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.bin.Cache;
26 import jalview.datamodel.GraphLine;
27 import jalview.datamodel.features.FeatureAttributes;
28 import jalview.datamodel.features.FeatureAttributes.Datatype;
29 import jalview.datamodel.features.FeatureMatcher;
30 import jalview.datamodel.features.FeatureMatcherI;
31 import jalview.datamodel.features.FeatureMatcherSet;
32 import jalview.datamodel.features.FeatureMatcherSetI;
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.math.BigDecimal;
52 import java.math.MathContext;
53 import java.text.DecimalFormat;
54 import java.util.ArrayList;
55 import java.util.List;
57 import javax.swing.BorderFactory;
58 import javax.swing.BoxLayout;
59 import javax.swing.ButtonGroup;
60 import javax.swing.JButton;
61 import javax.swing.JCheckBox;
62 import javax.swing.JColorChooser;
63 import javax.swing.JComboBox;
64 import javax.swing.JLabel;
65 import javax.swing.JPanel;
66 import javax.swing.JRadioButton;
67 import javax.swing.JTextField;
68 import javax.swing.border.EmptyBorder;
69 import javax.swing.border.LineBorder;
70 import javax.swing.event.ChangeEvent;
71 import javax.swing.event.ChangeListener;
74 * A dialog where the user can configure colour scheme, and any filters, for one
77 * (Was FeatureColourChooser prior to Jalview 1.11, renamed with the addition of
80 public class FeatureTypeSettings extends JalviewDialog
82 private final static MathContext FOUR_SIG_FIG = new MathContext(4);
84 private final static String LABEL_18N = MessageManager
85 .getString("label.label");
87 private final static String SCORE_18N = MessageManager
88 .getString("label.score");
90 private static final int RADIO_WIDTH = 130;
92 private static final String COLON = ":";
94 private static final int MAX_TOOLTIP_LENGTH = 50;
96 private static final int NO_COLOUR_OPTION = 0;
98 private static final int MIN_COLOUR_OPTION = 1;
100 private static final int MAX_COLOUR_OPTION = 2;
102 private static final int ABOVE_THRESHOLD_OPTION = 1;
104 private static final int BELOW_THRESHOLD_OPTION = 2;
106 private static final DecimalFormat DECFMT_2_2 = new DecimalFormat(
110 * FeatureRenderer holds colour scheme and filters for feature types
112 private final FeatureRenderer fr; // todo refactor to allow interface type
116 * the view panel to update when settings change
118 private final AlignmentViewPanel ap;
120 private final String featureType;
123 * the colour and filters to reset to on Cancel
125 private final FeatureColourI originalColour;
127 private final FeatureMatcherSetI originalFilter;
130 * set flag to true when setting values programmatically,
131 * to avoid invocation of action handlers
133 private boolean adjusting = false;
136 * minimum of the value range for graduated colour
137 * (may be for feature score or for a numeric attribute)
142 * maximum of the value range for graduated colour
147 * radio button group, to select what to colour by:
148 * simple colour, by category (text), or graduated
150 private JRadioButton simpleColour = new JRadioButton();
152 private JRadioButton byCategory = new JRadioButton();
154 private JRadioButton graduatedColour = new JRadioButton();
157 * colours and filters are shown in tabbed view or single content pane
159 JPanel coloursPanel, filtersPanel;
161 JPanel singleColour = new JPanel();
163 private JPanel minColour = new JPanel();
165 private JPanel maxColour = new JPanel();
167 private JComboBox<Object> threshold = new JComboBox<>();
169 private Slider slider;
171 private JTextField thresholdValue = new JTextField(20);
173 private JCheckBox thresholdIsMin = new JCheckBox();
175 private GraphLine threshline;
177 private ActionListener featureSettings = null;
179 private ActionListener changeColourAction;
182 * choice of option for 'colour for no value'
184 private JComboBox<Object> noValueCombo;
187 * choice of what to colour by text (Label or attribute)
189 private JComboBox<Object> colourByTextCombo;
192 * choice of what to colour by range (Score or attribute)
194 private JComboBox<Object> colourByRangeCombo;
196 private JRadioButton andFilters;
198 private JRadioButton orFilters;
201 * filters for the currently selected feature type
203 private List<FeatureMatcherI> filters;
205 private JPanel chooseFiltersPanel;
213 public FeatureTypeSettings(FeatureRenderer frender, String theType)
216 this.featureType = theType;
218 originalFilter = fr.getFeatureFilter(theType);
219 originalColour = fr.getFeatureColours().get(theType);
226 } catch (Exception ex)
228 ex.printStackTrace();
238 colourChanged(false);
240 String title = MessageManager
241 .formatMessage("label.display_settings_for", new String[]
243 initDialogFrame(this, true, false, title, 580, 500);
248 * Configures the widgets on the Colours tab according to the current feature
251 private void updateColoursTab()
253 FeatureColourI fc = fr.getFeatureColours().get(featureType);
256 * suppress action handling while updating values programmatically
264 if (fc.isSimpleColour())
266 singleColour.setBackground(fc.getColour());
267 singleColour.setForeground(fc.getColour());
268 simpleColour.setSelected(true);
272 * colour by text (Label or attribute text)
274 if (fc.isColourByLabel())
276 byCategory.setSelected(true);
277 colourByTextCombo.setEnabled(colourByTextCombo.getItemCount() > 1);
278 if (fc.isColourByAttribute())
280 String[] attributeName = fc.getAttributeName();
281 colourByTextCombo.setSelectedItem(
282 FeatureMatcher.toAttributeDisplayName(attributeName));
286 colourByTextCombo.setSelectedItem(LABEL_18N);
291 colourByTextCombo.setEnabled(false);
294 if (!fc.isGraduatedColour())
296 colourByRangeCombo.setEnabled(false);
297 minColour.setEnabled(false);
298 maxColour.setEnabled(false);
299 noValueCombo.setEnabled(false);
300 threshold.setEnabled(false);
301 slider.setEnabled(false);
302 thresholdValue.setEnabled(false);
303 thresholdIsMin.setEnabled(false);
308 * Graduated colour, by score or attribute value range
310 graduatedColour.setSelected(true);
311 updateColourMinMax(); // ensure min, max are set
312 colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
313 minColour.setEnabled(true);
314 maxColour.setEnabled(true);
315 noValueCombo.setEnabled(true);
316 threshold.setEnabled(true);
317 minColour.setBackground(fc.getMinColour());
318 maxColour.setBackground(fc.getMaxColour());
320 if (fc.isColourByAttribute())
322 String[] attributeName = fc.getAttributeName();
323 colourByRangeCombo.setSelectedItem(
324 FeatureMatcher.toAttributeDisplayName(attributeName));
328 colourByRangeCombo.setSelectedItem(SCORE_18N);
330 Color noColour = fc.getNoColour();
331 if (noColour == null)
333 noValueCombo.setSelectedIndex(NO_COLOUR_OPTION);
335 else if (noColour.equals(fc.getMinColour()))
337 noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION);
339 else if (noColour.equals(fc.getMaxColour()))
341 noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION);
345 * update min-max scaling if there is a range to work with,
346 * else disable the widgets (this shouldn't happen if only
347 * valid options are offered in the combo box)
348 * offset slider to have only non-negative values if necessary (JAL-2983)
350 slider.setSliderModel(min, max, min);
351 slider.setMajorTickSpacing(
352 (int) ((slider.getMaximum() - slider.getMinimum()) / 10f));
354 threshline = new GraphLine((max - min) / 2f, "Threshold",
356 threshline.value = fc.getThreshold();
358 if (fc.hasThreshold())
360 threshold.setSelectedIndex(
361 fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
362 : BELOW_THRESHOLD_OPTION);
363 slider.setEnabled(true);
364 slider.setSliderValue(fc.getThreshold());
365 setThresholdValueText(fc.getThreshold());
366 thresholdValue.setEnabled(true);
367 thresholdIsMin.setEnabled(true);
371 slider.setEnabled(false);
372 thresholdValue.setEnabled(false);
373 thresholdIsMin.setEnabled(false);
375 thresholdIsMin.setSelected(!fc.isAutoScaled());
383 * Configures the initial layout
385 private void initialise()
387 this.setLayout(new BorderLayout());
390 * an ActionListener that applies colour changes
392 changeColourAction = new ActionListener()
395 public void actionPerformed(ActionEvent e)
402 * first panel/tab: colour options
404 JPanel coloursPanel = initialiseColoursPanel();
405 this.add(coloursPanel, BorderLayout.NORTH);
408 * second panel/tab: 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 * if not set, default max colour to last plain colour,
563 * and make min colour a pale version of max colour
565 Color max = originalColour.getMaxColour();
568 max = originalColour.getColour();
569 minColour.setBackground(ColorUtils.bleachColour(max, 0.9f));
573 maxColour.setBackground(max);
574 minColour.setBackground(originalColour.getMinColour());
577 noValueCombo = new JComboBox<>();
578 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
579 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
580 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
581 noValueCombo.addItemListener(new ItemListener()
584 public void itemStateChanged(ItemEvent e)
590 JLabel minText = new JLabel(
591 MessageManager.getString("label.min_value") + COLON);
592 minText.setFont(JvSwingUtils.getLabelFont());
593 JLabel maxText = new JLabel(
594 MessageManager.getString("label.max_value") + COLON);
595 maxText.setFont(JvSwingUtils.getLabelFont());
596 JLabel noText = new JLabel(
597 MessageManager.getString("label.no_value") + COLON);
598 noText.setFont(JvSwingUtils.getLabelFont());
600 colourRangePanel.add(minText);
601 colourRangePanel.add(minColour);
602 colourRangePanel.add(maxText);
603 colourRangePanel.add(maxColour);
604 colourRangePanel.add(noText);
605 colourRangePanel.add(noValueCombo);
608 * third row - threshold options and value
610 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
611 thresholdPanel.setBackground(Color.white);
612 graduatedColourPanel.add(thresholdPanel);
614 threshold.addActionListener(changeColourAction);
615 threshold.setToolTipText(MessageManager
616 .getString("label.threshold_feature_display_by_score"));
617 threshold.addItem(MessageManager
618 .getString("label.threshold_feature_no_threshold")); // index 0
619 threshold.addItem(MessageManager
620 .getString("label.threshold_feature_above_threshold")); // index 1
621 threshold.addItem(MessageManager
622 .getString("label.threshold_feature_below_threshold")); // index 2
624 thresholdValue.addActionListener(new ActionListener()
627 public void actionPerformed(ActionEvent e)
629 thresholdValue_actionPerformed();
632 thresholdValue.addFocusListener(new FocusAdapter()
635 public void focusLost(FocusEvent e)
637 thresholdValue_actionPerformed();
640 slider = new Slider(0f, 100f, 50f);
641 slider.setPaintLabels(false);
642 slider.setPaintTicks(true);
643 slider.setBackground(Color.white);
644 slider.setEnabled(false);
645 slider.setOpaque(false);
646 slider.setPreferredSize(new Dimension(100, 32));
647 slider.setToolTipText(
648 MessageManager.getString("label.adjust_threshold"));
650 slider.addChangeListener(new ChangeListener()
653 public void stateChanged(ChangeEvent evt)
657 setThresholdValueText(slider.getSliderValue());
658 thresholdValue.setBackground(Color.white); // to reset red for invalid
659 sliderValueChanged();
663 slider.addMouseListener(new MouseAdapter()
666 public void mouseReleased(MouseEvent evt)
669 * only update Overview and/or structure colouring
670 * when threshold slider drag ends (mouse up)
674 ap.paintAlignment(true, true);
679 thresholdValue.setEnabled(false);
680 thresholdValue.setColumns(7);
682 thresholdPanel.add(threshold);
683 thresholdPanel.add(slider);
684 thresholdPanel.add(thresholdValue);
686 thresholdIsMin.setBackground(Color.white);
688 .setText(MessageManager.getString("label.threshold_minmax"));
689 thresholdIsMin.setToolTipText(MessageManager
690 .getString("label.toggle_absolute_relative_display_threshold"));
691 thresholdIsMin.addActionListener(changeColourAction);
692 thresholdPanel.add(thresholdIsMin);
694 return graduatedColourPanel;
698 * Lay out OK and Cancel buttons
702 private JPanel initialiseOkCancelPanel()
704 JPanel okCancelPanel = new JPanel();
705 // okCancelPanel.setBackground(Color.white);
706 okCancelPanel.add(ok);
707 okCancelPanel.add(cancel);
708 return okCancelPanel;
712 * Lay out Colour options panel, containing
714 * <li>plain colour, with colour picker</li>
715 * <li>colour by text, with choice of Label or other attribute</li>
716 * <li>colour by range, of score or other attribute, when available</li>
721 private JPanel initialiseColoursPanel()
723 JPanel colourByPanel = new JPanel();
724 colourByPanel.setBackground(Color.white);
725 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
726 JvSwingUtils.createTitledBorder(colourByPanel,
727 MessageManager.getString("action.colour"), true);
730 * simple colour radio button and colour picker
732 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
733 simpleColourPanel.setBackground(Color.white);
734 colourByPanel.add(simpleColourPanel);
736 simpleColour = new JRadioButton(
737 MessageManager.getString("label.simple_colour"));
738 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
739 simpleColour.addItemListener(new ItemListener()
742 public void itemStateChanged(ItemEvent e)
744 if (simpleColour.isSelected() && !adjusting)
751 singleColour.setFont(JvSwingUtils.getLabelFont());
752 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
753 singleColour.setPreferredSize(new Dimension(40, 20));
754 // if (originalColour.isGraduatedColour())
756 // singleColour.setBackground(originalColour.getMaxColour());
757 // singleColour.setForeground(originalColour.getMaxColour());
761 singleColour.setBackground(originalColour.getColour());
762 singleColour.setForeground(originalColour.getColour());
764 singleColour.addMouseListener(new MouseAdapter()
767 public void mousePressed(MouseEvent e)
769 if (simpleColour.isSelected())
771 showColourChooser(singleColour, "label.select_colour");
775 simpleColourPanel.add(simpleColour); // radio button
776 simpleColourPanel.add(singleColour); // colour picker button
779 * colour by text (category) radio button and drop-down choice list
781 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
782 byTextPanel.setBackground(Color.white);
783 JvSwingUtils.createTitledBorder(byTextPanel,
784 MessageManager.getString("label.colour_by_text"), true);
785 colourByPanel.add(byTextPanel);
786 byCategory = new JRadioButton(
787 MessageManager.getString("label.by_text_of") + COLON);
788 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
789 byCategory.addItemListener(new ItemListener()
792 public void itemStateChanged(ItemEvent e)
794 if (byCategory.isSelected())
800 byTextPanel.add(byCategory);
802 List<String[]> attNames = FeatureAttributes.getInstance()
803 .getAttributes(featureType);
804 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
805 colourByTextCombo.addItemListener(new ItemListener()
808 public void itemStateChanged(ItemEvent e)
813 byTextPanel.add(colourByTextCombo);
816 * graduated colour panel
818 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
819 colourByPanel.add(graduatedColourPanel);
822 * 3 radio buttons select between simple colour,
823 * by category (text), or graduated
825 ButtonGroup bg = new ButtonGroup();
826 bg.add(simpleColour);
828 bg.add(graduatedColour);
830 return colourByPanel;
833 private void showColourChooser(JPanel colourPanel, String key)
835 Color col = JColorChooser.showDialog(this,
836 MessageManager.getString(key), colourPanel.getBackground());
839 colourPanel.setBackground(col);
840 colourPanel.setForeground(col);
842 colourPanel.repaint();
847 * Constructs and sets the selected colour options as the colour for the
848 * feature type, and repaints the alignment, and optionally the Overview
849 * and/or structure viewer if open
851 * @param updateStructsAndOverview
853 void colourChanged(boolean updateStructsAndOverview)
858 * ignore action handlers while setting values programmatically
864 * ensure min-max range is for the latest choice of
865 * 'graduated colour by'
867 updateColourMinMax();
869 FeatureColourI acg = makeColourFromInputs();
872 * save the colour, and repaint stuff
874 fr.setColour(featureType, acg);
875 ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
881 * Converts the input values into an instance of FeatureColour
885 private FeatureColourI makeColourFromInputs()
888 * min-max range is to (or from) threshold value if
889 * 'threshold is min/max' is selected
895 thresh = Float.valueOf(thresholdValue.getText());
896 } catch (NumberFormatException e)
898 // invalid inputs are already handled on entry
900 float minValue = min;
901 float maxValue = max;
902 final int thresholdOption = threshold.getSelectedIndex();
903 if (thresholdIsMin.isSelected()
904 && thresholdOption == ABOVE_THRESHOLD_OPTION)
908 if (thresholdIsMin.isSelected()
909 && thresholdOption == BELOW_THRESHOLD_OPTION)
913 Color noColour = null;
914 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
916 noColour = minColour.getBackground();
918 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
920 noColour = maxColour.getBackground();
924 * construct a colour that 'remembers' all the options, including
925 * those not currently selected
927 FeatureColourI fc = new FeatureColour(singleColour.getBackground(),
928 minColour.getBackground(), maxColour.getBackground(), noColour,
932 * easiest case - a single colour
934 if (simpleColour.isSelected())
936 ((FeatureColour) fc).setGraduatedColour(false);
941 * next easiest case - colour by Label, or attribute text
943 if (byCategory.isSelected())
945 fc.setColourByLabel(true);
946 String byWhat = (String) colourByTextCombo.getSelectedItem();
947 if (!LABEL_18N.equals(byWhat))
950 FeatureMatcher.fromAttributeDisplayName(byWhat));
956 * remaining case - graduated colour by score, or attribute value;
957 * set attribute to colour by if selected
959 String byWhat = (String) colourByRangeCombo.getSelectedItem();
960 if (!SCORE_18N.equals(byWhat))
962 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
966 * set threshold options and 'autoscaled' which is
967 * false if 'threshold is min/max' is selected
968 * else true (colour range is on actual range of values)
970 fc.setThreshold(thresh);
971 fc.setAutoScaled(!thresholdIsMin.isSelected());
972 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
973 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
975 if (threshline == null)
978 * todo not yet implemented: visual indication of feature threshold
980 threshline = new GraphLine((max - min) / 2f, "Threshold",
988 protected void raiseClosed()
990 if (this.featureSettings != null)
992 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
997 * Action on OK is just to dismiss the dialog - any changes have already been
1001 public void okPressed()
1006 * Action on Cancel is to restore colour scheme and filters as they were when
1007 * the dialog was opened
1010 public void cancelPressed()
1012 fr.setColour(featureType, originalColour);
1013 fr.setFeatureFilter(featureType, originalFilter);
1014 ap.paintAlignment(true, true);
1018 * Action on text entry of a threshold value
1020 protected void thresholdValue_actionPerformed()
1025 * set 'adjusting' flag while moving the slider, so it
1026 * doesn't then in turn change the value (with rounding)
1029 float f = Float.parseFloat(thresholdValue.getText());
1030 f = Float.max(f, this.min);
1031 f = Float.min(f, this.max);
1032 setThresholdValueText(f);
1033 slider.setSliderValue(f);
1034 threshline.value = f;
1035 thresholdValue.setBackground(Color.white); // ok
1037 colourChanged(true);
1038 } catch (NumberFormatException ex)
1040 thresholdValue.setBackground(Color.red); // not ok
1046 * Sets the text field for threshold value, rounded to four significant figures
1050 void setThresholdValueText(float f)
1052 BigDecimal formatted = new BigDecimal(f).round(FOUR_SIG_FIG)
1053 .stripTrailingZeros();
1054 thresholdValue.setText(formatted.toPlainString());
1058 * Action on change of threshold slider value. This may be done interactively
1059 * (by moving the slider), or programmatically (to update the slider after
1060 * manual input of a threshold value).
1062 protected void sliderValueChanged()
1064 threshline.value = slider.getSliderValue();
1067 * repaint alignment, but not Overview or structure,
1068 * to avoid overload while dragging the slider
1070 colourChanged(false);
1073 void addActionListener(ActionListener listener)
1075 if (featureSettings != null)
1078 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1080 featureSettings = listener;
1084 * A helper method to build the drop-down choice of attributes for a feature.
1085 * If 'withRange' is true, then Score, and any attributes with a min-max
1086 * range, are added. If 'withText' is true, Label and any known attributes are
1087 * added. This allows 'categorical numerical' attributes e.g. codon position
1088 * to be coloured by text.
1090 * Where metadata is available with a description for an attribute, that is
1091 * added as a tooltip.
1093 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1094 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1096 * This method does not add any ActionListener to the JComboBox.
1102 protected JComboBox<Object> populateAttributesDropdown(
1103 List<String[]> attNames, boolean withRange, boolean withText)
1105 List<String> displayAtts = new ArrayList<>();
1106 List<String> tooltips = new ArrayList<>();
1110 displayAtts.add(LABEL_18N);
1111 tooltips.add(MessageManager.getString("label.description"));
1115 float[][] minMax = fr.getMinMax().get(featureType);
1116 if (minMax != null && minMax[0][0] != minMax[0][1])
1118 displayAtts.add(SCORE_18N);
1119 tooltips.add(SCORE_18N);
1123 FeatureAttributes fa = FeatureAttributes.getInstance();
1124 for (String[] attName : attNames)
1126 float[] minMax = fa.getMinMax(featureType, attName);
1127 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1128 if (!withText && !hasRange)
1132 displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
1133 String desc = fa.getDescription(featureType, attName);
1134 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1136 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1138 tooltips.add(desc == null ? "" : desc);
1141 // now convert String List to Object List for buildComboWithTooltips
1142 List<Object> displayAttsObjects = new ArrayList<>(displayAtts);
1143 JComboBox<Object> attCombo = JvSwingUtils
1144 .buildComboWithTooltips(displayAttsObjects, tooltips);
1150 * Populates initial layout of the feature attribute filters panel
1152 private JPanel initialiseFiltersPanel()
1154 filters = new ArrayList<>();
1156 JPanel filtersPanel = new JPanel();
1157 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1158 filtersPanel.setBackground(Color.white);
1159 JvSwingUtils.createTitledBorder(filtersPanel,
1160 MessageManager.getString("label.filters"), true);
1162 JPanel andOrPanel = initialiseAndOrPanel();
1163 filtersPanel.add(andOrPanel);
1166 * panel with filters - populated by refreshFiltersDisplay,
1167 * which also sets the layout manager
1169 chooseFiltersPanel = new JPanel();
1170 chooseFiltersPanel.setBackground(Color.white);
1171 filtersPanel.add(chooseFiltersPanel);
1173 return filtersPanel;
1177 * Lays out the panel with radio buttons to AND or OR filter conditions
1181 private JPanel initialiseAndOrPanel()
1183 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1184 andOrPanel.setBackground(Color.white);
1185 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1186 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1187 ActionListener actionListener = new ActionListener()
1190 public void actionPerformed(ActionEvent e)
1195 andFilters.addActionListener(actionListener);
1196 orFilters.addActionListener(actionListener);
1197 ButtonGroup andOr = new ButtonGroup();
1198 andOr.add(andFilters);
1199 andOr.add(orFilters);
1200 andFilters.setSelected(true);
1202 new JLabel(MessageManager.getString("label.join_conditions")));
1203 andOrPanel.add(andFilters);
1204 andOrPanel.add(orFilters);
1209 * Refreshes the display to show any filters currently configured for the
1210 * selected feature type (editable, with 'remove' option), plus one extra row
1211 * for adding a condition. This should be called after a filter has been
1212 * removed, added or amended.
1214 private void updateFiltersTab()
1217 * clear the panel and list of filter conditions
1219 chooseFiltersPanel.removeAll();
1223 * look up attributes known for feature type
1225 List<String[]> attNames = FeatureAttributes.getInstance()
1226 .getAttributes(featureType);
1229 * if this feature type has filters set, load them first
1231 FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
1232 if (featureFilters != null)
1234 if (!featureFilters.isAnded())
1236 orFilters.setSelected(true);
1238 featureFilters.getMatchers().forEach(matcher -> filters.add(matcher));
1242 * and an empty filter for the user to populate (add)
1244 filters.add(FeatureMatcher.NULL_MATCHER);
1247 * use GridLayout to 'justify' rows to the top of the panel, until
1248 * there are too many to fit in, then fall back on BoxLayout
1250 if (filters.size() <= 5)
1252 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1256 chooseFiltersPanel.setLayout(
1257 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1261 * render the conditions in rows, each in its own JPanel
1263 int filterIndex = 0;
1264 for (FeatureMatcherI filter : filters)
1266 JPanel row = addFilter(filter, attNames, filterIndex);
1267 chooseFiltersPanel.add(row);
1276 * A helper method that constructs a row (panel) with one filter condition:
1278 * <li>a drop-down list of Label, Score and attribute names to choose
1280 * <li>a drop-down list of conditions to choose from</li>
1281 * <li>a text field for input of a match pattern</li>
1282 * <li>optionally, a 'remove' button</li>
1284 * The filter values are set as defaults for the input fields. The 'remove'
1285 * button is added unless the pattern is empty (incomplete filter condition).
1287 * Action handlers on these fields provide for
1289 * <li>validate pattern field - should be numeric if condition is numeric</li>
1290 * <li>save filters and refresh display on any (valid) change</li>
1291 * <li>remove filter and refresh on 'Remove'</li>
1292 * <li>update conditions list on change of Label/Score/Attribute</li>
1293 * <li>refresh value field tooltip with min-max range on change of
1299 * @param filterIndex
1302 protected JPanel addFilter(FeatureMatcherI filter,
1303 List<String[]> attNames, int filterIndex)
1305 String[] attName = filter.getAttribute();
1306 Condition cond = filter.getMatcher().getCondition();
1307 String pattern = filter.getMatcher().getPattern();
1309 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1310 filterRow.setBackground(Color.white);
1313 * drop-down choice of attribute, with description as a tooltip
1314 * if we can obtain it
1316 final JComboBox<Object> attCombo = populateAttributesDropdown(attNames,
1318 String filterBy = setSelectedAttribute(attCombo, filter);
1320 JComboBox<Condition> condCombo = new JComboBox<>();
1322 JTextField patternField = new JTextField(8);
1323 patternField.setText(pattern);
1326 * action handlers that validate and (if valid) apply changes
1328 ActionListener actionListener = new ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 if (validateFilter(patternField, condCombo))
1335 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1342 ItemListener itemListener = new ItemListener()
1345 public void itemStateChanged(ItemEvent e)
1347 actionListener.actionPerformed(null);
1351 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1353 attCombo.setSelectedIndex(0);
1357 attCombo.setSelectedItem(
1358 FeatureMatcher.toAttributeDisplayName(attName));
1360 attCombo.addItemListener(new ItemListener()
1363 public void itemStateChanged(ItemEvent e)
1366 * on change of attribute, refresh the conditions list to
1367 * ensure it is appropriate for the attribute datatype
1369 populateConditions((String) attCombo.getSelectedItem(),
1370 (Condition) condCombo.getSelectedItem(), condCombo,
1372 actionListener.actionPerformed(null);
1376 filterRow.add(attCombo);
1379 * drop-down choice of test condition
1381 populateConditions(filterBy, cond, condCombo, patternField);
1382 condCombo.setPreferredSize(new Dimension(150, 20));
1383 condCombo.addItemListener(itemListener);
1384 filterRow.add(condCombo);
1387 * pattern to match against
1389 patternField.addActionListener(actionListener);
1390 patternField.addFocusListener(new FocusAdapter()
1393 public void focusLost(FocusEvent e)
1395 actionListener.actionPerformed(null);
1398 filterRow.add(patternField);
1401 * disable pattern field for condition 'Present / NotPresent'
1403 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1404 patternField.setEnabled(selectedCondition.needsAPattern());
1407 * if a numeric condition is selected, show the value range
1408 * as a tooltip on the value input field
1410 setNumericHints(filterBy, selectedCondition, patternField);
1413 * add remove button if filter is populated (non-empty pattern)
1415 if (!patternField.isEnabled()
1416 || (pattern != null && pattern.trim().length() > 0))
1418 JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x
1419 removeCondition.setToolTipText(
1420 MessageManager.getString("label.delete_condition"));
1421 removeCondition.setBorder(new EmptyBorder(0, 0, 0, 0));
1422 removeCondition.addActionListener(new ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 filters.remove(filterIndex);
1431 filterRow.add(removeCondition);
1438 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1444 private String setSelectedAttribute(JComboBox<Object> attCombo,
1445 FeatureMatcherI filter)
1448 if (filter.isByScore())
1452 else if (filter.isByLabel())
1458 item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
1460 attCombo.setSelectedItem(item);
1465 * If a numeric comparison condition is selected, retrieves the min-max range
1466 * for the value (score or attribute), and sets it as a tooltip on the value
1467 * field. If the field is currently empty, then pre-populates it with
1469 * <li>the minimum value, if condition is > or >=</li>
1470 * <li>the maximum value, if condition is < or <=</li>
1474 * @param selectedCondition
1475 * @param patternField
1477 private void setNumericHints(String attName, Condition selectedCondition,
1478 JTextField patternField)
1480 patternField.setToolTipText("");
1482 if (selectedCondition.isNumeric())
1484 float[] minMax = getMinMax(attName);
1487 String minFormatted = DECFMT_2_2.format(minMax[0]);
1488 String maxFormatted = DECFMT_2_2.format(minMax[1]);
1489 String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
1490 patternField.setToolTipText(tip);
1491 if (patternField.getText().isEmpty())
1493 if (selectedCondition == Condition.GE
1494 || selectedCondition == Condition.GT)
1496 patternField.setText(minFormatted);
1500 if (selectedCondition == Condition.LE
1501 || selectedCondition == Condition.LT)
1503 patternField.setText(maxFormatted);
1512 * Populates the drop-down list of comparison conditions for the given
1513 * attribute name. The conditions added depend on the datatype of the
1514 * attribute values. The supplied condition is set as the selected item in the
1515 * list, provided it is in the list. If the pattern is now invalid
1516 * (non-numeric pattern for a numeric condition), it is cleared.
1521 * @param patternField
1523 private void populateConditions(String attName, Condition cond,
1524 JComboBox<Condition> condCombo, JTextField patternField)
1526 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1527 FeatureMatcher.fromAttributeDisplayName(attName));
1528 if (LABEL_18N.equals(attName))
1530 type = Datatype.Character;
1532 else if (SCORE_18N.equals(attName))
1534 type = Datatype.Number;
1538 * remove itemListener before starting
1540 ItemListener listener = condCombo.getItemListeners()[0];
1541 condCombo.removeItemListener(listener);
1542 boolean condIsValid = false;
1544 condCombo.removeAllItems();
1545 for (Condition c : Condition.values())
1547 if ((c.isNumeric() && type == Datatype.Number)
1548 || (!c.isNumeric() && type != Datatype.Number))
1550 condCombo.addItem(c);
1559 * set the selected condition (does nothing if not in the list)
1563 condCombo.setSelectedItem(cond);
1567 condCombo.setSelectedIndex(0);
1571 * clear pattern if it is now invalid for condition
1573 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1577 String pattern = patternField.getText().trim();
1578 if (pattern.length() > 0)
1580 Float.valueOf(pattern);
1582 } catch (NumberFormatException e)
1584 patternField.setText("");
1589 * restore the listener
1591 condCombo.addItemListener(listener);
1595 * Answers true unless a numeric condition has been selected with a
1596 * non-numeric value. Sets the value field to RED with a tooltip if in error.
1598 * If the pattern is expected but is empty, this method returns false, but
1599 * does not mark the field as invalid. This supports selecting an attribute
1600 * for a new condition before a match pattern has been entered.
1605 protected boolean validateFilter(JTextField value,
1606 JComboBox<Condition> condCombo)
1608 if (value == null || condCombo == null)
1610 return true; // fields not populated
1613 Condition cond = (Condition) condCombo.getSelectedItem();
1614 if (!cond.needsAPattern())
1619 value.setBackground(Color.white);
1620 value.setToolTipText("");
1621 String v1 = value.getText().trim();
1622 if (v1.length() == 0)
1627 if (cond.isNumeric() && v1.length() > 0)
1632 } catch (NumberFormatException e)
1634 value.setBackground(Color.red);
1635 value.setToolTipText(
1636 MessageManager.getString("label.numeric_required"));
1645 * Constructs a filter condition from the given input fields, and replaces the
1646 * condition at filterIndex with the new one. Does nothing if the pattern
1647 * field is blank (unless the match condition is one that doesn't require a
1648 * pattern, e.g. 'Is present'). Answers true if the filter was updated, else
1651 * This method may update the tooltip on the filter value field to show the
1652 * value range, if a numeric condition is selected. This ensures the tooltip
1653 * is updated when a numeric valued attribute is chosen on the last 'add a
1659 * @param filterIndex
1661 protected boolean updateFilter(JComboBox<Object> attCombo,
1662 JComboBox<Condition> condCombo, JTextField valueField,
1668 attName = (String) attCombo.getSelectedItem();
1669 } catch (Exception e)
1671 Cache.log.error("Problem casting Combo box entry to String");
1672 attName = attCombo.getSelectedItem().toString();
1674 Condition cond = (Condition) condCombo.getSelectedItem();
1675 String pattern = valueField.getText().trim();
1677 setNumericHints(attName, cond, valueField);
1679 if (pattern.length() == 0 && cond.needsAPattern())
1681 valueField.setEnabled(true); // ensure pattern field is enabled!
1686 * Construct a matcher that operates on Label, Score,
1687 * or named attribute
1689 FeatureMatcherI km = null;
1690 if (LABEL_18N.equals(attName))
1692 km = FeatureMatcher.byLabel(cond, pattern);
1694 else if (SCORE_18N.equals(attName))
1696 km = FeatureMatcher.byScore(cond, pattern);
1700 km = FeatureMatcher.byAttribute(cond, pattern,
1701 FeatureMatcher.fromAttributeDisplayName(attName));
1704 filters.set(filterIndex, km);
1710 * Action on any change to feature filtering, namely
1712 * <li>change of selected attribute</li>
1713 * <li>change of selected condition</li>
1714 * <li>change of match pattern</li>
1715 * <li>removal of a condition</li>
1717 * The inputs are parsed into a combined filter and this is set for the
1718 * feature type, and the alignment redrawn.
1720 protected void filtersChanged()
1723 * update the filter conditions for the feature type
1725 boolean anded = andFilters.isSelected();
1726 FeatureMatcherSetI combined = new FeatureMatcherSet();
1728 for (FeatureMatcherI filter : filters)
1730 String pattern = filter.getMatcher().getPattern();
1731 Condition condition = filter.getMatcher().getCondition();
1732 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1736 combined.and(filter);
1740 combined.or(filter);
1746 * save the filter conditions in the FeatureRenderer
1747 * (note this might now be an empty filter with no conditions)
1749 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1750 ap.paintAlignment(true, true);