2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.FeatureColourI;
25 import jalview.datamodel.GraphLine;
26 import jalview.datamodel.features.FeatureAttributes;
27 import jalview.datamodel.features.FeatureAttributes.Datatype;
28 import jalview.datamodel.features.FeatureMatcher;
29 import jalview.datamodel.features.FeatureMatcherI;
30 import jalview.datamodel.features.FeatureMatcherSet;
31 import jalview.datamodel.features.FeatureMatcherSetI;
32 import jalview.schemes.FeatureColour;
33 import jalview.util.ColorUtils;
34 import jalview.util.MessageManager;
35 import jalview.util.matcher.Condition;
37 import java.awt.BorderLayout;
38 import java.awt.Color;
39 import java.awt.Dimension;
40 import java.awt.FlowLayout;
41 import java.awt.GridLayout;
42 import java.awt.event.ActionEvent;
43 import java.awt.event.ActionListener;
44 import java.awt.event.FocusAdapter;
45 import java.awt.event.FocusEvent;
46 import java.awt.event.ItemEvent;
47 import java.awt.event.ItemListener;
48 import java.awt.event.MouseAdapter;
49 import java.awt.event.MouseEvent;
50 import java.text.DecimalFormat;
51 import java.util.ArrayList;
52 import java.util.List;
54 import javax.swing.BorderFactory;
55 import javax.swing.BoxLayout;
56 import javax.swing.ButtonGroup;
57 import javax.swing.JButton;
58 import javax.swing.JCheckBox;
59 import javax.swing.JColorChooser;
60 import javax.swing.JComboBox;
61 import javax.swing.JLabel;
62 import javax.swing.JPanel;
63 import javax.swing.JRadioButton;
64 import javax.swing.JSlider;
65 import javax.swing.JTextField;
66 import javax.swing.SwingConstants;
67 import javax.swing.border.LineBorder;
68 import javax.swing.event.ChangeEvent;
69 import javax.swing.event.ChangeListener;
70 import javax.swing.plaf.basic.BasicArrowButton;
73 * A dialog where the user can configure colour scheme, and any filters, for one
76 * (Was FeatureColourChooser prior to Jalview 1.11, renamed with the addition of
79 public class FeatureTypeSettings extends JalviewDialog
81 private final static String LABEL_18N = MessageManager
82 .getString("label.label");
84 private final static String SCORE_18N = MessageManager
85 .getString("label.score");
87 private static final int RADIO_WIDTH = 130;
89 private static final String COLON = ":";
91 private static final int MAX_TOOLTIP_LENGTH = 50;
93 private static final int NO_COLOUR_OPTION = 0;
95 private static final int MIN_COLOUR_OPTION = 1;
97 private static final int MAX_COLOUR_OPTION = 2;
99 private static final int ABOVE_THRESHOLD_OPTION = 1;
101 private static final int BELOW_THRESHOLD_OPTION = 2;
103 private static final DecimalFormat DECFMT_2_2 = new DecimalFormat(
107 * FeatureRenderer holds colour scheme and filters for feature types
109 private final FeatureRenderer fr; // todo refactor to allow interface type
113 * the view panel to update when settings change
115 private final AlignmentViewPanel ap;
117 private final String featureType;
120 * the colour and filters to reset to on Cancel
122 private final FeatureColourI originalColour;
124 private final FeatureMatcherSetI originalFilter;
127 * set flag to true when setting values programmatically,
128 * to avoid invocation of action handlers
130 private boolean adjusting = false;
133 * minimum of the value range for graduated colour
134 * (may be for feature score or for a numeric attribute)
139 * maximum of the value range for graduated colour
144 * scale factor for conversion between absolute min-max and slider
146 private float scaleFactor;
149 * radio button group, to select what to colour by:
150 * simple colour, by category (text), or graduated
152 private JRadioButton simpleColour = new JRadioButton();
154 private JRadioButton byCategory = new JRadioButton();
156 private JRadioButton graduatedColour = new JRadioButton();
159 * colours and filters are shown in tabbed view or single content pane
161 JPanel coloursPanel, filtersPanel;
163 JPanel singleColour = new JPanel();
165 private JPanel minColour = new JPanel();
167 private JPanel maxColour = new JPanel();
169 private JComboBox<String> threshold = new JComboBox<>();
171 private JSlider slider = new JSlider();
173 private JTextField thresholdValue = new JTextField(20);
175 private JCheckBox thresholdIsMin = new JCheckBox();
177 private GraphLine threshline;
179 private ActionListener featureSettings = null;
181 private ActionListener changeColourAction;
184 * choice of option for 'colour for no value'
186 private JComboBox<String> noValueCombo;
189 * choice of what to colour by text (Label or attribute)
191 private JComboBox<String> colourByTextCombo;
194 * choice of what to colour by range (Score or attribute)
196 private JComboBox<String> colourByRangeCombo;
198 private JRadioButton andFilters;
200 private JRadioButton orFilters;
203 * filters for the currently selected feature type
205 private List<FeatureMatcherI> filters;
207 private JPanel chooseFiltersPanel;
215 public FeatureTypeSettings(FeatureRenderer frender, String theType)
217 this(frender, false, theType);
221 * Constructor, with option to make a blocking dialog (has to complete in the
222 * AWT event queue thread). Currently this option is always set to false.
228 FeatureTypeSettings(FeatureRenderer frender, boolean blocking,
232 this.featureType = theType;
234 originalFilter = fr.getFeatureFilter(theType);
235 originalColour = fr.getFeatureColours().get(theType);
242 } catch (Exception ex)
244 ex.printStackTrace();
254 colourChanged(false);
256 String title = MessageManager
257 .formatMessage("label.display_settings_for", new String[]
259 initDialogFrame(this, true, blocking, title, 500, 500);
265 * Configures the widgets on the Colours tab according to the current feature
268 private void updateColoursTab()
270 FeatureColourI fc = fr.getFeatureColours().get(featureType);
273 * suppress action handling while updating values programmatically
281 if (fc.isSimpleColour())
283 simpleColour.setSelected(true);
284 singleColour.setBackground(fc.getColour());
285 singleColour.setForeground(fc.getColour());
289 * colour by text (Label or attribute text)
291 if (fc.isColourByLabel())
293 byCategory.setSelected(true);
294 colourByTextCombo.setEnabled(colourByTextCombo.getItemCount() > 1);
295 if (fc.isColourByAttribute())
297 String[] attributeName = fc.getAttributeName();
298 colourByTextCombo.setSelectedItem(
299 FeatureMatcher.toAttributeDisplayName(attributeName));
303 colourByTextCombo.setSelectedItem(LABEL_18N);
308 colourByTextCombo.setEnabled(false);
311 if (!fc.isGraduatedColour())
313 colourByRangeCombo.setEnabled(false);
314 minColour.setEnabled(false);
315 maxColour.setEnabled(false);
316 noValueCombo.setEnabled(false);
317 threshold.setEnabled(false);
318 slider.setEnabled(false);
319 thresholdValue.setEnabled(false);
320 thresholdIsMin.setEnabled(false);
325 * Graduated colour, by score or attribute value range
327 graduatedColour.setSelected(true);
328 updateColourMinMax(); // ensure min, max are set
329 colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
330 minColour.setEnabled(true);
331 maxColour.setEnabled(true);
332 noValueCombo.setEnabled(true);
333 threshold.setEnabled(true);
334 minColour.setBackground(fc.getMinColour());
335 maxColour.setBackground(fc.getMaxColour());
337 if (fc.isColourByAttribute())
339 String[] attributeName = fc.getAttributeName();
340 colourByRangeCombo.setSelectedItem(
341 FeatureMatcher.toAttributeDisplayName(attributeName));
345 colourByRangeCombo.setSelectedItem(SCORE_18N);
347 Color noColour = fc.getNoColour();
348 if (noColour == null)
350 noValueCombo.setSelectedIndex(NO_COLOUR_OPTION);
352 else if (noColour.equals(fc.getMinColour()))
354 noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION);
356 else if (noColour.equals(fc.getMaxColour()))
358 noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION);
362 * update min-max scaling if there is a range to work with,
363 * else disable the widgets (this shouldn't happen if only
364 * valid options are offered in the combo box)
366 scaleFactor = (max == min) ? 1f : 100f / (max - min);
367 float range = (max - min) * scaleFactor;
368 slider.setMinimum((int) (min * scaleFactor));
369 slider.setMaximum((int) (max * scaleFactor));
370 slider.setMajorTickSpacing((int) (range / 10f));
372 threshline = new GraphLine((max - min) / 2f, "Threshold",
374 threshline.value = fc.getThreshold();
376 if (fc.hasThreshold())
378 threshold.setSelectedIndex(
379 fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
380 : BELOW_THRESHOLD_OPTION);
381 slider.setEnabled(true);
382 slider.setValue((int) (fc.getThreshold() * scaleFactor));
383 thresholdValue.setText(String.valueOf(getRoundedSliderValue()));
384 thresholdValue.setEnabled(true);
385 thresholdIsMin.setEnabled(true);
389 slider.setEnabled(false);
390 thresholdValue.setEnabled(false);
391 thresholdIsMin.setEnabled(false);
393 thresholdIsMin.setSelected(!fc.isAutoScaled());
401 * Configures the initial layout
403 private void initialise()
405 this.setLayout(new BorderLayout());
408 * an ActionListener that applies colour changes
410 changeColourAction = new ActionListener()
413 public void actionPerformed(ActionEvent e)
420 * first panel/tab: colour options
422 JPanel coloursPanel = initialiseColoursPanel();
423 this.add(coloursPanel, BorderLayout.NORTH);
426 * second panel/tab: filter options
428 JPanel filtersPanel = initialiseFiltersPanel();
429 this.add(filtersPanel, BorderLayout.CENTER);
431 JPanel okCancelPanel = initialiseOkCancelPanel();
433 this.add(okCancelPanel, BorderLayout.SOUTH);
437 * Updates the min-max range if Colour By selected item is Score, or an
438 * attribute, with a min-max range
440 protected void updateColourMinMax()
442 if (!graduatedColour.isSelected())
447 String colourBy = (String) colourByRangeCombo.getSelectedItem();
448 float[] minMax = getMinMax(colourBy);
458 * Retrieves the min-max range:
460 * <li>of feature score, if colour or filter is by Score</li>
461 * <li>else of the selected attribute</li>
467 private float[] getMinMax(String attName)
469 float[] minMax = null;
470 if (SCORE_18N.equals(attName))
472 minMax = fr.getMinMax().get(featureType)[0];
476 // colour by attribute range
477 minMax = FeatureAttributes.getInstance().getMinMax(featureType,
478 FeatureMatcher.fromAttributeDisplayName(attName));
484 * Lay out fields for graduated colour (by score or attribute value)
488 private JPanel initialiseGraduatedColourPanel()
490 JPanel graduatedColourPanel = new JPanel();
491 graduatedColourPanel.setLayout(
492 new BoxLayout(graduatedColourPanel, BoxLayout.Y_AXIS));
493 JvSwingUtils.createTitledBorder(graduatedColourPanel,
494 MessageManager.getString("label.graduated_colour"), true);
495 graduatedColourPanel.setBackground(Color.white);
498 * first row: graduated colour radio button, score/attribute drop-down
500 JPanel graduatedChoicePanel = new JPanel(
501 new FlowLayout(FlowLayout.LEFT));
502 graduatedChoicePanel.setBackground(Color.white);
503 graduatedColour = new JRadioButton(
504 MessageManager.getString("label.by_range_of") + COLON);
505 graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
506 graduatedColour.addItemListener(new ItemListener()
509 public void itemStateChanged(ItemEvent e)
511 if (graduatedColour.isSelected())
517 graduatedChoicePanel.add(graduatedColour);
519 List<String[]> attNames = FeatureAttributes.getInstance()
520 .getAttributes(featureType);
521 colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
522 colourByRangeCombo.addItemListener(new ItemListener()
525 public void itemStateChanged(ItemEvent e)
532 * disable graduated colour option if no range found
534 graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
536 graduatedChoicePanel.add(colourByRangeCombo);
537 graduatedColourPanel.add(graduatedChoicePanel);
540 * second row - min/max/no colours
542 JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
543 colourRangePanel.setBackground(Color.white);
544 graduatedColourPanel.add(colourRangePanel);
546 minColour.setFont(JvSwingUtils.getLabelFont());
547 minColour.setBorder(BorderFactory.createLineBorder(Color.black));
548 minColour.setPreferredSize(new Dimension(40, 20));
549 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
550 minColour.addMouseListener(new MouseAdapter()
553 public void mousePressed(MouseEvent e)
555 if (minColour.isEnabled())
557 showColourChooser(minColour, "label.select_colour_minimum_value");
562 maxColour.setFont(JvSwingUtils.getLabelFont());
563 maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
564 maxColour.setPreferredSize(new Dimension(40, 20));
565 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
566 maxColour.addMouseListener(new MouseAdapter()
569 public void mousePressed(MouseEvent e)
571 if (maxColour.isEnabled())
573 showColourChooser(maxColour, "label.select_colour_maximum_value");
577 maxColour.setBorder(new LineBorder(Color.black));
580 * default max colour to current colour (if a plain colour),
581 * or to Black if colour by label; make min colour a pale
582 * version of max colour
584 FeatureColourI fc = fr.getFeatureColours().get(featureType);
585 Color bg = fc.isSimpleColour() ? fc.getColour() : Color.BLACK;
586 maxColour.setBackground(bg);
587 minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
589 noValueCombo = new JComboBox<>();
590 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
591 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
592 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
593 noValueCombo.addItemListener(new ItemListener()
596 public void itemStateChanged(ItemEvent e)
602 JLabel minText = new JLabel(
603 MessageManager.getString("label.min_value") + COLON);
604 minText.setFont(JvSwingUtils.getLabelFont());
605 JLabel maxText = new JLabel(
606 MessageManager.getString("label.max_value") + COLON);
607 maxText.setFont(JvSwingUtils.getLabelFont());
608 JLabel noText = new JLabel(
609 MessageManager.getString("label.no_value") + COLON);
610 noText.setFont(JvSwingUtils.getLabelFont());
612 colourRangePanel.add(minText);
613 colourRangePanel.add(minColour);
614 colourRangePanel.add(maxText);
615 colourRangePanel.add(maxColour);
616 colourRangePanel.add(noText);
617 colourRangePanel.add(noValueCombo);
620 * third row - threshold options and value
622 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
623 thresholdPanel.setBackground(Color.white);
624 graduatedColourPanel.add(thresholdPanel);
626 threshold.addActionListener(changeColourAction);
627 threshold.setToolTipText(MessageManager
628 .getString("label.threshold_feature_display_by_score"));
629 threshold.addItem(MessageManager
630 .getString("label.threshold_feature_no_threshold")); // index 0
631 threshold.addItem(MessageManager
632 .getString("label.threshold_feature_above_threshold")); // index 1
633 threshold.addItem(MessageManager
634 .getString("label.threshold_feature_below_threshold")); // index 2
636 thresholdValue.addActionListener(new ActionListener()
639 public void actionPerformed(ActionEvent e)
641 thresholdValue_actionPerformed();
644 thresholdValue.addFocusListener(new FocusAdapter()
647 public void focusLost(FocusEvent e)
649 thresholdValue_actionPerformed();
652 slider.setPaintLabels(false);
653 slider.setPaintTicks(true);
654 slider.setBackground(Color.white);
655 slider.setEnabled(false);
656 slider.setOpaque(false);
657 slider.setPreferredSize(new Dimension(100, 32));
658 slider.setToolTipText(
659 MessageManager.getString("label.adjust_threshold"));
661 slider.addChangeListener(new ChangeListener()
664 public void stateChanged(ChangeEvent evt)
669 .setText(String.valueOf(slider.getValue() / scaleFactor));
670 sliderValueChanged();
674 slider.addMouseListener(new MouseAdapter()
677 public void mouseReleased(MouseEvent evt)
680 * only update Overview and/or structure colouring
681 * when threshold slider drag ends (mouse up)
685 ap.paintAlignment(true, true);
690 thresholdValue.setEnabled(false);
691 thresholdValue.setColumns(7);
693 thresholdPanel.add(threshold);
694 thresholdPanel.add(slider);
695 thresholdPanel.add(thresholdValue);
697 thresholdIsMin.setBackground(Color.white);
699 .setText(MessageManager.getString("label.threshold_minmax"));
700 thresholdIsMin.setToolTipText(MessageManager
701 .getString("label.toggle_absolute_relative_display_threshold"));
702 thresholdIsMin.addActionListener(changeColourAction);
703 thresholdPanel.add(thresholdIsMin);
705 return graduatedColourPanel;
709 * Lay out OK and Cancel buttons
713 private JPanel initialiseOkCancelPanel()
715 JPanel okCancelPanel = new JPanel();
716 // okCancelPanel.setBackground(Color.white);
717 okCancelPanel.add(ok);
718 okCancelPanel.add(cancel);
719 return okCancelPanel;
723 * Lay out Colour options panel, containing
725 * <li>plain colour, with colour picker</li>
726 * <li>colour by text, with choice of Label or other attribute</li>
727 * <li>colour by range, of score or other attribute, when available</li>
732 private JPanel initialiseColoursPanel()
734 JPanel colourByPanel = new JPanel();
735 colourByPanel.setBackground(Color.white);
736 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
737 JvSwingUtils.createTitledBorder(colourByPanel,
738 MessageManager.getString("action.colour"), true);
741 * simple colour radio button and colour picker
743 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
744 simpleColourPanel.setBackground(Color.white);
745 // JvSwingUtils.createTitledBorder(simpleColourPanel,
746 // MessageManager.getString("label.simple"), true);
747 colourByPanel.add(simpleColourPanel);
749 simpleColour = new JRadioButton(
750 MessageManager.getString("label.simple_colour"));
751 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
752 simpleColour.addItemListener(new ItemListener()
755 public void itemStateChanged(ItemEvent e)
757 if (simpleColour.isSelected() && !adjusting)
759 showColourChooser(singleColour, "label.select_colour");
765 singleColour.setFont(JvSwingUtils.getLabelFont());
766 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
767 singleColour.setPreferredSize(new Dimension(40, 20));
768 singleColour.addMouseListener(new MouseAdapter()
771 public void mousePressed(MouseEvent e)
773 if (simpleColour.isSelected())
775 showColourChooser(singleColour, "label.select_colour");
779 simpleColourPanel.add(simpleColour); // radio button
780 simpleColourPanel.add(singleColour); // colour picker button
783 * colour by text (category) radio button and drop-down choice list
785 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
786 byTextPanel.setBackground(Color.white);
787 JvSwingUtils.createTitledBorder(byTextPanel,
788 MessageManager.getString("label.colour_by_text"), true);
789 colourByPanel.add(byTextPanel);
790 byCategory = new JRadioButton(
791 MessageManager.getString("label.by_text_of") + COLON);
792 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
793 byCategory.addItemListener(new ItemListener()
796 public void itemStateChanged(ItemEvent e)
798 if (byCategory.isSelected())
804 byTextPanel.add(byCategory);
806 List<String[]> attNames = FeatureAttributes.getInstance()
807 .getAttributes(featureType);
808 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
809 colourByTextCombo.addItemListener(new ItemListener()
812 public void itemStateChanged(ItemEvent e)
817 byTextPanel.add(colourByTextCombo);
820 * graduated colour panel
822 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
823 colourByPanel.add(graduatedColourPanel);
826 * 3 radio buttons select between simple colour,
827 * by category (text), or graduated
829 ButtonGroup bg = new ButtonGroup();
830 bg.add(simpleColour);
832 bg.add(graduatedColour);
834 return colourByPanel;
837 private void showColourChooser(JPanel colourPanel, String key)
839 Color col = JColorChooser.showDialog(this,
840 MessageManager.getString(key), colourPanel.getBackground());
843 colourPanel.setBackground(col);
844 colourPanel.setForeground(col);
846 colourPanel.repaint();
851 * Constructs and sets the selected colour options as the colour for the
852 * feature type, and repaints the alignment, and optionally the Overview
853 * and/or structure viewer if open
855 * @param updateStructsAndOverview
857 void colourChanged(boolean updateStructsAndOverview)
862 * ignore action handlers while setting values programmatically
868 * ensure min-max range is for the latest choice of
869 * 'graduated colour by'
871 updateColourMinMax();
873 FeatureColourI acg = makeColourFromInputs();
876 * save the colour, and repaint stuff
878 fr.setColour(featureType, acg);
879 ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
885 * Converts the input values into an instance of FeatureColour
889 private FeatureColourI makeColourFromInputs()
892 * easiest case - a single colour
894 if (simpleColour.isSelected())
896 return new FeatureColour(singleColour.getBackground());
900 * next easiest case - colour by Label, or attribute text
902 if (byCategory.isSelected())
904 Color c = this.getBackground();
905 FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f);
906 fc.setColourByLabel(true);
907 String byWhat = (String) colourByTextCombo.getSelectedItem();
908 if (!LABEL_18N.equals(byWhat))
911 FeatureMatcher.fromAttributeDisplayName(byWhat));
917 * remaining case - graduated colour by score, or attribute value
919 Color noColour = null;
920 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
922 noColour = minColour.getBackground();
924 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
926 noColour = maxColour.getBackground();
932 thresh = Float.valueOf(thresholdValue.getText());
933 } catch (NumberFormatException e)
935 // invalid inputs are already handled on entry
939 * min-max range is to (or from) threshold value if
940 * 'threshold is min/max' is selected
942 float minValue = min;
943 float maxValue = max;
944 final int thresholdOption = threshold.getSelectedIndex();
945 if (thresholdIsMin.isSelected()
946 && thresholdOption == ABOVE_THRESHOLD_OPTION)
950 if (thresholdIsMin.isSelected()
951 && thresholdOption == BELOW_THRESHOLD_OPTION)
957 * make the graduated colour
959 FeatureColourI fc = new FeatureColour(minColour.getBackground(),
960 maxColour.getBackground(), noColour, minValue, maxValue);
963 * set attribute to colour by if selected
965 String byWhat = (String) colourByRangeCombo.getSelectedItem();
966 if (!SCORE_18N.equals(byWhat))
968 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
972 * set threshold options and 'autoscaled' which is
973 * false if 'threshold is min/max' is selected
974 * else true (colour range is on actual range of values)
976 fc.setThreshold(thresh);
977 fc.setAutoScaled(!thresholdIsMin.isSelected());
978 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
979 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
981 if (threshline == null)
984 * todo not yet implemented: visual indication of feature threshold
986 threshline = new GraphLine((max - min) / 2f, "Threshold",
994 protected void raiseClosed()
996 if (this.featureSettings != null)
998 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
1003 * Action on OK is just to dismiss the dialog - any changes have already been
1007 public void okPressed()
1012 * Action on Cancel is to restore colour scheme and filters as they were when
1013 * the dialog was opened
1016 public void cancelPressed()
1018 fr.setColour(featureType, originalColour);
1019 fr.setFeatureFilter(featureType, originalFilter);
1020 ap.paintAlignment(true, true);
1024 * Action on text entry of a threshold value
1026 protected void thresholdValue_actionPerformed()
1031 float f = Float.parseFloat(thresholdValue.getText());
1032 slider.setValue((int) (f * scaleFactor));
1033 threshline.value = f;
1034 thresholdValue.setBackground(Color.white); // ok
1037 * force repaint of any Overview window or structure
1039 ap.paintAlignment(true, true);
1040 } catch (NumberFormatException ex)
1042 thresholdValue.setBackground(Color.red); // not ok
1050 * Action on change of threshold slider value. This may be done interactively
1051 * (by moving the slider), or programmatically (to update the slider after
1052 * manual input of a threshold value).
1054 protected void sliderValueChanged()
1056 threshline.value = getRoundedSliderValue();
1059 * repaint alignment, but not Overview or structure,
1060 * to avoid overload while dragging the slider
1062 colourChanged(false);
1066 * Converts the slider value to its absolute value by dividing by the
1067 * scaleFactor. Rounding errors are squashed by forcing min/max of slider
1068 * range to the actual min/max of feature score range
1072 private float getRoundedSliderValue()
1074 int value = slider.getValue();
1075 float f = value == slider.getMaximum() ? max
1076 : (value == slider.getMinimum() ? min : value / scaleFactor);
1080 void addActionListener(ActionListener listener)
1082 if (featureSettings != null)
1085 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1087 featureSettings = listener;
1091 * A helper method to build the drop-down choice of attributes for a feature.
1092 * If 'withRange' is true, then Score, and any attributes with a min-max
1093 * range, are added. If 'withText' is true, Label and any known attributes are
1094 * added. This allows 'categorical numerical' attributes e.g. codon position
1095 * to be coloured by text.
1097 * Where metadata is available with a description for an attribute, that is
1098 * added as a tooltip.
1100 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1101 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1103 * This method does not add any ActionListener to the JComboBox.
1109 protected JComboBox<String> populateAttributesDropdown(
1110 List<String[]> attNames, boolean withRange, boolean withText)
1112 List<String> displayAtts = new ArrayList<>();
1113 List<String> tooltips = new ArrayList<>();
1117 displayAtts.add(LABEL_18N);
1118 tooltips.add(MessageManager.getString("label.description"));
1122 float[][] minMax = fr.getMinMax().get(featureType);
1123 if (minMax != null && minMax[0][0] != minMax[0][1])
1125 displayAtts.add(SCORE_18N);
1126 tooltips.add(SCORE_18N);
1130 FeatureAttributes fa = FeatureAttributes.getInstance();
1131 for (String[] attName : attNames)
1133 float[] minMax = fa.getMinMax(featureType, attName);
1134 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1135 if (!withText && !hasRange)
1139 displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
1140 String desc = fa.getDescription(featureType, attName);
1141 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1143 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1145 tooltips.add(desc == null ? "" : desc);
1148 JComboBox<String> attCombo = JvSwingUtils
1149 .buildComboWithTooltips(displayAtts, tooltips);
1155 * Populates initial layout of the feature attribute filters panel
1157 private JPanel initialiseFiltersPanel()
1159 filters = new ArrayList<>();
1161 JPanel filtersPanel = new JPanel();
1162 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1163 filtersPanel.setBackground(Color.white);
1164 JvSwingUtils.createTitledBorder(filtersPanel,
1165 MessageManager.getString("label.filters"), true);
1167 JPanel andOrPanel = initialiseAndOrPanel();
1168 filtersPanel.add(andOrPanel);
1171 * panel with filters - populated by refreshFiltersDisplay,
1172 * which also sets the layout manager
1174 chooseFiltersPanel = new JPanel();
1175 chooseFiltersPanel.setBackground(Color.white);
1176 filtersPanel.add(chooseFiltersPanel);
1178 return filtersPanel;
1182 * Lays out the panel with radio buttons to AND or OR filter conditions
1186 private JPanel initialiseAndOrPanel()
1188 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1189 andOrPanel.setBackground(Color.white);
1190 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1191 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1192 ActionListener actionListener = new ActionListener()
1195 public void actionPerformed(ActionEvent e)
1200 andFilters.addActionListener(actionListener);
1201 orFilters.addActionListener(actionListener);
1202 ButtonGroup andOr = new ButtonGroup();
1203 andOr.add(andFilters);
1204 andOr.add(orFilters);
1205 andFilters.setSelected(true);
1207 new JLabel(MessageManager.getString("label.join_conditions")));
1208 andOrPanel.add(andFilters);
1209 andOrPanel.add(orFilters);
1214 * Refreshes the display to show any filters currently configured for the
1215 * selected feature type (editable, with 'remove' option), plus one extra row
1216 * for adding a condition. This should be called after a filter has been
1217 * removed, added or amended.
1219 private void updateFiltersTab()
1222 * clear the panel and list of filter conditions
1224 chooseFiltersPanel.removeAll();
1228 * look up attributes known for feature type
1230 List<String[]> attNames = FeatureAttributes.getInstance()
1231 .getAttributes(featureType);
1234 * if this feature type has filters set, load them first
1236 FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
1237 if (featureFilters != null)
1239 if (!featureFilters.isAnded())
1241 orFilters.setSelected(true);
1243 featureFilters.getMatchers().forEach(matcher -> filters.add(matcher));
1247 * and an empty filter for the user to populate (add)
1249 filters.add(FeatureMatcher.NULL_MATCHER);
1252 * use GridLayout to 'justify' rows to the top of the panel, until
1253 * there are too many to fit in, then fall back on BoxLayout
1255 if (filters.size() <= 5)
1257 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1261 chooseFiltersPanel.setLayout(
1262 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1266 * render the conditions in rows, each in its own JPanel
1268 int filterIndex = 0;
1269 for (FeatureMatcherI filter : filters)
1271 JPanel row = addFilter(filter, attNames, filterIndex);
1272 chooseFiltersPanel.add(row);
1281 * A helper method that constructs a row (panel) with one filter condition:
1283 * <li>a drop-down list of Label, Score and attribute names to choose
1285 * <li>a drop-down list of conditions to choose from</li>
1286 * <li>a text field for input of a match pattern</li>
1287 * <li>optionally, a 'remove' button</li>
1289 * The filter values are set as defaults for the input fields. The 'remove'
1290 * button is added unless the pattern is empty (incomplete filter condition).
1292 * Action handlers on these fields provide for
1294 * <li>validate pattern field - should be numeric if condition is numeric</li>
1295 * <li>save filters and refresh display on any (valid) change</li>
1296 * <li>remove filter and refresh on 'Remove'</li>
1297 * <li>update conditions list on change of Label/Score/Attribute</li>
1298 * <li>refresh value field tooltip with min-max range on change of
1304 * @param filterIndex
1307 protected JPanel addFilter(FeatureMatcherI filter,
1308 List<String[]> attNames, int filterIndex)
1310 String[] attName = filter.getAttribute();
1311 Condition cond = filter.getMatcher().getCondition();
1312 String pattern = filter.getMatcher().getPattern();
1314 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1315 filterRow.setBackground(Color.white);
1318 * drop-down choice of attribute, with description as a tooltip
1319 * if we can obtain it
1321 final JComboBox<String> attCombo = populateAttributesDropdown(attNames,
1323 String filterBy = setSelectedAttribute(attCombo, filter);
1325 JComboBox<Condition> condCombo = new JComboBox<>();
1327 JTextField patternField = new JTextField(8);
1328 patternField.setText(pattern);
1331 * action handlers that validate and (if valid) apply changes
1333 ActionListener actionListener = new ActionListener()
1336 public void actionPerformed(ActionEvent e)
1338 if (validateFilter(patternField, condCombo))
1340 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1347 ItemListener itemListener = new ItemListener()
1350 public void itemStateChanged(ItemEvent e)
1352 actionListener.actionPerformed(null);
1356 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1358 attCombo.setSelectedIndex(0);
1362 attCombo.setSelectedItem(
1363 FeatureMatcher.toAttributeDisplayName(attName));
1365 attCombo.addItemListener(new ItemListener()
1368 public void itemStateChanged(ItemEvent e)
1371 * on change of attribute, refresh the conditions list to
1372 * ensure it is appropriate for the attribute datatype
1374 populateConditions((String) attCombo.getSelectedItem(),
1375 (Condition) condCombo.getSelectedItem(), condCombo,
1377 actionListener.actionPerformed(null);
1381 filterRow.add(attCombo);
1384 * drop-down choice of test condition
1386 populateConditions(filterBy, cond, condCombo, patternField);
1387 condCombo.setPreferredSize(new Dimension(150, 20));
1388 condCombo.addItemListener(itemListener);
1389 filterRow.add(condCombo);
1392 * pattern to match against
1394 patternField.addActionListener(actionListener);
1395 patternField.addFocusListener(new FocusAdapter()
1398 public void focusLost(FocusEvent e)
1400 actionListener.actionPerformed(null);
1403 filterRow.add(patternField);
1406 * disable pattern field for condition 'Present / NotPresent'
1408 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1409 patternField.setEnabled(selectedCondition.needsAPattern());
1412 * if a numeric condition is selected, show the value range
1413 * as a tooltip on the value input field
1415 setNumericHints(filterBy, selectedCondition, patternField);
1418 * add remove button if filter is populated (non-empty pattern)
1420 if (!patternField.isEnabled()
1421 || (pattern != null && pattern.trim().length() > 0))
1423 // todo: gif for button drawing '-' or 'x'
1424 JButton removeCondition = new BasicArrowButton(SwingConstants.WEST);
1426 .setToolTipText(MessageManager.getString("label.delete_row"));
1427 removeCondition.addActionListener(new ActionListener()
1430 public void actionPerformed(ActionEvent e)
1432 filters.remove(filterIndex);
1436 filterRow.add(removeCondition);
1443 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1449 private String setSelectedAttribute(JComboBox<String> attCombo,
1450 FeatureMatcherI filter)
1453 if (filter.isByScore())
1457 else if (filter.isByLabel())
1463 item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
1465 attCombo.setSelectedItem(item);
1470 * If a numeric comparison condition is selected, retrieves the min-max range
1471 * for the value (score or attribute), and sets it as a tooltip on the value
1472 * field. If the field is currently empty, then pre-populates it with
1474 * <li>the minimum value, if condition is > or >=</li>
1475 * <li>the maximum value, if condition is < or <=</li>
1479 * @param selectedCondition
1480 * @param patternField
1482 private void setNumericHints(String attName, Condition selectedCondition,
1483 JTextField patternField)
1485 patternField.setToolTipText("");
1487 if (selectedCondition.isNumeric())
1489 float[] minMax = getMinMax(attName);
1492 String minFormatted = DECFMT_2_2.format(minMax[0]);
1493 String maxFormatted = DECFMT_2_2.format(minMax[1]);
1494 String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
1495 patternField.setToolTipText(tip);
1496 if (patternField.getText().isEmpty())
1498 if (selectedCondition == Condition.GE
1499 || selectedCondition == Condition.GT)
1501 patternField.setText(minFormatted);
1505 if (selectedCondition == Condition.LE
1506 || selectedCondition == Condition.LT)
1508 patternField.setText(maxFormatted);
1517 * Populates the drop-down list of comparison conditions for the given
1518 * attribute name. The conditions added depend on the datatype of the
1519 * attribute values. The supplied condition is set as the selected item in the
1520 * list, provided it is in the list. If the pattern is now invalid
1521 * (non-numeric pattern for a numeric condition), it is cleared.
1526 * @param patternField
1528 private void populateConditions(String attName, Condition cond,
1529 JComboBox<Condition> condCombo, JTextField patternField)
1531 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1532 FeatureMatcher.fromAttributeDisplayName(attName));
1533 if (LABEL_18N.equals(attName))
1535 type = Datatype.Character;
1537 else if (SCORE_18N.equals(attName))
1539 type = Datatype.Number;
1543 * remove itemListener before starting
1545 ItemListener listener = condCombo.getItemListeners()[0];
1546 condCombo.removeItemListener(listener);
1547 boolean condIsValid = false;
1549 condCombo.removeAllItems();
1550 for (Condition c : Condition.values())
1552 if ((c.isNumeric() && type == Datatype.Number)
1553 || (!c.isNumeric() && type != Datatype.Number))
1555 condCombo.addItem(c);
1564 * set the selected condition (does nothing if not in the list)
1568 condCombo.setSelectedItem(cond);
1572 condCombo.setSelectedIndex(0);
1576 * clear pattern if it is now invalid for condition
1578 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1582 String pattern = patternField.getText().trim();
1583 if (pattern.length() > 0)
1585 Float.valueOf(pattern);
1587 } catch (NumberFormatException e)
1589 patternField.setText("");
1594 * restore the listener
1596 condCombo.addItemListener(listener);
1600 * Answers true unless a numeric condition has been selected with a
1601 * non-numeric value. Sets the value field to RED with a tooltip if in error.
1603 * If the pattern is expected but is empty, this method returns false, but
1604 * does not mark the field as invalid. This supports selecting an attribute
1605 * for a new condition before a match pattern has been entered.
1610 protected boolean validateFilter(JTextField value,
1611 JComboBox<Condition> condCombo)
1613 if (value == null || condCombo == null)
1615 return true; // fields not populated
1618 Condition cond = (Condition) condCombo.getSelectedItem();
1619 if (!cond.needsAPattern())
1624 value.setBackground(Color.white);
1625 value.setToolTipText("");
1626 String v1 = value.getText().trim();
1627 if (v1.length() == 0)
1632 if (cond.isNumeric() && v1.length() > 0)
1637 } catch (NumberFormatException e)
1639 value.setBackground(Color.red);
1640 value.setToolTipText(
1641 MessageManager.getString("label.numeric_required"));
1650 * Constructs a filter condition from the given input fields, and replaces the
1651 * condition at filterIndex with the new one. Does nothing if the pattern
1652 * field is blank (unless the match condition is one that doesn't require a
1653 * pattern, e.g. 'Is present'). Answers true if the filter was updated, else
1656 * This method may update the tooltip on the filter value field to show the
1657 * value range, if a numeric condition is selected. This ensures the tooltip
1658 * is updated when a numeric valued attribute is chosen on the last 'add a
1664 * @param filterIndex
1666 protected boolean updateFilter(JComboBox<String> attCombo,
1667 JComboBox<Condition> condCombo, JTextField valueField,
1670 String attName = (String) attCombo.getSelectedItem();
1671 Condition cond = (Condition) condCombo.getSelectedItem();
1672 String pattern = valueField.getText().trim();
1674 setNumericHints(attName, cond, valueField);
1676 if (pattern.length() == 0 && cond.needsAPattern())
1678 valueField.setEnabled(true); // ensure pattern field is enabled!
1683 * Construct a matcher that operates on Label, Score,
1684 * or named attribute
1686 FeatureMatcherI km = null;
1687 if (LABEL_18N.equals(attName))
1689 km = FeatureMatcher.byLabel(cond, pattern);
1691 else if (SCORE_18N.equals(attName))
1693 km = FeatureMatcher.byScore(cond, pattern);
1697 km = FeatureMatcher.byAttribute(cond, pattern,
1698 FeatureMatcher.fromAttributeDisplayName(attName));
1701 filters.set(filterIndex, km);
1707 * Action on any change to feature filtering, namely
1709 * <li>change of selected attribute</li>
1710 * <li>change of selected condition</li>
1711 * <li>change of match pattern</li>
1712 * <li>removal of a condition</li>
1714 * The inputs are parsed into a combined filter and this is set for the
1715 * feature type, and the alignment redrawn.
1717 protected void filtersChanged()
1720 * update the filter conditions for the feature type
1722 boolean anded = andFilters.isSelected();
1723 FeatureMatcherSetI combined = new FeatureMatcherSet();
1725 for (FeatureMatcherI filter : filters)
1727 String pattern = filter.getMatcher().getPattern();
1728 Condition condition = filter.getMatcher().getCondition();
1729 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1733 combined.and(filter);
1737 combined.or(filter);
1743 * save the filter conditions in the FeatureRenderer
1744 * (note this might now be an empty filter with no conditions)
1746 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1747 ap.paintAlignment(true, true);