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.JTabbedPane;
66 import javax.swing.JTextField;
67 import javax.swing.SwingConstants;
68 import javax.swing.border.LineBorder;
69 import javax.swing.event.ChangeEvent;
70 import javax.swing.event.ChangeListener;
71 import javax.swing.plaf.basic.BasicArrowButton;
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 String LABEL_18N = MessageManager
83 .getString("label.label");
85 private final static String SCORE_18N = MessageManager
86 .getString("label.score");
88 private static final int RADIO_WIDTH = 130;
90 private static final String COLON = ":";
92 private static final int MAX_TOOLTIP_LENGTH = 50;
94 private static final int NO_COLOUR_OPTION = 0;
96 private static final int MIN_COLOUR_OPTION = 1;
98 private static final int MAX_COLOUR_OPTION = 2;
100 private static final int ABOVE_THRESHOLD_OPTION = 1;
102 private static final int BELOW_THRESHOLD_OPTION = 2;
104 private static final DecimalFormat DECFMT_2_2 = new DecimalFormat(
108 * FeatureRenderer holds colour scheme and filters for feature types
110 private final FeatureRenderer fr; // todo refactor to allow interface type here
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();
158 private JPanel singleColour = new JPanel();
160 private JPanel minColour = new JPanel();
162 private JPanel maxColour = new JPanel();
164 private JComboBox<String> threshold = new JComboBox<>();
166 private JSlider slider = new JSlider();
168 private JTextField thresholdValue = new JTextField(20);
170 private JCheckBox thresholdIsMin = new JCheckBox();
172 private GraphLine threshline;
174 private ActionListener featureSettings = null;
176 private ActionListener changeColourAction;
179 * choice of option for 'colour for no value'
181 private JComboBox<String> noValueCombo;
184 * choice of what to colour by text (Label or attribute)
186 private JComboBox<String> colourByTextCombo;
189 * choice of what to colour by range (Score or attribute)
191 private JComboBox<String> colourByRangeCombo;
193 private JRadioButton andFilters;
195 private JRadioButton orFilters;
198 * filters for the currently selected feature type
200 private List<FeatureMatcherI> filters;
202 // set white normally, black to debug layout
203 private Color debugBorderColour = Color.white;
205 private JPanel chooseFiltersPanel;
207 private JTabbedPane tabbedPane;
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, 600, 360);
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());
406 tabbedPane = new JTabbedPane();
407 this.add(tabbedPane, BorderLayout.CENTER);
410 * an ActionListener that applies colour changes
412 changeColourAction = new ActionListener()
415 public void actionPerformed(ActionEvent e)
422 * first tab: colour options
424 JPanel coloursPanel = initialiseColoursPanel();
425 tabbedPane.addTab(MessageManager.getString("action.colour"),
429 * second tab: filter options
431 JPanel filtersPanel = initialiseFiltersPanel();
432 tabbedPane.addTab(MessageManager.getString("label.filters"),
435 JPanel okCancelPanel = initialiseOkCancelPanel();
437 this.add(okCancelPanel, BorderLayout.SOUTH);
441 * Updates the min-max range if Colour By selected item is Score, or an
442 * attribute, with a min-max range
444 protected void updateColourMinMax()
446 if (!graduatedColour.isSelected())
451 String colourBy = (String) colourByRangeCombo.getSelectedItem();
452 float[] minMax = getMinMax(colourBy);
462 * Retrieves the min-max range:
464 * <li>of feature score, if colour or filter is by Score</li>
465 * <li>else of the selected attribute</li>
471 private float[] getMinMax(String attName)
473 float[] minMax = null;
474 if (SCORE_18N.equals(attName))
476 minMax = fr.getMinMax().get(featureType)[0];
480 // colour by attribute range
481 minMax = FeatureAttributes.getInstance().getMinMax(featureType,
482 FeatureMatcher.fromAttributeDisplayName(attName));
488 * Lay out fields for graduated colour (by score or attribute value)
492 private JPanel initialiseGraduatedColourPanel()
494 JPanel graduatedColourPanel = new JPanel();
495 graduatedColourPanel.setLayout(
496 new BoxLayout(graduatedColourPanel, BoxLayout.Y_AXIS));
497 JvSwingUtils.createTitledBorder(graduatedColourPanel,
498 MessageManager.getString("label.graduated_colour"), true);
499 graduatedColourPanel.setBackground(Color.white);
502 * first row: graduated colour radio button, score/attribute drop-down
504 JPanel graduatedChoicePanel = new JPanel(
505 new FlowLayout(FlowLayout.LEFT));
506 graduatedChoicePanel.setBackground(Color.white);
507 graduatedColour = new JRadioButton(
508 MessageManager.getString("label.by_range_of") + COLON);
509 graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
510 graduatedColour.addItemListener(new ItemListener()
513 public void itemStateChanged(ItemEvent e)
515 if (graduatedColour.isSelected())
521 graduatedChoicePanel.add(graduatedColour);
523 List<String[]> attNames = FeatureAttributes.getInstance()
524 .getAttributes(featureType);
525 colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
526 colourByRangeCombo.addItemListener(new ItemListener()
529 public void itemStateChanged(ItemEvent e)
536 * disable graduated colour option if no range found
538 graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
540 graduatedChoicePanel.add(colourByRangeCombo);
541 graduatedColourPanel.add(graduatedChoicePanel);
544 * second row - min/max/no colours
546 JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
547 colourRangePanel.setBackground(Color.white);
548 graduatedColourPanel.add(colourRangePanel);
550 minColour.setFont(JvSwingUtils.getLabelFont());
551 minColour.setBorder(BorderFactory.createLineBorder(Color.black));
552 minColour.setPreferredSize(new Dimension(40, 20));
553 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
554 minColour.addMouseListener(new MouseAdapter()
557 public void mousePressed(MouseEvent e)
559 if (minColour.isEnabled())
561 showColourChooser(minColour, "label.select_colour_minimum_value");
566 maxColour.setFont(JvSwingUtils.getLabelFont());
567 maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
568 maxColour.setPreferredSize(new Dimension(40, 20));
569 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
570 maxColour.addMouseListener(new MouseAdapter()
573 public void mousePressed(MouseEvent e)
575 if (maxColour.isEnabled())
577 showColourChooser(maxColour, "label.select_colour_maximum_value");
581 maxColour.setBorder(new LineBorder(Color.black));
584 * default max colour to current colour (if a plain colour),
585 * or to Black if colour by label; make min colour a pale
586 * version of max colour
588 FeatureColourI fc = fr.getFeatureColours().get(featureType);
589 Color bg = fc.isSimpleColour() ? fc.getColour() : Color.BLACK;
590 maxColour.setBackground(bg);
591 minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
593 noValueCombo = new JComboBox<>();
594 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
595 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
596 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
597 noValueCombo.addItemListener(new ItemListener()
600 public void itemStateChanged(ItemEvent e)
606 JLabel minText = new JLabel(
607 MessageManager.getString("label.min_value") + COLON);
608 minText.setFont(JvSwingUtils.getLabelFont());
609 JLabel maxText = new JLabel(
610 MessageManager.getString("label.max_value") + COLON);
611 maxText.setFont(JvSwingUtils.getLabelFont());
612 JLabel noText = new JLabel(
613 MessageManager.getString("label.no_value") + COLON);
614 noText.setFont(JvSwingUtils.getLabelFont());
616 colourRangePanel.add(minText);
617 colourRangePanel.add(minColour);
618 colourRangePanel.add(maxText);
619 colourRangePanel.add(maxColour);
620 colourRangePanel.add(noText);
621 colourRangePanel.add(noValueCombo);
624 * third row - threshold options and value
626 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
627 thresholdPanel.setBackground(Color.white);
628 graduatedColourPanel.add(thresholdPanel);
630 threshold.addActionListener(changeColourAction);
631 threshold.setToolTipText(MessageManager
632 .getString("label.threshold_feature_display_by_score"));
633 threshold.addItem(MessageManager
634 .getString("label.threshold_feature_no_threshold")); // index 0
635 threshold.addItem(MessageManager
636 .getString("label.threshold_feature_above_threshold")); // index 1
637 threshold.addItem(MessageManager
638 .getString("label.threshold_feature_below_threshold")); // index 2
640 thresholdValue.addActionListener(new ActionListener()
643 public void actionPerformed(ActionEvent e)
645 thresholdValue_actionPerformed();
648 thresholdValue.addFocusListener(new FocusAdapter()
651 public void focusLost(FocusEvent e)
653 thresholdValue_actionPerformed();
656 slider.setPaintLabels(false);
657 slider.setPaintTicks(true);
658 slider.setBackground(Color.white);
659 slider.setEnabled(false);
660 slider.setOpaque(false);
661 slider.setPreferredSize(new Dimension(100, 32));
662 slider.setToolTipText(
663 MessageManager.getString("label.adjust_threshold"));
665 slider.addChangeListener(new ChangeListener()
668 public void stateChanged(ChangeEvent evt)
673 .setText(String.valueOf(slider.getValue() / scaleFactor));
674 sliderValueChanged();
678 slider.addMouseListener(new MouseAdapter()
681 public void mouseReleased(MouseEvent evt)
684 * only update Overview and/or structure colouring
685 * when threshold slider drag ends (mouse up)
689 ap.paintAlignment(true, true);
694 thresholdValue.setEnabled(false);
695 thresholdValue.setColumns(7);
697 thresholdPanel.add(threshold);
698 thresholdPanel.add(slider);
699 thresholdPanel.add(thresholdValue);
701 thresholdIsMin.setBackground(Color.white);
703 .setText(MessageManager.getString("label.threshold_minmax"));
704 thresholdIsMin.setToolTipText(MessageManager
705 .getString("label.toggle_absolute_relative_display_threshold"));
706 thresholdIsMin.addActionListener(changeColourAction);
707 thresholdPanel.add(thresholdIsMin);
709 return graduatedColourPanel;
713 * Lay out OK and Cancel buttons
717 private JPanel initialiseOkCancelPanel()
719 JPanel okCancelPanel = new JPanel();
720 // okCancelPanel.setBackground(Color.white);
721 okCancelPanel.add(ok);
722 okCancelPanel.add(cancel);
723 return okCancelPanel;
727 * Lay out Colour options panel, containing
729 * <li>plain colour, with colour picker</li>
730 * <li>colour by text, with choice of Label or other attribute</li>
731 * <li>colour by range, of score or other attribute, when available</li>
736 private JPanel initialiseColoursPanel()
738 JPanel colourByPanel = new JPanel();
739 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
742 * simple colour radio button and colour picker
744 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
745 simpleColourPanel.setBackground(Color.white);
746 JvSwingUtils.createTitledBorder(simpleColourPanel,
747 MessageManager.getString("label.simple"), true);
748 colourByPanel.add(simpleColourPanel);
750 simpleColour = new JRadioButton(
751 MessageManager.getString("label.simple_colour"));
752 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
753 simpleColour.addItemListener(new ItemListener()
756 public void itemStateChanged(ItemEvent e)
758 if (simpleColour.isSelected() && !adjusting)
760 showColourChooser(singleColour, "label.select_colour");
766 singleColour.setFont(JvSwingUtils.getLabelFont());
767 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
768 singleColour.setPreferredSize(new Dimension(40, 20));
769 singleColour.addMouseListener(new MouseAdapter()
772 public void mousePressed(MouseEvent e)
774 if (simpleColour.isSelected())
776 showColourChooser(singleColour, "label.select_colour");
780 simpleColourPanel.add(simpleColour); // radio button
781 simpleColourPanel.add(singleColour); // colour picker button
784 * colour by text (category) radio button and drop-down choice list
786 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
787 byTextPanel.setBackground(Color.white);
788 JvSwingUtils.createTitledBorder(byTextPanel,
789 MessageManager.getString("label.colour_by_text"), true);
790 colourByPanel.add(byTextPanel);
791 byCategory = new JRadioButton(
792 MessageManager.getString("label.by_text_of") + COLON);
793 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
794 byCategory.addItemListener(new ItemListener()
797 public void itemStateChanged(ItemEvent e)
799 if (byCategory.isSelected())
805 byTextPanel.add(byCategory);
807 List<String[]> attNames = FeatureAttributes.getInstance()
808 .getAttributes(featureType);
809 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
810 colourByTextCombo.addItemListener(new ItemListener()
813 public void itemStateChanged(ItemEvent e)
818 byTextPanel.add(colourByTextCombo);
821 * graduated colour panel
823 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
824 colourByPanel.add(graduatedColourPanel);
827 * 3 radio buttons select between simple colour,
828 * by category (text), or graduated
830 ButtonGroup bg = new ButtonGroup();
831 bg.add(simpleColour);
833 bg.add(graduatedColour);
835 return colourByPanel;
838 private void showColourChooser(JPanel colourPanel, String key)
840 Color col = JColorChooser.showDialog(this,
841 MessageManager.getString(key), colourPanel.getBackground());
844 colourPanel.setBackground(col);
845 colourPanel.setForeground(col);
847 colourPanel.repaint();
852 * Constructs and sets the selected colour options as the colour for the feature
853 * type, and repaints the alignment, and optionally the Overview and/or
854 * structure viewer if open
856 * @param updateStructsAndOverview
858 void colourChanged(boolean updateStructsAndOverview)
863 * ignore action handlers while setting values programmatically
869 * ensure min-max range is for the latest choice of
870 * 'graduated colour by'
872 updateColourMinMax();
874 FeatureColourI acg = makeColourFromInputs();
877 * save the colour, and repaint stuff
879 fr.setColour(featureType, acg);
880 ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
886 * Converts the input values into an instance of FeatureColour
890 private FeatureColourI makeColourFromInputs()
893 * easiest case - a single colour
895 if (simpleColour.isSelected())
897 return new FeatureColour(singleColour.getBackground());
901 * next easiest case - colour by Label, or attribute text
903 if (byCategory.isSelected())
905 Color c = this.getBackground();
906 FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f);
907 fc.setColourByLabel(true);
908 String byWhat = (String) colourByTextCombo.getSelectedItem();
909 if (!LABEL_18N.equals(byWhat))
912 FeatureMatcher.fromAttributeDisplayName(byWhat));
918 * remaining case - graduated colour by score, or attribute value
920 Color noColour = null;
921 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
923 noColour = minColour.getBackground();
925 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
927 noColour = maxColour.getBackground();
933 thresh = Float.valueOf(thresholdValue.getText());
934 } catch (NumberFormatException e)
936 // invalid inputs are already handled on entry
940 * min-max range is to (or from) threshold value if
941 * 'threshold is min/max' is selected
943 float minValue = min;
944 float maxValue = max;
945 final int thresholdOption = threshold.getSelectedIndex();
946 if (thresholdIsMin.isSelected()
947 && thresholdOption == ABOVE_THRESHOLD_OPTION)
951 if (thresholdIsMin.isSelected()
952 && thresholdOption == BELOW_THRESHOLD_OPTION)
958 * make the graduated colour
960 FeatureColourI fc = new FeatureColour(minColour.getBackground(),
961 maxColour.getBackground(), noColour, minValue, maxValue);
964 * set attribute to colour by if selected
966 String byWhat = (String) colourByRangeCombo.getSelectedItem();
967 if (!SCORE_18N.equals(byWhat))
969 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
973 * set threshold options and 'autoscaled' which is
974 * false if 'threshold is min/max' is selected
975 * else true (colour range is on actual range of values)
977 fc.setThreshold(thresh);
978 fc.setAutoScaled(!thresholdIsMin.isSelected());
979 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
980 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
982 if (threshline == null)
985 * todo not yet implemented: visual indication of feature threshold
987 threshline = new GraphLine((max - min) / 2f, "Threshold",
995 protected void raiseClosed()
997 if (this.featureSettings != null)
999 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
1004 * Action on OK is just to dismiss the dialog - any changes have already been
1008 public void okPressed()
1013 * Action on Cancel is to restore colour scheme and filters as they were when
1014 * the dialog was opened
1017 public void cancelPressed()
1019 fr.setColour(featureType, originalColour);
1020 fr.setFeatureFilter(featureType, originalFilter);
1021 ap.paintAlignment(true, true);
1025 * Action on text entry of a threshold value
1027 protected void thresholdValue_actionPerformed()
1032 float f = Float.parseFloat(thresholdValue.getText());
1033 slider.setValue((int) (f * scaleFactor));
1034 threshline.value = f;
1035 thresholdValue.setBackground(Color.white); // ok
1038 * force repaint of any Overview window or structure
1040 ap.paintAlignment(true, true);
1041 } catch (NumberFormatException ex)
1043 thresholdValue.setBackground(Color.red); // not ok
1051 * Action on change of threshold slider value. This may be done interactively
1052 * (by moving the slider), or programmatically (to update the slider after
1053 * manual input of a threshold value).
1055 protected void sliderValueChanged()
1057 threshline.value = getRoundedSliderValue();
1060 * repaint alignment, but not Overview or structure,
1061 * to avoid overload while dragging the slider
1063 colourChanged(false);
1067 * Converts the slider value to its absolute value by dividing by the
1068 * scaleFactor. Rounding errors are squashed by forcing min/max of slider range
1069 * to the actual min/max of feature score range
1073 private float getRoundedSliderValue()
1075 int value = slider.getValue();
1076 float f = value == slider.getMaximum() ? max
1077 : (value == slider.getMinimum() ? min : value / scaleFactor);
1081 void addActionListener(ActionListener listener)
1083 if (featureSettings != null)
1086 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1088 featureSettings = listener;
1092 * A helper method to build the drop-down choice of attributes for a feature. If
1093 * 'withRange' is true, then Score, and any attributes with a min-max range, are
1094 * added. If 'withText' is true, Label and any known attributes are added. This
1095 * allows 'categorical numerical' attributes e.g. codon position to be coloured
1098 * Where metadata is available with a description for an attribute, that is
1099 * added as a tooltip.
1101 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1102 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1104 * This method does not add any ActionListener to the JComboBox.
1110 protected JComboBox<String> populateAttributesDropdown(
1111 List<String[]> attNames, boolean withRange, boolean withText)
1113 List<String> displayAtts = new ArrayList<>();
1114 List<String> tooltips = new ArrayList<>();
1118 displayAtts.add(LABEL_18N);
1119 tooltips.add(MessageManager.getString("label.description"));
1123 float[][] minMax = fr.getMinMax().get(featureType);
1124 if (minMax != null && minMax[0][0] != minMax[0][1])
1126 displayAtts.add(SCORE_18N);
1127 tooltips.add(SCORE_18N);
1131 FeatureAttributes fa = FeatureAttributes.getInstance();
1132 for (String[] attName : attNames)
1134 float[] minMax = fa.getMinMax(featureType, attName);
1135 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1136 if (!withText && !hasRange)
1140 displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
1141 String desc = fa.getDescription(featureType, attName);
1142 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1144 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1146 tooltips.add(desc == null ? "" : desc);
1149 JComboBox<String> attCombo = JvSwingUtils
1150 .buildComboWithTooltips(displayAtts, tooltips);
1156 * Populates initial layout of the feature attribute filters panel
1158 private JPanel initialiseFiltersPanel()
1160 filters = new ArrayList<>();
1162 JPanel filtersPanel = new JPanel();
1163 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1164 filtersPanel.setBackground(Color.white);
1165 JvSwingUtils.createTitledBorder(filtersPanel,
1166 MessageManager.getString("label.filters"), true);
1168 JPanel andOrPanel = initialiseAndOrPanel();
1169 filtersPanel.add(andOrPanel);
1172 * panel with filters - populated by refreshFiltersDisplay,
1173 * which also sets the layout manager
1175 chooseFiltersPanel = new JPanel();
1176 chooseFiltersPanel.setBackground(Color.white);
1177 filtersPanel.add(chooseFiltersPanel);
1179 return filtersPanel;
1183 * Lays out the panel with radio buttons to AND or OR filter conditions
1187 private JPanel initialiseAndOrPanel()
1189 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1190 andOrPanel.setBackground(Color.white);
1191 andOrPanel.setBorder(BorderFactory.createLineBorder(debugBorderColour));
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 updateFiltersTab()
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 featureFilters.getMatchers().forEach(matcher -> filters.add(matcher));
1249 * and an empty filter for the user to populate (add)
1251 filters.add(FeatureMatcher.NULL_MATCHER);
1254 * use GridLayout to 'justify' rows to the top of the panel, until
1255 * there are too many to fit in, then fall back on BoxLayout
1257 if (filters.size() <= 5)
1259 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1263 chooseFiltersPanel.setLayout(
1264 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1268 * render the conditions in rows, each in its own JPanel
1270 int filterIndex = 0;
1271 for (FeatureMatcherI filter : filters)
1273 JPanel row = addFilter(filter, attNames, filterIndex);
1274 row.setBorder(BorderFactory.createLineBorder(debugBorderColour));
1275 chooseFiltersPanel.add(row);
1284 * A helper method that constructs a row (panel) with one filter condition:
1286 * <li>a drop-down list of Label, Score and attribute names to choose from</li>
1287 * <li>a drop-down list of conditions to choose from</li>
1288 * <li>a text field for input of a match pattern</li>
1289 * <li>optionally, a 'remove' button</li>
1291 * The filter values are set as defaults for the input fields. The 'remove'
1292 * button is added unless the pattern is empty (incomplete filter condition).
1294 * Action handlers on these fields provide for
1296 * <li>validate pattern field - should be numeric if condition is numeric</li>
1297 * <li>save filters and refresh display on any (valid) change</li>
1298 * <li>remove filter and refresh on 'Remove'</li>
1299 * <li>update conditions list on change of Label/Score/Attribute</li>
1300 * <li>refresh value field tooltip with min-max range on change of
1306 * @param filterIndex
1309 protected JPanel addFilter(FeatureMatcherI filter,
1310 List<String[]> attNames, int filterIndex)
1312 String[] attName = filter.getAttribute();
1313 Condition cond = filter.getMatcher().getCondition();
1314 String pattern = filter.getMatcher().getPattern();
1316 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1317 filterRow.setBackground(Color.white);
1320 * drop-down choice of attribute, with description as a tooltip
1321 * if we can obtain it
1323 final JComboBox<String> attCombo = populateAttributesDropdown(attNames,
1325 String filterBy = setSelectedAttribute(attCombo, filter);
1327 JComboBox<Condition> condCombo = new JComboBox<>();
1329 JTextField patternField = new JTextField(8);
1330 patternField.setText(pattern);
1333 * action handlers that validate and (if valid) apply changes
1335 ActionListener actionListener = new ActionListener()
1338 public void actionPerformed(ActionEvent e)
1340 if (validateFilter(patternField, condCombo))
1342 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1349 ItemListener itemListener = new ItemListener()
1352 public void itemStateChanged(ItemEvent e)
1354 actionListener.actionPerformed(null);
1358 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1360 attCombo.setSelectedIndex(0);
1364 attCombo.setSelectedItem(
1365 FeatureMatcher.toAttributeDisplayName(attName));
1367 attCombo.addItemListener(new ItemListener()
1370 public void itemStateChanged(ItemEvent e)
1373 * on change of attribute, refresh the conditions list to
1374 * ensure it is appropriate for the attribute datatype
1376 populateConditions((String) attCombo.getSelectedItem(),
1377 (Condition) condCombo.getSelectedItem(), condCombo,
1379 actionListener.actionPerformed(null);
1383 filterRow.add(attCombo);
1386 * drop-down choice of test condition
1388 populateConditions(filterBy, cond, condCombo, patternField);
1389 condCombo.setPreferredSize(new Dimension(150, 20));
1390 condCombo.addItemListener(itemListener);
1391 filterRow.add(condCombo);
1394 * pattern to match against
1396 patternField.addActionListener(actionListener);
1397 patternField.addFocusListener(new FocusAdapter()
1400 public void focusLost(FocusEvent e)
1402 actionListener.actionPerformed(null);
1405 filterRow.add(patternField);
1408 * disable pattern field for condition 'Present / NotPresent'
1410 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1411 patternField.setEnabled(selectedCondition.needsAPattern());
1414 * if a numeric condition is selected, show the value range
1415 * as a tooltip on the value input field
1417 setNumericHints(filterBy, selectedCondition, patternField);
1420 * add remove button if filter is populated (non-empty pattern)
1422 if (!patternField.isEnabled()
1423 || (pattern != null && pattern.trim().length() > 0))
1425 // todo: gif for button drawing '-' or 'x'
1426 JButton removeCondition = new BasicArrowButton(SwingConstants.WEST);
1428 .setToolTipText(MessageManager.getString("label.delete_row"));
1429 removeCondition.addActionListener(new ActionListener()
1432 public void actionPerformed(ActionEvent e)
1434 filters.remove(filterIndex);
1438 filterRow.add(removeCondition);
1445 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1451 private String setSelectedAttribute(JComboBox<String> attCombo,
1452 FeatureMatcherI filter)
1455 if (filter.isByScore())
1459 else if (filter.isByLabel())
1465 item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
1467 attCombo.setSelectedItem(item);
1472 * If a numeric comparison condition is selected, retrieves the min-max range
1473 * for the value (score or attribute), and sets it as a tooltip on the value
1474 * field. If the field is currently empty, then pre-populates it with
1476 * <li>the minimum value, if condition is > or >=</li>
1477 * <li>the maximum value, if condition is < or <=</li>
1481 * @param selectedCondition
1482 * @param patternField
1484 private void setNumericHints(String attName,
1485 Condition selectedCondition, JTextField patternField)
1487 patternField.setToolTipText("");
1489 if (selectedCondition.isNumeric())
1491 float[] minMax = getMinMax(attName);
1494 String minFormatted = DECFMT_2_2.format(minMax[0]);
1495 String maxFormatted = DECFMT_2_2.format(minMax[1]);
1496 String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
1497 patternField.setToolTipText(tip);
1498 if (patternField.getText().isEmpty())
1500 if (selectedCondition == Condition.GE
1501 || selectedCondition == Condition.GT)
1503 patternField.setText(minFormatted);
1507 if (selectedCondition == Condition.LE
1508 || selectedCondition == Condition.LT)
1510 patternField.setText(maxFormatted);
1519 * Populates the drop-down list of comparison conditions for the given attribute
1520 * name. The conditions added depend on the datatype of the attribute values.
1521 * The supplied condition is set as the selected item in the list, provided it
1522 * is in the list. If the pattern is now invalid (non-numeric pattern for a
1523 * numeric condition), it is cleared.
1528 * @param patternField
1530 private void populateConditions(String attName, Condition cond,
1531 JComboBox<Condition> condCombo, JTextField patternField)
1533 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1534 FeatureMatcher.fromAttributeDisplayName(attName));
1535 if (LABEL_18N.equals(attName))
1537 type = Datatype.Character;
1539 else if (SCORE_18N.equals(attName))
1541 type = Datatype.Number;
1545 * remove itemListener before starting
1547 ItemListener listener = condCombo.getItemListeners()[0];
1548 condCombo.removeItemListener(listener);
1549 boolean condIsValid = false;
1551 condCombo.removeAllItems();
1552 for (Condition c : Condition.values())
1554 if ((c.isNumeric() && type == Datatype.Number)
1555 || (!c.isNumeric() && type != Datatype.Number))
1557 condCombo.addItem(c);
1566 * set the selected condition (does nothing if not in the list)
1570 condCombo.setSelectedItem(cond);
1574 condCombo.setSelectedIndex(0);
1578 * clear pattern if it is now invalid for condition
1580 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1584 String pattern = patternField.getText().trim();
1585 if (pattern.length() > 0)
1587 Float.valueOf(pattern);
1589 } catch (NumberFormatException e)
1591 patternField.setText("");
1596 * restore the listener
1598 condCombo.addItemListener(listener);
1602 * Answers true unless a numeric condition has been selected with a non-numeric
1603 * value. Sets the value field to RED with a tooltip if in error.
1605 * If the pattern is expected but is empty, this method returns false, but does
1606 * not mark the field as invalid. This supports selecting an attribute for a new
1607 * condition before a match pattern has been entered.
1612 protected boolean validateFilter(JTextField value,
1613 JComboBox<Condition> condCombo)
1615 if (value == null || condCombo == null)
1617 return true; // fields not populated
1620 Condition cond = (Condition) condCombo.getSelectedItem();
1621 if (!cond.needsAPattern())
1626 value.setBackground(Color.white);
1627 value.setToolTipText("");
1628 String v1 = value.getText().trim();
1629 if (v1.length() == 0)
1634 if (cond.isNumeric() && v1.length() > 0)
1639 } catch (NumberFormatException e)
1641 value.setBackground(Color.red);
1642 value.setToolTipText(
1643 MessageManager.getString("label.numeric_required"));
1652 * Constructs a filter condition from the given input fields, and replaces the
1653 * condition at filterIndex with the new one. Does nothing if the pattern field
1654 * is blank (unless the match condition is one that doesn't require a pattern,
1655 * e.g. 'Is present'). Answers true if the filter was updated, else false.
1657 * This method may update the tooltip on the filter value field to show the
1658 * value range, if a numeric condition is selected. This ensures the tooltip is
1659 * updated when a numeric valued attribute is chosen on the last 'add a filter'
1665 * @param filterIndex
1667 protected boolean updateFilter(JComboBox<String> attCombo,
1668 JComboBox<Condition> condCombo, JTextField valueField,
1671 String attName = (String) attCombo.getSelectedItem();
1672 Condition cond = (Condition) condCombo.getSelectedItem();
1673 String pattern = valueField.getText().trim();
1675 setNumericHints(attName, cond, valueField);
1677 if (pattern.length() == 0 && cond.needsAPattern())
1679 valueField.setEnabled(true); // ensure pattern field is enabled!
1684 * Construct a matcher that operates on Label, Score,
1685 * or named attribute
1687 FeatureMatcherI km = null;
1688 if (LABEL_18N.equals(attName))
1690 km = FeatureMatcher.byLabel(cond, pattern);
1692 else if (SCORE_18N.equals(attName))
1694 km = FeatureMatcher.byScore(cond, pattern);
1698 km = FeatureMatcher.byAttribute(cond, pattern,
1699 FeatureMatcher.fromAttributeDisplayName(attName));
1702 filters.set(filterIndex, km);
1708 * Makes the dialog visible, at the Feature Colour tab or at the Filters tab
1712 public void showTab(boolean coloursTab)
1715 tabbedPane.setSelectedIndex(coloursTab ? 0 : 1);
1719 * Action on any change to feature filtering, namely
1721 * <li>change of selected attribute</li>
1722 * <li>change of selected condition</li>
1723 * <li>change of match pattern</li>
1724 * <li>removal of a condition</li>
1726 * The inputs are parsed into a combined filter and this is set for the feature
1727 * type, and the alignment redrawn.
1729 protected void filtersChanged()
1732 * update the filter conditions for the feature type
1734 boolean anded = andFilters.isSelected();
1735 FeatureMatcherSetI combined = new FeatureMatcherSet();
1737 for (FeatureMatcherI filter : filters)
1739 String pattern = filter.getMatcher().getPattern();
1740 Condition condition = filter.getMatcher().getCondition();
1741 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1745 combined.and(filter);
1749 combined.or(filter);
1755 * save the filter conditions in the FeatureRenderer
1756 * (note this might now be an empty filter with no conditions)
1758 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1759 ap.paintAlignment(true, true);