < or <=</li>
1492 * @param selectedCondition
1493 * @param patternField
1495 private void setNumericHints(String attName, Condition selectedCondition,
1496 JTextField patternField)
1498 patternField.setToolTipText("");
1500 if (selectedCondition.isNumeric())
1502 float[] minMax = getMinMax(attName);
1505 String minFormatted = DECFMT_2_2.format(minMax[0]);
1506 String maxFormatted = DECFMT_2_2.format(minMax[1]);
1507 String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
1508 patternField.setToolTipText(tip);
1509 if (patternField.getText().isEmpty())
1511 if (selectedCondition == Condition.GE
1512 || selectedCondition == Condition.GT)
1514 patternField.setText(minFormatted);
1518 if (selectedCondition == Condition.LE
1519 || selectedCondition == Condition.LT)
1521 patternField.setText(maxFormatted);
1530 * Populates the drop-down list of comparison conditions for the given
1531 * attribute name. The conditions added depend on the datatype of the
1532 * attribute values. The supplied condition is set as the selected item in the
1533 * list, provided it is in the list. If the pattern is now invalid
1534 * (non-numeric pattern for a numeric condition), it is cleared.
1539 * @param patternField
1541 void populateConditions(String attName, Condition cond,
1542 JComboBox<Condition> condCombo, JTextField patternField)
1544 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1545 FeatureMatcher.fromAttributeDisplayName(attName));
1546 if (LABEL_18N.equals(attName))
1548 type = Datatype.Character;
1550 else if (SCORE_18N.equals(attName))
1552 type = Datatype.Number;
1556 * remove itemListener before starting
1558 ItemListener listener = condCombo.getItemListeners()[0];
1559 condCombo.removeItemListener(listener);
1560 boolean condIsValid = false;
1562 condCombo.removeAllItems();
1563 for (Condition c : Condition.values())
1565 if ((c.isNumeric() && type == Datatype.Number)
1566 || (!c.isNumeric() && type != Datatype.Number))
1568 condCombo.addItem(c);
1577 * set the selected condition (does nothing if not in the list)
1581 condCombo.setSelectedItem(cond);
1585 condCombo.setSelectedIndex(0);
1589 * clear pattern if it is now invalid for condition
1591 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1595 String pattern = patternField.getText().trim();
1596 if (pattern.length() > 0)
1598 Float.valueOf(pattern);
1600 } catch (NumberFormatException e)
1602 patternField.setText("");
1607 * restore the listener
1609 condCombo.addItemListener(listener);
1613 * Answers true unless a numeric condition has been selected with a
1614 * non-numeric value. Sets the value field to RED with a tooltip if in error.
1616 * If the pattern is expected but is empty, this method returns false, but
1617 * does not mark the field as invalid. This supports selecting an attribute
1618 * for a new condition before a match pattern has been entered.
1623 protected boolean validateFilter(JTextField value,
1624 JComboBox<Condition> condCombo)
1626 if (value == null || condCombo == null)
1628 return true; // fields not populated
1631 Condition cond = (Condition) condCombo.getSelectedItem();
1632 if (!cond.needsAPattern())
1637 value.setBackground(Color.white);
1638 value.setToolTipText("");
1639 String v1 = value.getText().trim();
1640 if (v1.length() == 0)
1645 if (cond.isNumeric() && v1.length() > 0)
1650 } catch (NumberFormatException e)
1652 value.setBackground(Color.red);
1653 value.setToolTipText(
1654 MessageManager.getString("label.numeric_required"));
1663 * Constructs a filter condition from the given input fields, and replaces the
1664 * condition at filterIndex with the new one. Does nothing if the pattern
1665 * field is blank (unless the match condition is one that doesn't require a
1666 * pattern, e.g. 'Is present'). Answers true if the filter was updated, else
1669 * This method may update the tooltip on the filter value field to show the
1670 * value range, if a numeric condition is selected. This ensures the tooltip
1671 * is updated when a numeric valued attribute is chosen on the last 'add a
1677 * @param filterIndex
1679 protected boolean updateFilter(JComboBox<String> attCombo,
1680 JComboBox<Condition> condCombo, JTextField valueField,
1683 String attName = (String) attCombo.getSelectedItem();
1684 Condition cond = (Condition) condCombo.getSelectedItem();
1685 String pattern = valueField.getText().trim();
1687 setNumericHints(attName, cond, valueField);
1689 if (pattern.length() == 0 && cond.needsAPattern())
1691 valueField.setEnabled(true); // ensure pattern field is enabled!
1696 * Construct a matcher that operates on Label, Score,
1697 * or named attribute
1699 FeatureMatcherI km = null;
1700 if (LABEL_18N.equals(attName))
1702 km = FeatureMatcher.byLabel(cond, pattern);
1704 else if (SCORE_18N.equals(attName))
1706 km = FeatureMatcher.byScore(cond, pattern);
1710 km = FeatureMatcher.byAttribute(cond, pattern,
1711 FeatureMatcher.fromAttributeDisplayName(attName));
1714 filters.set(filterIndex, km);
1720 * Action on any change to feature filtering, namely
1722 * <li>change of selected attribute</li>
1723 * <li>change of selected condition</li>
1724 * <li>change of match pattern</li>
1725 * <li>removal of a condition</li>
1727 * The inputs are parsed into a combined filter and this is set for the
1728 * feature type, and the alignment redrawn.
1730 protected void filtersChanged()
1733 * update the filter conditions for the feature type
1735 boolean anded = andFilters.isSelected();
1736 FeatureMatcherSetI combined = new FeatureMatcherSet();
1738 for (FeatureMatcherI filter : filters)
1740 String pattern = filter.getMatcher().getPattern();
1741 Condition condition = filter.getMatcher().getCondition();
1742 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1746 combined.and(filter);
1750 combined.or(filter);
1756 * save the filter conditions in the FeatureRenderer
1757 * (note this might now be an empty filter with no conditions)
1759 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1760 ap.paintAlignment(true, true);
1762 updateFiltersPanel();