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 private final String featureType;
118 * the colour and filters to reset to on Cancel
120 private final FeatureColourI originalColour;
122 private final FeatureMatcherSetI originalFilter;
125 * set flag to true when setting values programmatically,
126 * to avoid invocation of action handlers
128 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.addItemListener(new ItemListener()
491 public void itemStateChanged(ItemEvent e)
493 if (graduatedColour.isSelected())
499 graduatedChoicePanel.add(graduatedColour);
501 List<String[]> attNames = FeatureAttributes.getInstance()
502 .getAttributes(featureType);
503 colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
504 colourByRangeCombo.addItemListener(new ItemListener()
507 public void itemStateChanged(ItemEvent e)
514 * disable graduated colour option if no range found
516 graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
518 graduatedChoicePanel.add(colourByRangeCombo);
519 graduatedColourPanel.add(graduatedChoicePanel);
522 * second row - min/max/no colours
524 JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
525 colourRangePanel.setBackground(Color.white);
526 graduatedColourPanel.add(colourRangePanel);
528 minColour.setFont(JvSwingUtils.getLabelFont());
529 minColour.setBorder(BorderFactory.createLineBorder(Color.black));
530 minColour.setPreferredSize(new Dimension(40, 20));
531 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
532 minColour.addMouseListener(new MouseAdapter()
535 public void mousePressed(MouseEvent e)
537 if (minColour.isEnabled())
539 showColourChooser(minColour, "label.select_colour_minimum_value");
544 maxColour.setFont(JvSwingUtils.getLabelFont());
545 maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
546 maxColour.setPreferredSize(new Dimension(40, 20));
547 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
548 maxColour.addMouseListener(new MouseAdapter()
551 public void mousePressed(MouseEvent e)
553 if (maxColour.isEnabled())
555 showColourChooser(maxColour, "label.select_colour_maximum_value");
559 maxColour.setBorder(new LineBorder(Color.black));
562 * default max colour to last plain colour;
563 * make min colour a pale version of max colour
565 FeatureColourI fc = fr.getFeatureColours().get(featureType);
566 Color bg = fc.getColour() == null ? Color.BLACK : fc.getColour();
567 maxColour.setBackground(bg);
568 minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
570 noValueCombo = new JComboBox<>();
571 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
572 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
573 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
574 noValueCombo.addItemListener(new ItemListener()
577 public void itemStateChanged(ItemEvent e)
583 JLabel minText = new JLabel(
584 MessageManager.getString("label.min_value") + COLON);
585 minText.setFont(JvSwingUtils.getLabelFont());
586 JLabel maxText = new JLabel(
587 MessageManager.getString("label.max_value") + COLON);
588 maxText.setFont(JvSwingUtils.getLabelFont());
589 JLabel noText = new JLabel(
590 MessageManager.getString("label.no_value") + COLON);
591 noText.setFont(JvSwingUtils.getLabelFont());
593 colourRangePanel.add(minText);
594 colourRangePanel.add(minColour);
595 colourRangePanel.add(maxText);
596 colourRangePanel.add(maxColour);
597 colourRangePanel.add(noText);
598 colourRangePanel.add(noValueCombo);
601 * third row - threshold options and value
603 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
604 thresholdPanel.setBackground(Color.white);
605 graduatedColourPanel.add(thresholdPanel);
607 threshold.addActionListener(changeColourAction);
608 threshold.setToolTipText(MessageManager
609 .getString("label.threshold_feature_display_by_score"));
610 threshold.addItem(MessageManager
611 .getString("label.threshold_feature_no_threshold")); // index 0
612 threshold.addItem(MessageManager
613 .getString("label.threshold_feature_above_threshold")); // index 1
614 threshold.addItem(MessageManager
615 .getString("label.threshold_feature_below_threshold")); // index 2
617 thresholdValue.addActionListener(new ActionListener()
620 public void actionPerformed(ActionEvent e)
622 thresholdValue_actionPerformed();
625 thresholdValue.addFocusListener(new FocusAdapter()
628 public void focusLost(FocusEvent e)
630 thresholdValue_actionPerformed();
633 slider.setPaintLabels(false);
634 slider.setPaintTicks(true);
635 slider.setBackground(Color.white);
636 slider.setEnabled(false);
637 slider.setOpaque(false);
638 slider.setPreferredSize(new Dimension(100, 32));
639 slider.setToolTipText(
640 MessageManager.getString("label.adjust_threshold"));
642 slider.addChangeListener(new ChangeListener()
645 public void stateChanged(ChangeEvent evt)
650 .setText(String.valueOf(slider.getValue() / scaleFactor));
651 sliderValueChanged();
655 slider.addMouseListener(new MouseAdapter()
658 public void mouseReleased(MouseEvent evt)
661 * only update Overview and/or structure colouring
662 * when threshold slider drag ends (mouse up)
666 ap.paintAlignment(true, true);
671 thresholdValue.setEnabled(false);
672 thresholdValue.setColumns(7);
674 thresholdPanel.add(threshold);
675 thresholdPanel.add(slider);
676 thresholdPanel.add(thresholdValue);
678 thresholdIsMin.setBackground(Color.white);
680 .setText(MessageManager.getString("label.threshold_minmax"));
681 thresholdIsMin.setToolTipText(MessageManager
682 .getString("label.toggle_absolute_relative_display_threshold"));
683 thresholdIsMin.addActionListener(changeColourAction);
684 thresholdPanel.add(thresholdIsMin);
686 return graduatedColourPanel;
690 * Lay out OK and Cancel buttons
694 private JPanel initialiseOkCancelPanel()
696 JPanel okCancelPanel = new JPanel();
697 // okCancelPanel.setBackground(Color.white);
698 okCancelPanel.add(ok);
699 okCancelPanel.add(cancel);
700 return okCancelPanel;
704 * Lay out Colour options panel, containing
706 * <li>plain colour, with colour picker</li>
707 * <li>colour by text, with choice of Label or other attribute</li>
708 * <li>colour by range, of score or other attribute, when available</li>
713 private JPanel initialiseColoursPanel()
715 JPanel colourByPanel = new JPanel();
716 colourByPanel.setBackground(Color.white);
717 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
718 JvSwingUtils.createTitledBorder(colourByPanel,
719 MessageManager.getString("action.colour"), true);
722 * simple colour radio button and colour picker
724 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
725 simpleColourPanel.setBackground(Color.white);
726 colourByPanel.add(simpleColourPanel);
728 simpleColour = new JRadioButton(
729 MessageManager.getString("label.simple_colour"));
730 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
731 simpleColour.addItemListener(new ItemListener()
734 public void itemStateChanged(ItemEvent e)
736 if (simpleColour.isSelected() && !adjusting)
743 singleColour.setFont(JvSwingUtils.getLabelFont());
744 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
745 singleColour.setPreferredSize(new Dimension(40, 20));
746 if (originalColour.isGraduatedColour())
748 singleColour.setBackground(originalColour.getMaxColour());
749 singleColour.setForeground(originalColour.getMaxColour());
753 singleColour.setBackground(originalColour.getColour());
754 singleColour.setForeground(originalColour.getColour());
756 singleColour.addMouseListener(new MouseAdapter()
759 public void mousePressed(MouseEvent e)
761 if (simpleColour.isSelected())
763 showColourChooser(singleColour, "label.select_colour");
767 simpleColourPanel.add(simpleColour); // radio button
768 simpleColourPanel.add(singleColour); // colour picker button
771 * colour by text (category) radio button and drop-down choice list
773 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
774 byTextPanel.setBackground(Color.white);
775 JvSwingUtils.createTitledBorder(byTextPanel,
776 MessageManager.getString("label.colour_by_text"), true);
777 colourByPanel.add(byTextPanel);
778 byCategory = new JRadioButton(
779 MessageManager.getString("label.by_text_of") + COLON);
780 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
781 byCategory.addItemListener(new ItemListener()
784 public void itemStateChanged(ItemEvent e)
786 if (byCategory.isSelected())
792 byTextPanel.add(byCategory);
794 List<String[]> attNames = FeatureAttributes.getInstance()
795 .getAttributes(featureType);
796 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
797 colourByTextCombo.addItemListener(new ItemListener()
800 public void itemStateChanged(ItemEvent e)
805 byTextPanel.add(colourByTextCombo);
808 * graduated colour panel
810 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
811 colourByPanel.add(graduatedColourPanel);
814 * 3 radio buttons select between simple colour,
815 * by category (text), or graduated
817 ButtonGroup bg = new ButtonGroup();
818 bg.add(simpleColour);
820 bg.add(graduatedColour);
822 return colourByPanel;
826 * Shows a colour chooser dialog, and if a selection is made, updates the
827 * colour of the given panel
830 * the panel whose background colour is being picked
832 * message bundle key for the dialog title
834 void showColourChooser(JPanel colourPanel, String key)
836 ColourChooserListener listener = new ColourChooserListener()
839 public void colourSelected(Color col)
841 colourPanel.setBackground(col);
842 colourPanel.setForeground(col);
843 colourPanel.repaint();
847 JalviewColourChooser.showColourChooser(this,
848 MessageManager.getString(key), colourPanel.getBackground(),
853 * Constructs and sets the selected colour options as the colour for the
854 * feature type, and repaints the alignment, and optionally the Overview
855 * and/or structure viewer if open
857 * @param updateStructsAndOverview
859 void colourChanged(boolean updateStructsAndOverview)
864 * ignore action handlers while setting values programmatically
870 * ensure min-max range is for the latest choice of
871 * 'graduated colour by'
873 updateColourMinMax();
875 FeatureColourI acg = makeColourFromInputs();
878 * save the colour, and repaint stuff
880 fr.setColour(featureType, acg);
881 ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
883 updateColoursPanel();
887 * Converts the input values into an instance of FeatureColour
891 private FeatureColourI makeColourFromInputs()
894 * easiest case - a single colour
896 if (simpleColour.isSelected())
898 return new FeatureColour(singleColour.getBackground());
902 * next easiest case - colour by Label, or attribute text
904 if (byCategory.isSelected())
906 Color c = singleColour.getBackground();
907 FeatureColourI fc = new FeatureColour(c);
908 fc.setColourByLabel(true);
909 String byWhat = (String) colourByTextCombo.getSelectedItem();
910 if (!LABEL_18N.equals(byWhat))
913 FeatureMatcher.fromAttributeDisplayName(byWhat));
919 * remaining case - graduated colour by score, or attribute value
921 Color noColour = null;
922 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
924 noColour = minColour.getBackground();
926 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
928 noColour = maxColour.getBackground();
934 thresh = Float.valueOf(thresholdValue.getText());
935 } catch (NumberFormatException e)
937 // invalid inputs are already handled on entry
941 * min-max range is to (or from) threshold value if
942 * 'threshold is min/max' is selected
944 float minValue = min;
945 float maxValue = max;
946 int thresholdOption = threshold.getSelectedIndex();
947 if (thresholdIsMin.isSelected()
948 && thresholdOption == ABOVE_THRESHOLD_OPTION)
952 if (thresholdIsMin.isSelected()
953 && thresholdOption == BELOW_THRESHOLD_OPTION)
959 * make the graduated colour
961 FeatureColourI fc = new FeatureColour(minColour.getBackground(),
962 maxColour.getBackground(), noColour, minValue, maxValue);
965 * set attribute to colour by if selected
967 String byWhat = (String) colourByRangeCombo.getSelectedItem();
968 if (!SCORE_18N.equals(byWhat))
970 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
974 * set threshold options and 'autoscaled' which is
975 * false if 'threshold is min/max' is selected
976 * else true (colour range is on actual range of values)
978 fc.setThreshold(thresh);
979 fc.setAutoScaled(!thresholdIsMin.isSelected());
980 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
981 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
983 if (threshline == null)
986 * todo not yet implemented: visual indication of feature threshold
988 threshline = new GraphLine((max - min) / 2f, "Threshold",
996 protected void raiseClosed()
998 if (this.featureSettings != null)
1000 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
1005 * Action on OK is just to dismiss the dialog - any changes have already been
1009 public void okPressed()
1014 * Action on Cancel is to restore colour scheme and filters as they were when
1015 * the dialog was opened
1018 public void cancelPressed()
1020 fr.setColour(featureType, originalColour);
1021 fr.setFeatureFilter(featureType, originalFilter);
1022 ap.paintAlignment(true, true);
1026 * Action on text entry of a threshold value
1028 protected void thresholdValue_actionPerformed()
1033 float f = Float.parseFloat(thresholdValue.getText());
1034 slider.setValue((int) (f * scaleFactor));
1035 threshline.value = f;
1036 thresholdValue.setBackground(Color.white); // ok
1039 * force repaint of any Overview window or structure
1041 ap.paintAlignment(true, true);
1042 } catch (NumberFormatException ex)
1044 thresholdValue.setBackground(Color.red); // not ok
1052 * Action on change of threshold slider value. This may be done interactively
1053 * (by moving the slider), or programmatically (to update the slider after
1054 * manual input of a threshold value).
1056 protected void sliderValueChanged()
1058 threshline.value = getRoundedSliderValue();
1061 * repaint alignment, but not Overview or structure,
1062 * to avoid overload while dragging the slider
1064 colourChanged(false);
1068 * Converts the slider value to its absolute value by dividing by the
1069 * scaleFactor. Rounding errors are squashed by forcing min/max of slider
1070 * range to the actual min/max of feature score range
1074 private float getRoundedSliderValue()
1076 int value = slider.getValue();
1077 float f = value == slider.getMaximum() ? max
1078 : (value == slider.getMinimum() ? min : value / scaleFactor);
1082 void addActionListener(ActionListener listener)
1084 if (featureSettings != null)
1087 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1089 featureSettings = listener;
1093 * A helper method to build the drop-down choice of attributes for a feature.
1094 * If 'withRange' is true, then Score, and any attributes with a min-max
1095 * range, are added. If 'withText' is true, Label and any known attributes are
1096 * added. This allows 'categorical numerical' attributes e.g. codon position
1097 * to be coloured by text.
1099 * Where metadata is available with a description for an attribute, that is
1100 * added as a tooltip.
1102 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1103 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1105 * This method does not add any ActionListener to the JComboBox.
1111 protected JComboBox<String> populateAttributesDropdown(
1112 List<String[]> attNames, boolean withRange, boolean withText)
1114 List<String> displayAtts = new ArrayList<>();
1115 List<String> tooltips = new ArrayList<>();
1119 displayAtts.add(LABEL_18N);
1120 tooltips.add(MessageManager.getString("label.description"));
1124 float[][] minMax = fr.getMinMax().get(featureType);
1125 if (minMax != null && minMax[0][0] != minMax[0][1])
1127 displayAtts.add(SCORE_18N);
1128 tooltips.add(SCORE_18N);
1132 FeatureAttributes fa = FeatureAttributes.getInstance();
1133 for (String[] attName : attNames)
1135 float[] minMax = fa.getMinMax(featureType, attName);
1136 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1137 if (!withText && !hasRange)
1141 displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
1142 String desc = fa.getDescription(featureType, attName);
1143 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1145 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1147 tooltips.add(desc == null ? "" : desc);
1150 JComboBox<String> attCombo = JvSwingUtils
1151 .buildComboWithTooltips(displayAtts, tooltips);
1157 * Populates initial layout of the feature attribute filters panel
1159 private JPanel initialiseFiltersPanel()
1161 filters = new ArrayList<>();
1163 JPanel filtersPanel = new JPanel();
1164 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1165 filtersPanel.setBackground(Color.white);
1166 JvSwingUtils.createTitledBorder(filtersPanel,
1167 MessageManager.getString("label.filters"), true);
1169 JPanel andOrPanel = initialiseAndOrPanel();
1170 filtersPanel.add(andOrPanel);
1173 * panel with filters - populated by refreshFiltersDisplay,
1174 * which also sets the layout manager
1176 chooseFiltersPanel = new JPanel();
1177 chooseFiltersPanel.setBackground(Color.white);
1178 filtersPanel.add(chooseFiltersPanel);
1180 return filtersPanel;
1184 * Lays out the panel with radio buttons to AND or OR filter conditions
1188 private JPanel initialiseAndOrPanel()
1190 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1191 andOrPanel.setBackground(Color.white);
1192 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1193 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1194 ActionListener actionListener = new ActionListener()
1197 public void actionPerformed(ActionEvent e)
1202 andFilters.addActionListener(actionListener);
1203 orFilters.addActionListener(actionListener);
1204 ButtonGroup andOr = new ButtonGroup();
1205 andOr.add(andFilters);
1206 andOr.add(orFilters);
1207 andFilters.setSelected(true);
1209 new JLabel(MessageManager.getString("label.join_conditions")));
1210 andOrPanel.add(andFilters);
1211 andOrPanel.add(orFilters);
1216 * Refreshes the display to show any filters currently configured for the
1217 * selected feature type (editable, with 'remove' option), plus one extra row
1218 * for adding a condition. This should be called after a filter has been
1219 * removed, added or amended.
1221 private void updateFiltersPanel()
1224 * clear the panel and list of filter conditions
1226 chooseFiltersPanel.removeAll();
1230 * look up attributes known for feature type
1232 List<String[]> attNames = FeatureAttributes.getInstance()
1233 .getAttributes(featureType);
1236 * if this feature type has filters set, load them first
1238 FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
1239 if (featureFilters != null)
1241 if (!featureFilters.isAnded())
1243 orFilters.setSelected(true);
1245 // avoid use of lambda expression to keep SwingJS happy
1246 // featureFilters.getMatchers().forEach(item -> filters.add(item));
1247 for (FeatureMatcherI matcher : featureFilters.getMatchers())
1249 filters.add(matcher);
1254 * and an empty filter for the user to populate (add)
1256 filters.add(FeatureMatcher.NULL_MATCHER);
1259 * use GridLayout to 'justify' rows to the top of the panel, until
1260 * there are too many to fit in, then fall back on BoxLayout
1262 if (filters.size() <= 5)
1264 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1268 chooseFiltersPanel.setLayout(
1269 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1273 * render the conditions in rows, each in its own JPanel
1275 int filterIndex = 0;
1276 for (FeatureMatcherI filter : filters)
1278 JPanel row = addFilter(filter, attNames, filterIndex);
1279 chooseFiltersPanel.add(row);
1288 * A helper method that constructs a row (panel) with one filter condition:
1290 * <li>a drop-down list of Label, Score and attribute names to choose
1292 * <li>a drop-down list of conditions to choose from</li>
1293 * <li>a text field for input of a match pattern</li>
1294 * <li>optionally, a 'remove' button</li>
1296 * The filter values are set as defaults for the input fields. The 'remove'
1297 * button is added unless the pattern is empty (incomplete filter condition).
1299 * Action handlers on these fields provide for
1301 * <li>validate pattern field - should be numeric if condition is numeric</li>
1302 * <li>save filters and refresh display on any (valid) change</li>
1303 * <li>remove filter and refresh on 'Remove'</li>
1304 * <li>update conditions list on change of Label/Score/Attribute</li>
1305 * <li>refresh value field tooltip with min-max range on change of
1311 * @param filterIndex
1314 protected JPanel addFilter(FeatureMatcherI filter,
1315 List<String[]> attNames, int filterIndex)
1317 String[] attName = filter.getAttribute();
1318 Condition cond = filter.getMatcher().getCondition();
1319 String pattern = filter.getMatcher().getPattern();
1321 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1322 filterRow.setBackground(Color.white);
1325 * drop-down choice of attribute, with description as a tooltip
1326 * if we can obtain it
1328 JComboBox<String> attCombo = populateAttributesDropdown(attNames, true,
1330 String filterBy = setSelectedAttribute(attCombo, filter);
1332 JComboBox<Condition> condCombo = new JComboBox<>();
1334 JTextField patternField = new JTextField(8);
1335 patternField.setText(pattern);
1338 * action handlers that validate and (if valid) apply changes
1340 ActionListener actionListener = new ActionListener()
1343 public void actionPerformed(ActionEvent e)
1345 if (validateFilter(patternField, condCombo))
1347 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1354 ItemListener itemListener = new ItemListener()
1357 public void itemStateChanged(ItemEvent e)
1359 actionListener.actionPerformed(null);
1363 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1365 attCombo.setSelectedIndex(0);
1369 attCombo.setSelectedItem(
1370 FeatureMatcher.toAttributeDisplayName(attName));
1372 attCombo.addItemListener(new ItemListener()
1375 public void itemStateChanged(ItemEvent e)
1378 * on change of attribute, refresh the conditions list to
1379 * ensure it is appropriate for the attribute datatype
1381 populateConditions((String) attCombo.getSelectedItem(),
1382 (Condition) condCombo.getSelectedItem(), condCombo,
1384 actionListener.actionPerformed(null);
1388 filterRow.add(attCombo);
1391 * drop-down choice of test condition
1393 populateConditions(filterBy, cond, condCombo, patternField);
1394 condCombo.setPreferredSize(new Dimension(150, 20));
1395 condCombo.addItemListener(itemListener);
1396 filterRow.add(condCombo);
1399 * pattern to match against
1401 patternField.addActionListener(actionListener);
1402 patternField.addFocusListener(new FocusAdapter()
1405 public void focusLost(FocusEvent e)
1407 actionListener.actionPerformed(null);
1410 filterRow.add(patternField);
1413 * disable pattern field for condition 'Present / NotPresent'
1415 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1416 patternField.setEnabled(selectedCondition.needsAPattern());
1419 * if a numeric condition is selected, show the value range
1420 * as a tooltip on the value input field
1422 setNumericHints(filterBy, selectedCondition, patternField);
1425 * add remove button if filter is populated (non-empty pattern)
1427 if (!patternField.isEnabled()
1428 || (pattern != null && pattern.trim().length() > 0))
1430 JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x
1431 removeCondition.setPreferredSize(new Dimension(23, 17));
1433 .setToolTipText(MessageManager.getString("label.delete_row"));
1434 removeCondition.addActionListener(new ActionListener()
1437 public void actionPerformed(ActionEvent e)
1439 filters.remove(filterIndex);
1443 filterRow.add(removeCondition);
1450 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1456 private String setSelectedAttribute(JComboBox<String> attCombo,
1457 FeatureMatcherI filter)
1460 if (filter.isByScore())
1464 else if (filter.isByLabel())
1470 item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
1472 attCombo.setSelectedItem(item);
1477 * If a numeric comparison condition is selected, retrieves the min-max range
1478 * for the value (score or attribute), and sets it as a tooltip on the value
1479 * field. If the field is currently empty, then pre-populates it with
1481 * <li>the minimum value, if condition is > or >=</li>
1482 * <li>the maximum value, if condition is < or <=</li>
1486 * @param selectedCondition
1487 * @param patternField
1489 private void setNumericHints(String attName, Condition selectedCondition,
1490 JTextField patternField)
1492 patternField.setToolTipText("");
1494 if (selectedCondition.isNumeric())
1496 float[] minMax = getMinMax(attName);
1499 String minFormatted = DECFMT_2_2.format(minMax[0]);
1500 String maxFormatted = DECFMT_2_2.format(minMax[1]);
1501 String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
1502 patternField.setToolTipText(tip);
1503 if (patternField.getText().isEmpty())
1505 if (selectedCondition == Condition.GE
1506 || selectedCondition == Condition.GT)
1508 patternField.setText(minFormatted);
1512 if (selectedCondition == Condition.LE
1513 || selectedCondition == Condition.LT)
1515 patternField.setText(maxFormatted);
1524 * Populates the drop-down list of comparison conditions for the given
1525 * attribute name. The conditions added depend on the datatype of the
1526 * attribute values. The supplied condition is set as the selected item in the
1527 * list, provided it is in the list. If the pattern is now invalid
1528 * (non-numeric pattern for a numeric condition), it is cleared.
1533 * @param patternField
1535 void populateConditions(String attName, Condition cond,
1536 JComboBox<Condition> condCombo, JTextField patternField)
1538 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1539 FeatureMatcher.fromAttributeDisplayName(attName));
1540 if (LABEL_18N.equals(attName))
1542 type = Datatype.Character;
1544 else if (SCORE_18N.equals(attName))
1546 type = Datatype.Number;
1550 * remove itemListener before starting
1552 ItemListener listener = condCombo.getItemListeners()[0];
1553 condCombo.removeItemListener(listener);
1554 boolean condIsValid = false;
1556 condCombo.removeAllItems();
1557 for (Condition c : Condition.values())
1559 if ((c.isNumeric() && type == Datatype.Number)
1560 || (!c.isNumeric() && type != Datatype.Number))
1562 condCombo.addItem(c);
1571 * set the selected condition (does nothing if not in the list)
1575 condCombo.setSelectedItem(cond);
1579 condCombo.setSelectedIndex(0);
1583 * clear pattern if it is now invalid for condition
1585 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1589 String pattern = patternField.getText().trim();
1590 if (pattern.length() > 0)
1592 Float.valueOf(pattern);
1594 } catch (NumberFormatException e)
1596 patternField.setText("");
1601 * restore the listener
1603 condCombo.addItemListener(listener);
1607 * Answers true unless a numeric condition has been selected with a
1608 * non-numeric value. Sets the value field to RED with a tooltip if in error.
1610 * If the pattern is expected but is empty, this method returns false, but
1611 * does not mark the field as invalid. This supports selecting an attribute
1612 * for a new condition before a match pattern has been entered.
1617 protected boolean validateFilter(JTextField value,
1618 JComboBox<Condition> condCombo)
1620 if (value == null || condCombo == null)
1622 return true; // fields not populated
1625 Condition cond = (Condition) condCombo.getSelectedItem();
1626 if (!cond.needsAPattern())
1631 value.setBackground(Color.white);
1632 value.setToolTipText("");
1633 String v1 = value.getText().trim();
1634 if (v1.length() == 0)
1639 if (cond.isNumeric() && v1.length() > 0)
1644 } catch (NumberFormatException e)
1646 value.setBackground(Color.red);
1647 value.setToolTipText(
1648 MessageManager.getString("label.numeric_required"));
1657 * Constructs a filter condition from the given input fields, and replaces the
1658 * condition at filterIndex with the new one. Does nothing if the pattern
1659 * field is blank (unless the match condition is one that doesn't require a
1660 * pattern, e.g. 'Is present'). Answers true if the filter was updated, else
1663 * This method may update the tooltip on the filter value field to show the
1664 * value range, if a numeric condition is selected. This ensures the tooltip
1665 * is updated when a numeric valued attribute is chosen on the last 'add a
1671 * @param filterIndex
1673 protected boolean updateFilter(JComboBox<String> attCombo,
1674 JComboBox<Condition> condCombo, JTextField valueField,
1677 String attName = (String) attCombo.getSelectedItem();
1678 Condition cond = (Condition) condCombo.getSelectedItem();
1679 String pattern = valueField.getText().trim();
1681 setNumericHints(attName, cond, valueField);
1683 if (pattern.length() == 0 && cond.needsAPattern())
1685 valueField.setEnabled(true); // ensure pattern field is enabled!
1690 * Construct a matcher that operates on Label, Score,
1691 * or named attribute
1693 FeatureMatcherI km = null;
1694 if (LABEL_18N.equals(attName))
1696 km = FeatureMatcher.byLabel(cond, pattern);
1698 else if (SCORE_18N.equals(attName))
1700 km = FeatureMatcher.byScore(cond, pattern);
1704 km = FeatureMatcher.byAttribute(cond, pattern,
1705 FeatureMatcher.fromAttributeDisplayName(attName));
1708 filters.set(filterIndex, km);
1714 * Action on any change to feature filtering, namely
1716 * <li>change of selected attribute</li>
1717 * <li>change of selected condition</li>
1718 * <li>change of match pattern</li>
1719 * <li>removal of a condition</li>
1721 * The inputs are parsed into a combined filter and this is set for the
1722 * feature type, and the alignment redrawn.
1724 protected void filtersChanged()
1727 * update the filter conditions for the feature type
1729 boolean anded = andFilters.isSelected();
1730 FeatureMatcherSetI combined = new FeatureMatcherSet();
1732 for (FeatureMatcherI filter : filters)
1734 String pattern = filter.getMatcher().getPattern();
1735 Condition condition = filter.getMatcher().getCondition();
1736 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1740 combined.and(filter);
1744 combined.or(filter);
1750 * save the filter conditions in the FeatureRenderer
1751 * (note this might now be an empty filter with no conditions)
1753 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1754 ap.paintAlignment(true, true);
1756 updateFiltersPanel();