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.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.api.FeatureColourI;
26 import jalview.bin.Cache;
27 import jalview.datamodel.GraphLine;
28 import jalview.datamodel.features.FeatureAttributes;
29 import jalview.datamodel.features.FeatureAttributes.Datatype;
30 import jalview.datamodel.features.FeatureMatcher;
31 import jalview.datamodel.features.FeatureMatcherI;
32 import jalview.datamodel.features.FeatureMatcherSet;
33 import jalview.datamodel.features.FeatureMatcherSetI;
34 import jalview.schemes.FeatureColour;
35 import jalview.util.ColorUtils;
36 import jalview.util.MessageManager;
37 import jalview.util.matcher.Condition;
39 import java.awt.BorderLayout;
40 import java.awt.Color;
41 import java.awt.Dimension;
42 import java.awt.FlowLayout;
43 import java.awt.GridLayout;
44 import java.awt.event.ActionEvent;
45 import java.awt.event.ActionListener;
46 import java.awt.event.FocusAdapter;
47 import java.awt.event.FocusEvent;
48 import java.awt.event.ItemEvent;
49 import java.awt.event.ItemListener;
50 import java.awt.event.MouseAdapter;
51 import java.awt.event.MouseEvent;
52 import java.text.DecimalFormat;
53 import java.util.ArrayList;
54 import java.util.List;
56 import javax.swing.BorderFactory;
57 import javax.swing.BoxLayout;
58 import javax.swing.ButtonGroup;
59 import javax.swing.JButton;
60 import javax.swing.JCheckBox;
61 import javax.swing.JColorChooser;
62 import javax.swing.JComboBox;
63 import javax.swing.JLabel;
64 import javax.swing.JPanel;
65 import javax.swing.JRadioButton;
66 import javax.swing.JSlider;
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 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
114 * the view panel to update when settings change
116 private final AlignmentViewPanel ap;
118 private final String featureType;
121 * the colour and filters to reset to on Cancel
123 private final FeatureColourI originalColour;
125 private final FeatureMatcherSetI originalFilter;
128 * set flag to true when setting values programmatically,
129 * to avoid invocation of action handlers
131 private boolean adjusting = false;
134 * minimum of the value range for graduated colour
135 * (may be for feature score or for a numeric attribute)
140 * maximum of the value range for graduated colour
145 * scale factor for conversion between absolute min-max and slider
147 private float scaleFactor;
150 * radio button group, to select what to colour by:
151 * simple colour, by category (text), or graduated
153 private JRadioButton simpleColour = new JRadioButton();
155 private JRadioButton byCategory = new JRadioButton();
157 private JRadioButton graduatedColour = new JRadioButton();
160 * colours and filters are shown in tabbed view or single content pane
162 JPanel coloursPanel, filtersPanel;
164 JPanel singleColour = new JPanel();
166 private JPanel minColour = new JPanel();
168 private JPanel maxColour = new JPanel();
170 private JComboBox<Object> threshold = new JComboBox<>();
172 private JSlider slider = new JSlider();
174 private JTextField thresholdValue = new JTextField(20);
176 private JCheckBox thresholdIsMin = new JCheckBox();
178 private GraphLine threshline;
180 private ActionListener featureSettings = null;
182 private ActionListener changeColourAction;
185 * choice of option for 'colour for no value'
187 private JComboBox<Object> noValueCombo;
190 * choice of what to colour by text (Label or attribute)
192 private JComboBox<Object> colourByTextCombo;
195 * choice of what to colour by range (Score or attribute)
197 private JComboBox<Object> colourByRangeCombo;
199 private JRadioButton andFilters;
201 private JRadioButton orFilters;
204 * filters for the currently selected feature type
206 private List<FeatureMatcherI> filters;
208 private JPanel chooseFiltersPanel;
216 public FeatureTypeSettings(FeatureRenderer frender, String theType)
219 this.featureType = theType;
221 originalFilter = fr.getFeatureFilter(theType);
222 originalColour = fr.getFeatureColours().get(theType);
229 } catch (Exception ex)
231 ex.printStackTrace();
241 colourChanged(false);
243 String title = MessageManager
244 .formatMessage("label.display_settings_for", new String[]
246 initDialogFrame(this, true, false, title, 580, 500);
251 * Configures the widgets on the Colours tab according to the current feature
254 private void updateColoursTab()
256 FeatureColourI fc = fr.getFeatureColours().get(featureType);
259 * suppress action handling while updating values programmatically
267 if (fc.isSimpleColour())
269 singleColour.setBackground(fc.getColour());
270 singleColour.setForeground(fc.getColour());
271 simpleColour.setSelected(true);
275 * colour by text (Label or attribute text)
277 if (fc.isColourByLabel())
279 byCategory.setSelected(true);
280 colourByTextCombo.setEnabled(colourByTextCombo.getItemCount() > 1);
281 if (fc.isColourByAttribute())
283 String[] attributeName = fc.getAttributeName();
284 colourByTextCombo.setSelectedItem(
285 FeatureMatcher.toAttributeDisplayName(attributeName));
289 colourByTextCombo.setSelectedItem(LABEL_18N);
294 colourByTextCombo.setEnabled(false);
297 if (!fc.isGraduatedColour())
299 colourByRangeCombo.setEnabled(false);
300 minColour.setEnabled(false);
301 maxColour.setEnabled(false);
302 noValueCombo.setEnabled(false);
303 threshold.setEnabled(false);
304 slider.setEnabled(false);
305 thresholdValue.setEnabled(false);
306 thresholdIsMin.setEnabled(false);
311 * Graduated colour, by score or attribute value range
313 graduatedColour.setSelected(true);
314 updateColourMinMax(); // ensure min, max are set
315 colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
316 minColour.setEnabled(true);
317 maxColour.setEnabled(true);
318 noValueCombo.setEnabled(true);
319 threshold.setEnabled(true);
320 minColour.setBackground(fc.getMinColour());
321 maxColour.setBackground(fc.getMaxColour());
323 if (fc.isColourByAttribute())
325 String[] attributeName = fc.getAttributeName();
326 colourByRangeCombo.setSelectedItem(
327 FeatureMatcher.toAttributeDisplayName(attributeName));
331 colourByRangeCombo.setSelectedItem(SCORE_18N);
333 Color noColour = fc.getNoColour();
334 if (noColour == null)
336 noValueCombo.setSelectedIndex(NO_COLOUR_OPTION);
338 else if (noColour.equals(fc.getMinColour()))
340 noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION);
342 else if (noColour.equals(fc.getMaxColour()))
344 noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION);
348 * update min-max scaling if there is a range to work with,
349 * else disable the widgets (this shouldn't happen if only
350 * valid options are offered in the combo box)
352 scaleFactor = (max == min) ? 1f : 100f / (max - min);
353 float range = (max - min) * scaleFactor;
354 slider.setMinimum((int) (min * scaleFactor));
355 slider.setMaximum((int) (max * scaleFactor));
356 slider.setMajorTickSpacing((int) (range / 10f));
358 threshline = new GraphLine((max - min) / 2f, "Threshold",
360 threshline.value = fc.getThreshold();
362 if (fc.hasThreshold())
364 threshold.setSelectedIndex(
365 fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
366 : BELOW_THRESHOLD_OPTION);
367 slider.setEnabled(true);
368 slider.setValue((int) (fc.getThreshold() * scaleFactor));
369 thresholdValue.setText(String.valueOf(fc.getThreshold()));
370 thresholdValue.setEnabled(true);
371 thresholdIsMin.setEnabled(true);
375 slider.setEnabled(false);
376 thresholdValue.setEnabled(false);
377 thresholdIsMin.setEnabled(false);
379 thresholdIsMin.setSelected(!fc.isAutoScaled());
387 * Configures the initial layout
389 private void initialise()
391 this.setLayout(new BorderLayout());
394 * an ActionListener that applies colour changes
396 changeColourAction = new ActionListener()
399 public void actionPerformed(ActionEvent e)
406 * first panel/tab: colour options
408 JPanel coloursPanel = initialiseColoursPanel();
409 this.add(coloursPanel, BorderLayout.NORTH);
412 * second panel/tab: filter options
414 JPanel filtersPanel = initialiseFiltersPanel();
415 this.add(filtersPanel, BorderLayout.CENTER);
417 JPanel okCancelPanel = initialiseOkCancelPanel();
419 this.add(okCancelPanel, BorderLayout.SOUTH);
423 * Updates the min-max range if Colour By selected item is Score, or an
424 * attribute, with a min-max range
426 protected void updateColourMinMax()
428 if (!graduatedColour.isSelected())
433 String colourBy = (String) colourByRangeCombo.getSelectedItem();
434 float[] minMax = getMinMax(colourBy);
444 * Retrieves the min-max range:
446 * <li>of feature score, if colour or filter is by Score</li>
447 * <li>else of the selected attribute</li>
453 private float[] getMinMax(String attName)
455 float[] minMax = null;
456 if (SCORE_18N.equals(attName))
458 minMax = fr.getMinMax().get(featureType)[0];
462 // colour by attribute range
463 minMax = FeatureAttributes.getInstance().getMinMax(featureType,
464 FeatureMatcher.fromAttributeDisplayName(attName));
470 * Lay out fields for graduated colour (by score or attribute value)
474 private JPanel initialiseGraduatedColourPanel()
476 JPanel graduatedColourPanel = new JPanel();
477 graduatedColourPanel.setLayout(
478 new BoxLayout(graduatedColourPanel, BoxLayout.Y_AXIS));
479 JvSwingUtils.createTitledBorder(graduatedColourPanel,
480 MessageManager.getString("label.graduated_colour"), true);
481 graduatedColourPanel.setBackground(Color.white);
484 * first row: graduated colour radio button, score/attribute drop-down
486 JPanel graduatedChoicePanel = new JPanel(
487 new FlowLayout(FlowLayout.LEFT));
488 graduatedChoicePanel.setBackground(Color.white);
489 graduatedColour = new JRadioButton(
490 MessageManager.getString("label.by_range_of") + COLON);
491 graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
492 graduatedColour.addItemListener(new ItemListener()
495 public void itemStateChanged(ItemEvent e)
497 if (graduatedColour.isSelected())
503 graduatedChoicePanel.add(graduatedColour);
505 List<String[]> attNames = FeatureAttributes.getInstance()
506 .getAttributes(featureType);
507 colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
508 colourByRangeCombo.addItemListener(new ItemListener()
511 public void itemStateChanged(ItemEvent e)
518 * disable graduated colour option if no range found
520 graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
522 graduatedChoicePanel.add(colourByRangeCombo);
523 graduatedColourPanel.add(graduatedChoicePanel);
526 * second row - min/max/no colours
528 JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
529 colourRangePanel.setBackground(Color.white);
530 graduatedColourPanel.add(colourRangePanel);
532 minColour.setFont(JvSwingUtils.getLabelFont());
533 minColour.setBorder(BorderFactory.createLineBorder(Color.black));
534 minColour.setPreferredSize(new Dimension(40, 20));
535 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
536 minColour.addMouseListener(new MouseAdapter()
539 public void mousePressed(MouseEvent e)
541 if (minColour.isEnabled())
543 showColourChooser(minColour, "label.select_colour_minimum_value");
548 maxColour.setFont(JvSwingUtils.getLabelFont());
549 maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
550 maxColour.setPreferredSize(new Dimension(40, 20));
551 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
552 maxColour.addMouseListener(new MouseAdapter()
555 public void mousePressed(MouseEvent e)
557 if (maxColour.isEnabled())
559 showColourChooser(maxColour, "label.select_colour_maximum_value");
563 maxColour.setBorder(new LineBorder(Color.black));
566 * if not set, default max colour to last plain colour,
567 * and make min colour a pale version of max colour
569 Color max = originalColour.getMaxColour();
572 max = originalColour.getColour();
573 minColour.setBackground(ColorUtils.bleachColour(max, 0.9f));
577 maxColour.setBackground(max);
578 minColour.setBackground(originalColour.getMinColour());
581 noValueCombo = new JComboBox<>();
582 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
583 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
584 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
585 noValueCombo.addItemListener(new ItemListener()
588 public void itemStateChanged(ItemEvent e)
594 JLabel minText = new JLabel(
595 MessageManager.getString("label.min_value") + COLON);
596 minText.setFont(JvSwingUtils.getLabelFont());
597 JLabel maxText = new JLabel(
598 MessageManager.getString("label.max_value") + COLON);
599 maxText.setFont(JvSwingUtils.getLabelFont());
600 JLabel noText = new JLabel(
601 MessageManager.getString("label.no_value") + COLON);
602 noText.setFont(JvSwingUtils.getLabelFont());
604 colourRangePanel.add(minText);
605 colourRangePanel.add(minColour);
606 colourRangePanel.add(maxText);
607 colourRangePanel.add(maxColour);
608 colourRangePanel.add(noText);
609 colourRangePanel.add(noValueCombo);
612 * third row - threshold options and value
614 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
615 thresholdPanel.setBackground(Color.white);
616 graduatedColourPanel.add(thresholdPanel);
618 threshold.addActionListener(changeColourAction);
619 threshold.setToolTipText(MessageManager
620 .getString("label.threshold_feature_display_by_score"));
621 threshold.addItem(MessageManager
622 .getString("label.threshold_feature_no_threshold")); // index 0
623 threshold.addItem(MessageManager
624 .getString("label.threshold_feature_above_threshold")); // index 1
625 threshold.addItem(MessageManager
626 .getString("label.threshold_feature_below_threshold")); // index 2
628 thresholdValue.addActionListener(new ActionListener()
631 public void actionPerformed(ActionEvent e)
633 thresholdValue_actionPerformed();
636 thresholdValue.addFocusListener(new FocusAdapter()
639 public void focusLost(FocusEvent e)
641 thresholdValue_actionPerformed();
644 slider.setPaintLabels(false);
645 slider.setPaintTicks(true);
646 slider.setBackground(Color.white);
647 slider.setEnabled(false);
648 slider.setOpaque(false);
649 slider.setPreferredSize(new Dimension(100, 32));
650 slider.setToolTipText(
651 MessageManager.getString("label.adjust_threshold"));
653 slider.addChangeListener(new ChangeListener()
656 public void stateChanged(ChangeEvent evt)
661 .setText(String.valueOf(slider.getValue() / scaleFactor));
662 thresholdValue.setBackground(Color.white); // to reset red for invalid
663 sliderValueChanged();
667 slider.addMouseListener(new MouseAdapter()
670 public void mouseReleased(MouseEvent evt)
673 * only update Overview and/or structure colouring
674 * when threshold slider drag ends (mouse up)
678 refreshDisplay(true);
683 thresholdValue.setEnabled(false);
684 thresholdValue.setColumns(7);
686 thresholdPanel.add(threshold);
687 thresholdPanel.add(slider);
688 thresholdPanel.add(thresholdValue);
690 thresholdIsMin.setBackground(Color.white);
692 .setText(MessageManager.getString("label.threshold_minmax"));
693 thresholdIsMin.setToolTipText(MessageManager
694 .getString("label.toggle_absolute_relative_display_threshold"));
695 thresholdIsMin.addActionListener(changeColourAction);
696 thresholdPanel.add(thresholdIsMin);
698 return graduatedColourPanel;
702 * Lay out OK and Cancel buttons
706 private JPanel initialiseOkCancelPanel()
708 JPanel okCancelPanel = new JPanel();
709 // okCancelPanel.setBackground(Color.white);
710 okCancelPanel.add(ok);
711 okCancelPanel.add(cancel);
712 return okCancelPanel;
716 * Lay out Colour options panel, containing
718 * <li>plain colour, with colour picker</li>
719 * <li>colour by text, with choice of Label or other attribute</li>
720 * <li>colour by range, of score or other attribute, when available</li>
725 private JPanel initialiseColoursPanel()
727 JPanel colourByPanel = new JPanel();
728 colourByPanel.setBackground(Color.white);
729 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
730 JvSwingUtils.createTitledBorder(colourByPanel,
731 MessageManager.getString("action.colour"), true);
734 * simple colour radio button and colour picker
736 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
737 simpleColourPanel.setBackground(Color.white);
738 colourByPanel.add(simpleColourPanel);
740 simpleColour = new JRadioButton(
741 MessageManager.getString("label.simple_colour"));
742 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
743 simpleColour.addItemListener(new ItemListener()
746 public void itemStateChanged(ItemEvent e)
748 if (simpleColour.isSelected() && !adjusting)
755 singleColour.setFont(JvSwingUtils.getLabelFont());
756 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
757 singleColour.setPreferredSize(new Dimension(40, 20));
758 // if (originalColour.isGraduatedColour())
760 // singleColour.setBackground(originalColour.getMaxColour());
761 // singleColour.setForeground(originalColour.getMaxColour());
765 singleColour.setBackground(originalColour.getColour());
766 singleColour.setForeground(originalColour.getColour());
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 refreshDisplay(updateStructsAndOverview);
885 * Converts the input values into an instance of FeatureColour
889 private FeatureColourI makeColourFromInputs()
892 * min-max range is to (or from) threshold value if
893 * 'threshold is min/max' is selected
899 thresh = Float.valueOf(thresholdValue.getText());
900 } catch (NumberFormatException e)
902 // invalid inputs are already handled on entry
904 float minValue = min;
905 float maxValue = max;
906 final int thresholdOption = threshold.getSelectedIndex();
907 if (thresholdIsMin.isSelected()
908 && thresholdOption == ABOVE_THRESHOLD_OPTION)
912 if (thresholdIsMin.isSelected()
913 && thresholdOption == BELOW_THRESHOLD_OPTION)
917 Color noColour = null;
918 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
920 noColour = minColour.getBackground();
922 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
924 noColour = maxColour.getBackground();
928 * construct a colour that 'remembers' all the options, including
929 * those not currently selected
931 FeatureColourI fc = new FeatureColour(singleColour.getBackground(),
932 minColour.getBackground(), maxColour.getBackground(), noColour,
936 * easiest case - a single colour
938 if (simpleColour.isSelected())
940 ((FeatureColour) fc).setGraduatedColour(false);
945 * next easiest case - colour by Label, or attribute text
947 if (byCategory.isSelected())
949 fc.setColourByLabel(true);
950 String byWhat = (String) colourByTextCombo.getSelectedItem();
951 if (!LABEL_18N.equals(byWhat))
954 FeatureMatcher.fromAttributeDisplayName(byWhat));
960 * remaining case - graduated colour by score, or attribute value;
961 * set attribute to colour by if selected
963 String byWhat = (String) colourByRangeCombo.getSelectedItem();
964 if (!SCORE_18N.equals(byWhat))
966 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
970 * set threshold options and 'autoscaled' which is
971 * false if 'threshold is min/max' is selected
972 * else true (colour range is on actual range of values)
974 fc.setThreshold(thresh);
975 fc.setAutoScaled(!thresholdIsMin.isSelected());
976 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
977 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
979 if (threshline == null)
982 * todo not yet implemented: visual indication of feature threshold
984 threshline = new GraphLine((max - min) / 2f, "Threshold",
992 protected void raiseClosed()
994 if (this.featureSettings != null)
996 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
1001 * Action on OK is just to dismiss the dialog - any changes have already been
1005 public void okPressed()
1010 * Action on Cancel is to restore colour scheme and filters as they were when
1011 * the dialog was opened
1014 public void cancelPressed()
1016 fr.setColour(featureType, originalColour);
1017 fr.setFeatureFilter(featureType, originalFilter);
1018 refreshDisplay(true);
1022 * Action on text entry of a threshold value
1024 protected void thresholdValue_actionPerformed()
1029 * set 'adjusting' flag while moving the slider, so it
1030 * doesn't then in turn change the value (with rounding)
1033 float f = Float.parseFloat(thresholdValue.getText());
1034 f = Float.max(f, this.min);
1035 f = Float.min(f, this.max);
1036 thresholdValue.setText(String.valueOf(f));
1037 slider.setValue((int) (f * scaleFactor));
1038 threshline.value = f;
1039 thresholdValue.setBackground(Color.white); // ok
1041 colourChanged(true);
1042 } catch (NumberFormatException ex)
1044 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<Object> 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 // now convert String List to Object List for buildComboWithTooltips
1149 List<Object> displayAttsObjects = new ArrayList<>(displayAtts);
1150 JComboBox<Object> attCombo = JvSwingUtils
1151 .buildComboWithTooltips(displayAttsObjects, tooltips);
1157 * Populates initial layout of the feature attribute filters panel
1159 private JPanel initialiseFiltersPanel()
1161 filters = new ArrayList<>();
1163 JPanel filtersPanel = new JPanel();
1164 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1165 filtersPanel.setBackground(Color.white);
1166 JvSwingUtils.createTitledBorder(filtersPanel,
1167 MessageManager.getString("label.filters"), true);
1169 JPanel andOrPanel = initialiseAndOrPanel();
1170 filtersPanel.add(andOrPanel);
1173 * panel with filters - populated by refreshFiltersDisplay,
1174 * which also sets the layout manager
1176 chooseFiltersPanel = new JPanel();
1177 chooseFiltersPanel.setBackground(Color.white);
1178 filtersPanel.add(chooseFiltersPanel);
1180 return filtersPanel;
1184 * Lays out the panel with radio buttons to AND or OR filter conditions
1188 private JPanel initialiseAndOrPanel()
1190 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1191 andOrPanel.setBackground(Color.white);
1192 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1193 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1194 ActionListener actionListener = new ActionListener()
1197 public void actionPerformed(ActionEvent e)
1202 andFilters.addActionListener(actionListener);
1203 orFilters.addActionListener(actionListener);
1204 ButtonGroup andOr = new ButtonGroup();
1205 andOr.add(andFilters);
1206 andOr.add(orFilters);
1207 andFilters.setSelected(true);
1209 new JLabel(MessageManager.getString("label.join_conditions")));
1210 andOrPanel.add(andFilters);
1211 andOrPanel.add(orFilters);
1216 * Refreshes the display to show any filters currently configured for the
1217 * selected feature type (editable, with 'remove' option), plus one extra row
1218 * for adding a condition. This should be called after a filter has been
1219 * removed, added or amended.
1221 private void 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 chooseFiltersPanel.add(row);
1283 * A helper method that constructs a row (panel) with one filter condition:
1285 * <li>a drop-down list of Label, Score and attribute names to choose
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<Object> 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 JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x
1426 removeCondition.setToolTipText(
1427 MessageManager.getString("label.delete_condition"));
1428 removeCondition.setBorder(new EmptyBorder(0, 0, 0, 0));
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<Object> 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, Condition selectedCondition,
1485 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
1520 * attribute name. The conditions added depend on the datatype of the
1521 * attribute values. The supplied condition is set as the selected item in the
1522 * list, provided it is in the list. If the pattern is now invalid
1523 * (non-numeric pattern for a 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
1603 * non-numeric 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
1606 * does not mark the field as invalid. This supports selecting an attribute
1607 * for a new 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
1654 * field is blank (unless the match condition is one that doesn't require a
1655 * pattern, e.g. 'Is present'). Answers true if the filter was updated, else
1658 * This method may update the tooltip on the filter value field to show the
1659 * value range, if a numeric condition is selected. This ensures the tooltip
1660 * is updated when a numeric valued attribute is chosen on the last 'add a
1666 * @param filterIndex
1668 protected boolean updateFilter(JComboBox<Object> attCombo,
1669 JComboBox<Condition> condCombo, JTextField valueField,
1675 attName = (String) attCombo.getSelectedItem();
1676 } catch (Exception e)
1678 Cache.log.error("Problem casting Combo box entry to String");
1679 attName = attCombo.getSelectedItem().toString();
1681 Condition cond = (Condition) condCombo.getSelectedItem();
1682 String pattern = valueField.getText().trim();
1684 setNumericHints(attName, cond, valueField);
1686 if (pattern.length() == 0 && cond.needsAPattern())
1688 valueField.setEnabled(true); // ensure pattern field is enabled!
1693 * Construct a matcher that operates on Label, Score,
1694 * or named attribute
1696 FeatureMatcherI km = null;
1697 if (LABEL_18N.equals(attName))
1699 km = FeatureMatcher.byLabel(cond, pattern);
1701 else if (SCORE_18N.equals(attName))
1703 km = FeatureMatcher.byScore(cond, pattern);
1707 km = FeatureMatcher.byAttribute(cond, pattern,
1708 FeatureMatcher.fromAttributeDisplayName(attName));
1711 filters.set(filterIndex, km);
1717 * Action on any change to feature filtering, namely
1719 * <li>change of selected attribute</li>
1720 * <li>change of selected condition</li>
1721 * <li>change of match pattern</li>
1722 * <li>removal of a condition</li>
1724 * The inputs are parsed into a combined filter and this is set for the
1725 * feature type, and the alignment redrawn.
1727 protected void filtersChanged()
1730 * update the filter conditions for the feature type
1732 boolean anded = andFilters.isSelected();
1733 FeatureMatcherSetI combined = new FeatureMatcherSet();
1735 for (FeatureMatcherI filter : filters)
1737 String pattern = filter.getMatcher().getPattern();
1738 Condition condition = filter.getMatcher().getCondition();
1739 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1743 combined.and(filter);
1747 combined.or(filter);
1753 * save the filter conditions in the FeatureRenderer
1754 * (note this might now be an empty filter with no conditions)
1756 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1757 refreshDisplay(true);
1763 * Repaints alignment, structure and overview (if shown). If there is a
1764 * complementary view which is showing this view's features, then also
1767 * @param updateStructsAndOverview
1769 void refreshDisplay(boolean updateStructsAndOverview)
1771 ap.paintAlignment(true, updateStructsAndOverview);
1772 AlignViewportI complement = ap.getAlignViewport().getCodingComplement();
1773 if (complement != null && complement.isShowComplementFeatures())
1775 AlignFrame af2 = Desktop.getAlignFrameFor(complement);
1776 af2.alignPanel.paintAlignment(true, updateStructsAndOverview);