2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.FeatureColourI;
25 import jalview.datamodel.GraphLine;
26 import jalview.datamodel.features.FeatureAttributes;
27 import jalview.datamodel.features.FeatureAttributes.Datatype;
28 import jalview.datamodel.features.FeatureMatcher;
29 import jalview.datamodel.features.FeatureMatcherI;
30 import jalview.datamodel.features.FeatureMatcherSet;
31 import jalview.datamodel.features.FeatureMatcherSetI;
32 import jalview.gui.JalviewColourChooser.ColourChooserListener;
33 import jalview.schemes.FeatureColour;
34 import jalview.util.ColorUtils;
35 import jalview.util.MessageManager;
36 import jalview.util.matcher.Condition;
38 import java.awt.BorderLayout;
39 import java.awt.Color;
40 import java.awt.Dimension;
41 import java.awt.FlowLayout;
42 import java.awt.GridLayout;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.awt.event.FocusAdapter;
46 import java.awt.event.FocusEvent;
47 import java.awt.event.ItemEvent;
48 import java.awt.event.ItemListener;
49 import java.awt.event.MouseAdapter;
50 import java.awt.event.MouseEvent;
51 import java.text.DecimalFormat;
52 import java.util.ArrayList;
53 import java.util.List;
55 import javax.swing.BorderFactory;
56 import javax.swing.BoxLayout;
57 import javax.swing.ButtonGroup;
58 import javax.swing.JButton;
59 import javax.swing.JCheckBox;
60 import javax.swing.JComboBox;
61 import javax.swing.JLabel;
62 import javax.swing.JPanel;
63 import javax.swing.JRadioButton;
64 import javax.swing.JSlider;
65 import javax.swing.JTabbedPane;
66 import javax.swing.JTextField;
67 import javax.swing.border.LineBorder;
68 import javax.swing.event.ChangeEvent;
69 import javax.swing.event.ChangeListener;
72 * A dialog where the user can configure colour scheme, and any filters, for one
75 * (Was FeatureColourChooser prior to Jalview 1.11, renamed with the addition of
78 public class FeatureTypeSettings extends JalviewDialog
80 private final static String LABEL_18N = MessageManager
81 .getString("label.label");
83 private final static String SCORE_18N = MessageManager
84 .getString("label.score");
86 private static final int RADIO_WIDTH = 130;
88 private static final String COLON = ":";
90 private static final int MAX_TOOLTIP_LENGTH = 50;
92 private static final int NO_COLOUR_OPTION = 0;
94 private static final int MIN_COLOUR_OPTION = 1;
96 private static final int MAX_COLOUR_OPTION = 2;
98 private static final int ABOVE_THRESHOLD_OPTION = 1;
100 private static final int BELOW_THRESHOLD_OPTION = 2;
102 private static final DecimalFormat DECFMT_2_2 = new DecimalFormat(
106 * FeatureRenderer holds colour scheme and filters for feature types
108 private final FeatureRenderer fr; // todo refactor to allow interface type
112 * the view panel to update when settings change
114 final AlignmentViewPanel ap;
116 private final String featureType;
119 * the colour and filters to reset to on Cancel
121 private final FeatureColourI originalColour;
123 private final FeatureMatcherSetI originalFilter;
126 * set flag to true when setting values programmatically,
127 * to avoid invocation of action handlers
129 boolean adjusting = false;
132 * minimum of the value range for graduated colour
133 * (may be for feature score or for a numeric attribute)
138 * maximum of the value range for graduated colour
143 * scale factor for conversion between absolute min-max and slider
148 * radio button group, to select what to colour by:
149 * simple colour, by category (text), or graduated
151 JRadioButton simpleColour = new JRadioButton();
153 JRadioButton byCategory = new JRadioButton();
155 JRadioButton graduatedColour = new JRadioButton();
158 * colours and filters are shown in tabbed view or single content pane
160 JPanel coloursPanel, filtersPanel;
162 JPanel singleColour = new JPanel();
164 JPanel minColour = new JPanel();
166 JPanel maxColour = new JPanel();
168 private JComboBox<String> threshold = new JComboBox<>();
170 JSlider slider = new JSlider();
172 JTextField thresholdValue = new JTextField(20);
174 private JCheckBox thresholdIsMin = new JCheckBox();
176 private GraphLine threshline;
178 private ActionListener featureSettings = null;
180 private ActionListener changeColourAction;
183 * choice of option for 'colour for no value'
185 private JComboBox<String> noValueCombo;
188 * choice of what to colour by text (Label or attribute)
190 private JComboBox<String> colourByTextCombo;
193 * choice of what to colour by range (Score or attribute)
195 private JComboBox<String> colourByRangeCombo;
197 private JRadioButton andFilters;
199 private JRadioButton orFilters;
202 * filters for the currently selected feature type
204 List<FeatureMatcherI> filters;
206 private JPanel chooseFiltersPanel;
214 public FeatureTypeSettings(FeatureRenderer frender, String theType)
216 this(frender, false, theType);
220 * Constructor, with option to make a blocking dialog (has to complete in the
221 * AWT event queue thread). Currently this option is always set to false.
227 FeatureTypeSettings(FeatureRenderer frender, boolean blocking,
231 this.featureType = theType;
233 originalFilter = fr.getFeatureFilter(theType);
234 originalColour = fr.getFeatureColours().get(theType);
241 } catch (Exception ex)
243 ex.printStackTrace();
253 colourChanged(false);
255 String title = MessageManager
256 .formatMessage("label.display_settings_for", new String[]
258 initDialogFrame(this, true, blocking, title, 500, 500);
264 * Configures the widgets on the Colours tab according to the current feature
267 private void updateColoursTab()
269 FeatureColourI fc = fr.getFeatureColours().get(featureType);
272 * suppress action handling while updating values programmatically
280 if (fc.isSimpleColour())
282 simpleColour.setSelected(true);
283 singleColour.setBackground(fc.getColour());
284 singleColour.setForeground(fc.getColour());
288 * colour by text (Label or attribute text)
290 if (fc.isColourByLabel())
292 byCategory.setSelected(true);
293 colourByTextCombo.setEnabled(colourByTextCombo.getItemCount() > 1);
294 if (fc.isColourByAttribute())
296 String[] attributeName = fc.getAttributeName();
297 colourByTextCombo.setSelectedItem(
298 FeatureMatcher.toAttributeDisplayName(attributeName));
302 colourByTextCombo.setSelectedItem(LABEL_18N);
307 colourByTextCombo.setEnabled(false);
310 if (!fc.isGraduatedColour())
312 colourByRangeCombo.setEnabled(false);
313 minColour.setEnabled(false);
314 maxColour.setEnabled(false);
315 noValueCombo.setEnabled(false);
316 threshold.setEnabled(false);
317 slider.setEnabled(false);
318 thresholdValue.setEnabled(false);
319 thresholdIsMin.setEnabled(false);
324 * Graduated colour, by score or attribute value range
326 graduatedColour.setSelected(true);
327 updateColourMinMax(); // ensure min, max are set
328 colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
329 minColour.setEnabled(true);
330 maxColour.setEnabled(true);
331 noValueCombo.setEnabled(true);
332 threshold.setEnabled(true);
333 minColour.setBackground(fc.getMinColour());
334 maxColour.setBackground(fc.getMaxColour());
336 if (fc.isColourByAttribute())
338 String[] attributeName = fc.getAttributeName();
339 colourByRangeCombo.setSelectedItem(
340 FeatureMatcher.toAttributeDisplayName(attributeName));
344 colourByRangeCombo.setSelectedItem(SCORE_18N);
346 Color noColour = fc.getNoColour();
347 if (noColour == null)
349 noValueCombo.setSelectedIndex(NO_COLOUR_OPTION);
351 else if (noColour.equals(fc.getMinColour()))
353 noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION);
355 else if (noColour.equals(fc.getMaxColour()))
357 noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION);
361 * update min-max scaling if there is a range to work with,
362 * else disable the widgets (this shouldn't happen if only
363 * valid options are offered in the combo box)
365 scaleFactor = (max == min) ? 1f : 100f / (max - min);
366 float range = (max - min) * scaleFactor;
367 slider.setMinimum((int) (min * scaleFactor));
368 slider.setMaximum((int) (max * scaleFactor));
369 slider.setMajorTickSpacing((int) (range / 10f));
371 threshline = new GraphLine((max - min) / 2f, "Threshold",
373 threshline.value = fc.getThreshold();
375 if (fc.hasThreshold())
377 threshold.setSelectedIndex(
378 fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
379 : BELOW_THRESHOLD_OPTION);
380 slider.setEnabled(true);
381 slider.setValue((int) (fc.getThreshold() * scaleFactor));
382 thresholdValue.setText(String.valueOf(getRoundedSliderValue()));
383 thresholdValue.setEnabled(true);
384 thresholdIsMin.setEnabled(true);
388 slider.setEnabled(false);
389 thresholdValue.setEnabled(false);
390 thresholdIsMin.setEnabled(false);
392 thresholdIsMin.setSelected(!fc.isAutoScaled());
400 * Configures the initial layout
402 private void initialise()
404 this.setLayout(new BorderLayout());
407 * an ActionListener that applies colour changes
409 changeColourAction = new ActionListener()
412 public void actionPerformed(ActionEvent e)
419 * first panel/tab: colour options
421 JPanel coloursPanel = initialiseColoursPanel();
422 this.add(coloursPanel, BorderLayout.NORTH);
425 * second panel/tab: filter options
427 JPanel filtersPanel = initialiseFiltersPanel();
428 this.add(filtersPanel, BorderLayout.CENTER);
430 JPanel okCancelPanel = initialiseOkCancelPanel();
432 this.add(okCancelPanel, BorderLayout.SOUTH);
436 * Updates the min-max range if Colour By selected item is Score, or an
437 * attribute, with a min-max range
439 protected void updateColourMinMax()
441 if (!graduatedColour.isSelected())
446 String colourBy = (String) colourByRangeCombo.getSelectedItem();
447 float[] minMax = getMinMax(colourBy);
457 * Retrieves the min-max range:
459 * <li>of feature score, if colour or filter is by Score</li>
460 * <li>else of the selected attribute</li>
466 private float[] getMinMax(String attName)
468 float[] minMax = null;
469 if (SCORE_18N.equals(attName))
471 minMax = fr.getMinMax().get(featureType)[0];
475 // colour by attribute range
476 minMax = FeatureAttributes.getInstance().getMinMax(featureType,
477 FeatureMatcher.fromAttributeDisplayName(attName));
483 * Lay out fields for graduated colour (by score or attribute value)
487 private JPanel initialiseGraduatedColourPanel()
489 JPanel graduatedColourPanel = new JPanel();
490 graduatedColourPanel.setLayout(
491 new BoxLayout(graduatedColourPanel, BoxLayout.Y_AXIS));
492 JvSwingUtils.createTitledBorder(graduatedColourPanel,
493 MessageManager.getString("label.graduated_colour"), true);
494 graduatedColourPanel.setBackground(Color.white);
497 * first row: graduated colour radio button, score/attribute drop-down
499 JPanel graduatedChoicePanel = new JPanel(
500 new FlowLayout(FlowLayout.LEFT));
501 graduatedChoicePanel.setBackground(Color.white);
502 graduatedColour = new JRadioButton(
503 MessageManager.getString("label.by_range_of") + COLON);
504 graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
505 graduatedColour.addItemListener(new ItemListener()
508 public void itemStateChanged(ItemEvent e)
510 if (graduatedColour.isSelected())
516 graduatedChoicePanel.add(graduatedColour);
518 List<String[]> attNames = FeatureAttributes.getInstance()
519 .getAttributes(featureType);
520 colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
521 colourByRangeCombo.addItemListener(new ItemListener()
524 public void itemStateChanged(ItemEvent e)
531 * disable graduated colour option if no range found
533 graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
535 graduatedChoicePanel.add(colourByRangeCombo);
536 graduatedColourPanel.add(graduatedChoicePanel);
539 * second row - min/max/no colours
541 JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
542 colourRangePanel.setBackground(Color.white);
543 graduatedColourPanel.add(colourRangePanel);
545 minColour.setFont(JvSwingUtils.getLabelFont());
546 minColour.setBorder(BorderFactory.createLineBorder(Color.black));
547 minColour.setPreferredSize(new Dimension(40, 20));
548 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
549 minColour.addMouseListener(new MouseAdapter()
552 public void mousePressed(MouseEvent e)
554 if (minColour.isEnabled())
556 showColourChooser(minColour, "label.select_colour_minimum_value");
561 maxColour.setFont(JvSwingUtils.getLabelFont());
562 maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
563 maxColour.setPreferredSize(new Dimension(40, 20));
564 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
565 maxColour.addMouseListener(new MouseAdapter()
568 public void mousePressed(MouseEvent e)
570 if (maxColour.isEnabled())
572 showColourChooser(maxColour, "label.select_colour_maximum_value");
576 maxColour.setBorder(new LineBorder(Color.black));
579 * default max colour to current colour (if a plain colour),
580 * or to Black if colour by label; make min colour a pale
581 * version of max colour
583 FeatureColourI fc = fr.getFeatureColours().get(featureType);
584 Color bg = fc.isSimpleColour() ? fc.getColour() : Color.BLACK;
585 maxColour.setBackground(bg);
586 minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
588 noValueCombo = new JComboBox<>();
589 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
590 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
591 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
592 noValueCombo.addItemListener(new ItemListener()
595 public void itemStateChanged(ItemEvent e)
601 JLabel minText = new JLabel(
602 MessageManager.getString("label.min_value") + COLON);
603 minText.setFont(JvSwingUtils.getLabelFont());
604 JLabel maxText = new JLabel(
605 MessageManager.getString("label.max_value") + COLON);
606 maxText.setFont(JvSwingUtils.getLabelFont());
607 JLabel noText = new JLabel(
608 MessageManager.getString("label.no_value") + COLON);
609 noText.setFont(JvSwingUtils.getLabelFont());
611 colourRangePanel.add(minText);
612 colourRangePanel.add(minColour);
613 colourRangePanel.add(maxText);
614 colourRangePanel.add(maxColour);
615 colourRangePanel.add(noText);
616 colourRangePanel.add(noValueCombo);
619 * third row - threshold options and value
621 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
622 thresholdPanel.setBackground(Color.white);
623 graduatedColourPanel.add(thresholdPanel);
625 threshold.addActionListener(changeColourAction);
626 threshold.setToolTipText(MessageManager
627 .getString("label.threshold_feature_display_by_score"));
628 threshold.addItem(MessageManager
629 .getString("label.threshold_feature_no_threshold")); // index 0
630 threshold.addItem(MessageManager
631 .getString("label.threshold_feature_above_threshold")); // index 1
632 threshold.addItem(MessageManager
633 .getString("label.threshold_feature_below_threshold")); // index 2
635 thresholdValue.addActionListener(new ActionListener()
638 public void actionPerformed(ActionEvent e)
640 thresholdValue_actionPerformed();
643 thresholdValue.addFocusListener(new FocusAdapter()
646 public void focusLost(FocusEvent e)
648 thresholdValue_actionPerformed();
651 slider.setPaintLabels(false);
652 slider.setPaintTicks(true);
653 slider.setBackground(Color.white);
654 slider.setEnabled(false);
655 slider.setOpaque(false);
656 slider.setPreferredSize(new Dimension(100, 32));
657 slider.setToolTipText(
658 MessageManager.getString("label.adjust_threshold"));
660 slider.addChangeListener(new ChangeListener()
663 public void stateChanged(ChangeEvent evt)
668 .setText(String.valueOf(slider.getValue() / scaleFactor));
669 sliderValueChanged();
673 slider.addMouseListener(new MouseAdapter()
676 public void mouseReleased(MouseEvent evt)
679 * only update Overview and/or structure colouring
680 * when threshold slider drag ends (mouse up)
684 ap.paintAlignment(true, true);
689 thresholdValue.setEnabled(false);
690 thresholdValue.setColumns(7);
692 thresholdPanel.add(threshold);
693 thresholdPanel.add(slider);
694 thresholdPanel.add(thresholdValue);
696 thresholdIsMin.setBackground(Color.white);
698 .setText(MessageManager.getString("label.threshold_minmax"));
699 thresholdIsMin.setToolTipText(MessageManager
700 .getString("label.toggle_absolute_relative_display_threshold"));
701 thresholdIsMin.addActionListener(changeColourAction);
702 thresholdPanel.add(thresholdIsMin);
704 return graduatedColourPanel;
708 * Lay out OK and Cancel buttons
712 private JPanel initialiseOkCancelPanel()
714 JPanel okCancelPanel = new JPanel();
715 // okCancelPanel.setBackground(Color.white);
716 okCancelPanel.add(ok);
717 okCancelPanel.add(cancel);
718 return okCancelPanel;
722 * Lay out Colour options panel, containing
724 * <li>plain colour, with colour picker</li>
725 * <li>colour by text, with choice of Label or other attribute</li>
726 * <li>colour by range, of score or other attribute, when available</li>
731 private JPanel initialiseColoursPanel()
733 JPanel colourByPanel = new JPanel();
734 colourByPanel.setBackground(Color.white);
735 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
736 JvSwingUtils.createTitledBorder(colourByPanel,
737 MessageManager.getString("action.colour"), true);
740 * simple colour radio button and colour picker
742 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
743 simpleColourPanel.setBackground(Color.white);
744 // JvSwingUtils.createTitledBorder(simpleColourPanel,
745 // MessageManager.getString("label.simple"), true);
746 colourByPanel.add(simpleColourPanel);
748 simpleColour = new JRadioButton(
749 MessageManager.getString("label.simple_colour"));
750 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
751 simpleColour.addItemListener(new ItemListener()
754 public void itemStateChanged(ItemEvent e)
756 if (simpleColour.isSelected() && !adjusting)
758 showColourChooser(singleColour, "label.select_colour");
763 singleColour.setFont(JvSwingUtils.getLabelFont());
764 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
765 singleColour.setPreferredSize(new Dimension(40, 20));
766 singleColour.addMouseListener(new MouseAdapter()
769 public void mousePressed(MouseEvent e)
771 if (simpleColour.isSelected())
773 showColourChooser(singleColour, "label.select_colour");
777 simpleColourPanel.add(simpleColour); // radio button
778 simpleColourPanel.add(singleColour); // colour picker button
781 * colour by text (category) radio button and drop-down choice list
783 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
784 byTextPanel.setBackground(Color.white);
785 JvSwingUtils.createTitledBorder(byTextPanel,
786 MessageManager.getString("label.colour_by_text"), true);
787 colourByPanel.add(byTextPanel);
788 byCategory = new JRadioButton(
789 MessageManager.getString("label.by_text_of") + COLON);
790 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
791 byCategory.addItemListener(new ItemListener()
794 public void itemStateChanged(ItemEvent e)
796 if (byCategory.isSelected())
802 byTextPanel.add(byCategory);
804 List<String[]> attNames = FeatureAttributes.getInstance()
805 .getAttributes(featureType);
806 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
807 colourByTextCombo.addItemListener(new ItemListener()
810 public void itemStateChanged(ItemEvent e)
815 byTextPanel.add(colourByTextCombo);
818 * graduated colour panel
820 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
821 colourByPanel.add(graduatedColourPanel);
824 * 3 radio buttons select between simple colour,
825 * by category (text), or graduated
827 ButtonGroup bg = new ButtonGroup();
828 bg.add(simpleColour);
830 bg.add(graduatedColour);
832 return colourByPanel;
836 * Shows a colour chooser dialog, and if a selection is made, updates the
837 * colour of the given panel
840 * the panel whose background colour is being picked
842 * message bundle key for the dialog title
844 void showColourChooser(JPanel colourPanel, String key)
846 ColourChooserListener listener = new ColourChooserListener()
849 public void colourSelected(Color col)
851 colourPanel.setBackground(col);
852 colourPanel.setForeground(col);
853 colourPanel.repaint();
857 JalviewColourChooser.showColourChooser(this,
858 MessageManager.getString(key), colourPanel.getBackground(),
863 * Constructs and sets the selected colour options as the colour for the
864 * feature type, and repaints the alignment, and optionally the Overview
865 * and/or structure viewer if open
867 * @param updateStructsAndOverview
869 void colourChanged(boolean updateStructsAndOverview)
874 * ignore action handlers while setting values programmatically
880 * ensure min-max range is for the latest choice of
881 * 'graduated colour by'
883 updateColourMinMax();
885 FeatureColourI acg = makeColourFromInputs();
888 * save the colour, and repaint stuff
890 fr.setColour(featureType, acg);
891 ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
897 * Converts the input values into an instance of FeatureColour
901 private FeatureColourI makeColourFromInputs()
904 * easiest case - a single colour
906 if (simpleColour.isSelected())
908 return new FeatureColour(singleColour.getBackground());
912 * next easiest case - colour by Label, or attribute text
914 if (byCategory.isSelected())
916 Color c = this.getBackground();
917 FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f);
918 fc.setColourByLabel(true);
919 String byWhat = (String) colourByTextCombo.getSelectedItem();
920 if (!LABEL_18N.equals(byWhat))
923 FeatureMatcher.fromAttributeDisplayName(byWhat));
929 * remaining case - graduated colour by score, or attribute value
931 Color noColour = null;
932 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
934 noColour = minColour.getBackground();
936 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
938 noColour = maxColour.getBackground();
944 thresh = Float.valueOf(thresholdValue.getText());
945 } catch (NumberFormatException e)
947 // invalid inputs are already handled on entry
951 * min-max range is to (or from) threshold value if
952 * 'threshold is min/max' is selected
954 float minValue = min;
955 float maxValue = max;
956 int thresholdOption = threshold.getSelectedIndex();
957 if (thresholdIsMin.isSelected()
958 && thresholdOption == ABOVE_THRESHOLD_OPTION)
962 if (thresholdIsMin.isSelected()
963 && thresholdOption == BELOW_THRESHOLD_OPTION)
969 * make the graduated colour
971 FeatureColourI fc = new FeatureColour(minColour.getBackground(),
972 maxColour.getBackground(), noColour, minValue, maxValue);
975 * set attribute to colour by if selected
977 String byWhat = (String) colourByRangeCombo.getSelectedItem();
978 if (!SCORE_18N.equals(byWhat))
980 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
984 * set threshold options and 'autoscaled' which is
985 * false if 'threshold is min/max' is selected
986 * else true (colour range is on actual range of values)
988 fc.setThreshold(thresh);
989 fc.setAutoScaled(!thresholdIsMin.isSelected());
990 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
991 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
993 if (threshline == null)
996 * todo not yet implemented: visual indication of feature threshold
998 threshline = new GraphLine((max - min) / 2f, "Threshold",
1006 protected void raiseClosed()
1008 if (this.featureSettings != null)
1010 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
1015 * Action on OK is just to dismiss the dialog - any changes have already been
1019 public void okPressed()
1024 * Action on Cancel is to restore colour scheme and filters as they were when
1025 * the dialog was opened
1028 public void cancelPressed()
1030 fr.setColour(featureType, originalColour);
1031 fr.setFeatureFilter(featureType, originalFilter);
1032 ap.paintAlignment(true, true);
1036 * Action on text entry of a threshold value
1038 protected void thresholdValue_actionPerformed()
1043 float f = Float.parseFloat(thresholdValue.getText());
1044 slider.setValue((int) (f * scaleFactor));
1045 threshline.value = f;
1046 thresholdValue.setBackground(Color.white); // ok
1049 * force repaint of any Overview window or structure
1051 ap.paintAlignment(true, true);
1052 } catch (NumberFormatException ex)
1054 thresholdValue.setBackground(Color.red); // not ok
1062 * Action on change of threshold slider value. This may be done interactively
1063 * (by moving the slider), or programmatically (to update the slider after
1064 * manual input of a threshold value).
1066 protected void sliderValueChanged()
1068 threshline.value = getRoundedSliderValue();
1071 * repaint alignment, but not Overview or structure,
1072 * to avoid overload while dragging the slider
1074 colourChanged(false);
1078 * Converts the slider value to its absolute value by dividing by the
1079 * scaleFactor. Rounding errors are squashed by forcing min/max of slider
1080 * range to the actual min/max of feature score range
1084 private float getRoundedSliderValue()
1086 int value = slider.getValue();
1087 float f = value == slider.getMaximum() ? max
1088 : (value == slider.getMinimum() ? min : value / scaleFactor);
1092 void addActionListener(ActionListener listener)
1094 if (featureSettings != null)
1097 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1099 featureSettings = listener;
1103 * A helper method to build the drop-down choice of attributes for a feature.
1104 * If 'withRange' is true, then Score, and any attributes with a min-max
1105 * range, are added. If 'withText' is true, Label and any known attributes are
1106 * added. This allows 'categorical numerical' attributes e.g. codon position
1107 * to be coloured by text.
1109 * Where metadata is available with a description for an attribute, that is
1110 * added as a tooltip.
1112 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1113 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1115 * This method does not add any ActionListener to the JComboBox.
1121 protected JComboBox<String> populateAttributesDropdown(
1122 List<String[]> attNames, boolean withRange, boolean withText)
1124 List<String> displayAtts = new ArrayList<>();
1125 List<String> tooltips = new ArrayList<>();
1129 displayAtts.add(LABEL_18N);
1130 tooltips.add(MessageManager.getString("label.description"));
1134 float[][] minMax = fr.getMinMax().get(featureType);
1135 if (minMax != null && minMax[0][0] != minMax[0][1])
1137 displayAtts.add(SCORE_18N);
1138 tooltips.add(SCORE_18N);
1142 FeatureAttributes fa = FeatureAttributes.getInstance();
1143 for (String[] attName : attNames)
1145 float[] minMax = fa.getMinMax(featureType, attName);
1146 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1147 if (!withText && !hasRange)
1151 displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
1152 String desc = fa.getDescription(featureType, attName);
1153 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1155 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1157 tooltips.add(desc == null ? "" : desc);
1160 JComboBox<String> attCombo = JvSwingUtils
1161 .buildComboWithTooltips(displayAtts, tooltips);
1167 * Populates initial layout of the feature attribute filters panel
1169 private JPanel initialiseFiltersPanel()
1171 filters = new ArrayList<>();
1173 JPanel filtersPanel = new JPanel();
1174 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1175 filtersPanel.setBackground(Color.white);
1176 JvSwingUtils.createTitledBorder(filtersPanel,
1177 MessageManager.getString("label.filters"), true);
1179 JPanel andOrPanel = initialiseAndOrPanel();
1180 filtersPanel.add(andOrPanel);
1183 * panel with filters - populated by refreshFiltersDisplay,
1184 * which also sets the layout manager
1186 chooseFiltersPanel = new JPanel();
1187 chooseFiltersPanel.setBackground(Color.white);
1188 filtersPanel.add(chooseFiltersPanel);
1190 return filtersPanel;
1194 * Lays out the panel with radio buttons to AND or OR filter conditions
1198 private JPanel initialiseAndOrPanel()
1200 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1201 andOrPanel.setBackground(Color.white);
1202 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1203 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1204 ActionListener actionListener = new ActionListener()
1207 public void actionPerformed(ActionEvent e)
1212 andFilters.addActionListener(actionListener);
1213 orFilters.addActionListener(actionListener);
1214 ButtonGroup andOr = new ButtonGroup();
1215 andOr.add(andFilters);
1216 andOr.add(orFilters);
1217 andFilters.setSelected(true);
1219 new JLabel(MessageManager.getString("label.join_conditions")));
1220 andOrPanel.add(andFilters);
1221 andOrPanel.add(orFilters);
1226 * Refreshes the display to show any filters currently configured for the
1227 * selected feature type (editable, with 'remove' option), plus one extra row
1228 * for adding a condition. This should be called after a filter has been
1229 * removed, added or amended.
1231 private void updateFiltersTab()
1234 * clear the panel and list of filter conditions
1236 chooseFiltersPanel.removeAll();
1240 * look up attributes known for feature type
1242 List<String[]> attNames = FeatureAttributes.getInstance()
1243 .getAttributes(featureType);
1246 * if this feature type has filters set, load them first
1248 FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
1249 if (featureFilters != null)
1251 if (!featureFilters.isAnded())
1253 orFilters.setSelected(true);
1255 // avoid use of lambda expression to keep SwingJS happy
1256 // featureFilters.getMatchers().forEach(item -> filters.add(item));
1257 for (FeatureMatcherI matcher : featureFilters.getMatchers())
1259 filters.add(matcher);
1264 * and an empty filter for the user to populate (add)
1266 filters.add(FeatureMatcher.NULL_MATCHER);
1269 * use GridLayout to 'justify' rows to the top of the panel, until
1270 * there are too many to fit in, then fall back on BoxLayout
1272 if (filters.size() <= 5)
1274 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1278 chooseFiltersPanel.setLayout(
1279 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1283 * render the conditions in rows, each in its own JPanel
1285 int filterIndex = 0;
1286 for (FeatureMatcherI filter : filters)
1288 JPanel row = addFilter(filter, attNames, filterIndex);
1289 chooseFiltersPanel.add(row);
1298 * A helper method that constructs a row (panel) with one filter condition:
1300 * <li>a drop-down list of Label, Score and attribute names to choose
1302 * <li>a drop-down list of conditions to choose from</li>
1303 * <li>a text field for input of a match pattern</li>
1304 * <li>optionally, a 'remove' button</li>
1306 * The filter values are set as defaults for the input fields. The 'remove'
1307 * button is added unless the pattern is empty (incomplete filter condition).
1309 * Action handlers on these fields provide for
1311 * <li>validate pattern field - should be numeric if condition is numeric</li>
1312 * <li>save filters and refresh display on any (valid) change</li>
1313 * <li>remove filter and refresh on 'Remove'</li>
1314 * <li>update conditions list on change of Label/Score/Attribute</li>
1315 * <li>refresh value field tooltip with min-max range on change of
1321 * @param filterIndex
1324 protected JPanel addFilter(FeatureMatcherI filter,
1325 List<String[]> attNames, int filterIndex)
1327 String[] attName = filter.getAttribute();
1328 Condition cond = filter.getMatcher().getCondition();
1329 String pattern = filter.getMatcher().getPattern();
1331 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1332 filterRow.setBackground(Color.white);
1335 * drop-down choice of attribute, with description as a tooltip
1336 * if we can obtain it
1338 JComboBox<String> attCombo = populateAttributesDropdown(attNames, true,
1340 String filterBy = setSelectedAttribute(attCombo, filter);
1342 JComboBox<Condition> condCombo = new JComboBox<>();
1344 JTextField patternField = new JTextField(8);
1345 patternField.setText(pattern);
1348 * action handlers that validate and (if valid) apply changes
1350 ActionListener actionListener = new ActionListener()
1353 public void actionPerformed(ActionEvent e)
1355 if (validateFilter(patternField, condCombo))
1357 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1364 ItemListener itemListener = new ItemListener()
1367 public void itemStateChanged(ItemEvent e)
1369 actionListener.actionPerformed(null);
1373 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1375 attCombo.setSelectedIndex(0);
1379 attCombo.setSelectedItem(
1380 FeatureMatcher.toAttributeDisplayName(attName));
1382 attCombo.addItemListener(new ItemListener()
1385 public void itemStateChanged(ItemEvent e)
1388 * on change of attribute, refresh the conditions list to
1389 * ensure it is appropriate for the attribute datatype
1391 populateConditions((String) attCombo.getSelectedItem(),
1392 (Condition) condCombo.getSelectedItem(), condCombo,
1394 actionListener.actionPerformed(null);
1398 filterRow.add(attCombo);
1401 * drop-down choice of test condition
1403 populateConditions(filterBy, cond, condCombo, patternField);
1404 condCombo.setPreferredSize(new Dimension(150, 20));
1405 condCombo.addItemListener(itemListener);
1406 filterRow.add(condCombo);
1409 * pattern to match against
1411 patternField.addActionListener(actionListener);
1412 patternField.addFocusListener(new FocusAdapter()
1415 public void focusLost(FocusEvent e)
1417 actionListener.actionPerformed(null);
1420 filterRow.add(patternField);
1423 * disable pattern field for condition 'Present / NotPresent'
1425 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1426 patternField.setEnabled(selectedCondition.needsAPattern());
1429 * if a numeric condition is selected, show the value range
1430 * as a tooltip on the value input field
1432 setNumericHints(filterBy, selectedCondition, patternField);
1435 * add remove button if filter is populated (non-empty pattern)
1437 if (!patternField.isEnabled()
1438 || (pattern != null && pattern.trim().length() > 0))
1440 JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x
1441 removeCondition.setPreferredSize(new Dimension(23, 17));
1443 .setToolTipText(MessageManager.getString("label.delete_row"));
1444 removeCondition.addActionListener(new ActionListener()
1447 public void actionPerformed(ActionEvent e)
1449 filters.remove(filterIndex);
1453 filterRow.add(removeCondition);
1460 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1466 private String setSelectedAttribute(JComboBox<String> attCombo,
1467 FeatureMatcherI filter)
1470 if (filter.isByScore())
1474 else if (filter.isByLabel())
1480 item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
1482 attCombo.setSelectedItem(item);
1487 * If a numeric comparison condition is selected, retrieves the min-max range
1488 * for the value (score or attribute), and sets it as a tooltip on the value
1489 * field. If the field is currently empty, then pre-populates it with
1491 * <li>the minimum value, if condition is > or >=</li>
1492 * <li>the maximum value, if condition is < or <=</li>
1496 * @param selectedCondition
1497 * @param patternField
1499 private void setNumericHints(String attName, Condition selectedCondition,
1500 JTextField patternField)
1502 patternField.setToolTipText("");
1504 if (selectedCondition.isNumeric())
1506 float[] minMax = getMinMax(attName);
1509 String minFormatted = DECFMT_2_2.format(minMax[0]);
1510 String maxFormatted = DECFMT_2_2.format(minMax[1]);
1511 String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
1512 patternField.setToolTipText(tip);
1513 if (patternField.getText().isEmpty())
1515 if (selectedCondition == Condition.GE
1516 || selectedCondition == Condition.GT)
1518 patternField.setText(minFormatted);
1522 if (selectedCondition == Condition.LE
1523 || selectedCondition == Condition.LT)
1525 patternField.setText(maxFormatted);
1534 * Populates the drop-down list of comparison conditions for the given
1535 * attribute name. The conditions added depend on the datatype of the
1536 * attribute values. The supplied condition is set as the selected item in the
1537 * list, provided it is in the list. If the pattern is now invalid
1538 * (non-numeric pattern for a numeric condition), it is cleared.
1543 * @param patternField
1545 void populateConditions(String attName, Condition cond,
1546 JComboBox<Condition> condCombo, JTextField patternField)
1548 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1549 FeatureMatcher.fromAttributeDisplayName(attName));
1550 if (LABEL_18N.equals(attName))
1552 type = Datatype.Character;
1554 else if (SCORE_18N.equals(attName))
1556 type = Datatype.Number;
1560 * remove itemListener before starting
1562 ItemListener listener = condCombo.getItemListeners()[0];
1563 condCombo.removeItemListener(listener);
1564 boolean condIsValid = false;
1566 condCombo.removeAllItems();
1567 for (Condition c : Condition.values())
1569 if ((c.isNumeric() && type == Datatype.Number)
1570 || (!c.isNumeric() && type != Datatype.Number))
1572 condCombo.addItem(c);
1581 * set the selected condition (does nothing if not in the list)
1585 condCombo.setSelectedItem(cond);
1589 condCombo.setSelectedIndex(0);
1593 * clear pattern if it is now invalid for condition
1595 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1599 String pattern = patternField.getText().trim();
1600 if (pattern.length() > 0)
1602 Float.valueOf(pattern);
1604 } catch (NumberFormatException e)
1606 patternField.setText("");
1611 * restore the listener
1613 condCombo.addItemListener(listener);
1617 * Answers true unless a numeric condition has been selected with a
1618 * non-numeric value. Sets the value field to RED with a tooltip if in error.
1620 * If the pattern is expected but is empty, this method returns false, but
1621 * does not mark the field as invalid. This supports selecting an attribute
1622 * for a new condition before a match pattern has been entered.
1627 protected boolean validateFilter(JTextField value,
1628 JComboBox<Condition> condCombo)
1630 if (value == null || condCombo == null)
1632 return true; // fields not populated
1635 Condition cond = (Condition) condCombo.getSelectedItem();
1636 if (!cond.needsAPattern())
1641 value.setBackground(Color.white);
1642 value.setToolTipText("");
1643 String v1 = value.getText().trim();
1644 if (v1.length() == 0)
1649 if (cond.isNumeric() && v1.length() > 0)
1654 } catch (NumberFormatException e)
1656 value.setBackground(Color.red);
1657 value.setToolTipText(
1658 MessageManager.getString("label.numeric_required"));
1667 * Constructs a filter condition from the given input fields, and replaces the
1668 * condition at filterIndex with the new one. Does nothing if the pattern
1669 * field is blank (unless the match condition is one that doesn't require a
1670 * pattern, e.g. 'Is present'). Answers true if the filter was updated, else
1673 * This method may update the tooltip on the filter value field to show the
1674 * value range, if a numeric condition is selected. This ensures the tooltip
1675 * is updated when a numeric valued attribute is chosen on the last 'add a
1681 * @param filterIndex
1683 protected boolean updateFilter(JComboBox<String> attCombo,
1684 JComboBox<Condition> condCombo, JTextField valueField,
1687 String attName = (String) attCombo.getSelectedItem();
1688 Condition cond = (Condition) condCombo.getSelectedItem();
1689 String pattern = valueField.getText().trim();
1691 setNumericHints(attName, cond, valueField);
1693 if (pattern.length() == 0 && cond.needsAPattern())
1695 valueField.setEnabled(true); // ensure pattern field is enabled!
1700 * Construct a matcher that operates on Label, Score,
1701 * or named attribute
1703 FeatureMatcherI km = null;
1704 if (LABEL_18N.equals(attName))
1706 km = FeatureMatcher.byLabel(cond, pattern);
1708 else if (SCORE_18N.equals(attName))
1710 km = FeatureMatcher.byScore(cond, pattern);
1714 km = FeatureMatcher.byAttribute(cond, pattern,
1715 FeatureMatcher.fromAttributeDisplayName(attName));
1718 filters.set(filterIndex, km);
1724 * Action on any change to feature filtering, namely
1726 * <li>change of selected attribute</li>
1727 * <li>change of selected condition</li>
1728 * <li>change of match pattern</li>
1729 * <li>removal of a condition</li>
1731 * The inputs are parsed into a combined filter and this is set for the
1732 * feature type, and the alignment redrawn.
1734 protected void filtersChanged()
1737 * update the filter conditions for the feature type
1739 boolean anded = andFilters.isSelected();
1740 FeatureMatcherSetI combined = new FeatureMatcherSet();
1742 for (FeatureMatcherI filter : filters)
1744 String pattern = filter.getMatcher().getPattern();
1745 Condition condition = filter.getMatcher().getCondition();
1746 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1750 combined.and(filter);
1754 combined.or(filter);
1760 * save the filter conditions in the FeatureRenderer
1761 * (note this might now be an empty filter with no conditions)
1763 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1764 ap.paintAlignment(true, true);