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();
299 .setSelectedItem(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 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();
340 .setSelectedItem(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());
405 tabbedPane = new JTabbedPane();
406 this.add(tabbedPane, BorderLayout.CENTER);
409 * an ActionListener that applies colour changes
411 changeColourAction = new ActionListener()
414 public void actionPerformed(ActionEvent e)
421 * first tab: colour options
423 JPanel coloursPanel = initialiseColoursPanel();
424 tabbedPane.addTab(MessageManager.getString("action.colour"),
428 * second tab: filter options
430 JPanel filtersPanel = initialiseFiltersPanel();
431 tabbedPane.addTab(MessageManager.getString("label.filters"),
434 JPanel okCancelPanel = initialiseOkCancelPanel();
436 this.add(okCancelPanel, BorderLayout.SOUTH);
440 * Updates the min-max range if Colour By selected item is Score, or an
441 * attribute, with a min-max range
443 protected void updateColourMinMax()
445 if (!graduatedColour.isSelected())
450 String colourBy = (String) colourByRangeCombo.getSelectedItem();
451 float[] minMax = getMinMax(colourBy);
461 * Retrieves the min-max range:
463 * <li>of feature score, if colour or filter is by Score</li>
464 * <li>else of the selected attribute</li>
470 private float[] getMinMax(String attName)
472 float[] minMax = null;
473 if (SCORE_18N.equals(attName))
475 minMax = fr.getMinMax().get(featureType)[0];
479 // colour by attribute range
480 minMax = FeatureAttributes.getInstance().getMinMax(featureType,
481 fromAttributeDisplayName(attName));
487 * Lay out fields for graduated colour (by score or attribute value)
491 private JPanel initialiseGraduatedColourPanel()
493 JPanel graduatedColourPanel = new JPanel();
494 graduatedColourPanel.setLayout(
495 new BoxLayout(graduatedColourPanel, BoxLayout.Y_AXIS));
496 JvSwingUtils.createTitledBorder(graduatedColourPanel,
497 MessageManager.getString("label.graduated_colour"), true);
498 graduatedColourPanel.setBackground(Color.white);
501 * first row: graduated colour radio button, score/attribute drop-down
503 JPanel graduatedChoicePanel = new JPanel(
504 new FlowLayout(FlowLayout.LEFT));
505 graduatedChoicePanel.setBackground(Color.white);
506 graduatedColour = new JRadioButton(
507 MessageManager.getString("label.by_range_of") + COLON);
508 graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
509 graduatedColour.addItemListener(new ItemListener()
512 public void itemStateChanged(ItemEvent e)
514 if (graduatedColour.isSelected())
520 graduatedChoicePanel.add(graduatedColour);
522 List<String[]> attNames = FeatureAttributes.getInstance()
523 .getAttributes(featureType);
524 colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
525 colourByRangeCombo.addItemListener(new ItemListener()
528 public void itemStateChanged(ItemEvent e)
535 * disable graduated colour option if no range found
537 graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
539 graduatedChoicePanel.add(colourByRangeCombo);
540 graduatedColourPanel.add(graduatedChoicePanel);
543 * second row - min/max/no colours
545 JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
546 colourRangePanel.setBackground(Color.white);
547 graduatedColourPanel.add(colourRangePanel);
549 minColour.setFont(JvSwingUtils.getLabelFont());
550 minColour.setBorder(BorderFactory.createLineBorder(Color.black));
551 minColour.setPreferredSize(new Dimension(40, 20));
552 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
553 minColour.addMouseListener(new MouseAdapter()
556 public void mousePressed(MouseEvent e)
558 if (minColour.isEnabled())
560 showColourChooser(minColour, "label.select_colour_minimum_value");
565 maxColour.setFont(JvSwingUtils.getLabelFont());
566 maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
567 maxColour.setPreferredSize(new Dimension(40, 20));
568 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
569 maxColour.addMouseListener(new MouseAdapter()
572 public void mousePressed(MouseEvent e)
574 if (maxColour.isEnabled())
576 showColourChooser(maxColour, "label.select_colour_maximum_value");
580 maxColour.setBorder(new LineBorder(Color.black));
583 * default max colour to current colour (if a plain colour),
584 * or to Black if colour by label; make min colour a pale
585 * version of max colour
587 FeatureColourI fc = fr.getFeatureColours().get(featureType);
588 Color bg = fc.isSimpleColour() ? fc.getColour() : Color.BLACK;
589 maxColour.setBackground(bg);
590 minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
592 noValueCombo = new JComboBox<>();
593 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
594 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
595 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
596 noValueCombo.addItemListener(new ItemListener()
599 public void itemStateChanged(ItemEvent e)
605 JLabel minText = new JLabel(
606 MessageManager.getString("label.min_value") + COLON);
607 minText.setFont(JvSwingUtils.getLabelFont());
608 JLabel maxText = new JLabel(
609 MessageManager.getString("label.max_value") + COLON);
610 maxText.setFont(JvSwingUtils.getLabelFont());
611 JLabel noText = new JLabel(
612 MessageManager.getString("label.no_value") + COLON);
613 noText.setFont(JvSwingUtils.getLabelFont());
615 colourRangePanel.add(minText);
616 colourRangePanel.add(minColour);
617 colourRangePanel.add(maxText);
618 colourRangePanel.add(maxColour);
619 colourRangePanel.add(noText);
620 colourRangePanel.add(noValueCombo);
623 * third row - threshold options and value
625 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
626 thresholdPanel.setBackground(Color.white);
627 graduatedColourPanel.add(thresholdPanel);
629 threshold.addActionListener(changeColourAction);
630 threshold.setToolTipText(MessageManager
631 .getString("label.threshold_feature_display_by_score"));
632 threshold.addItem(MessageManager
633 .getString("label.threshold_feature_no_threshold")); // index 0
634 threshold.addItem(MessageManager
635 .getString("label.threshold_feature_above_threshold")); // index 1
636 threshold.addItem(MessageManager
637 .getString("label.threshold_feature_below_threshold")); // index 2
639 thresholdValue.addActionListener(new ActionListener()
642 public void actionPerformed(ActionEvent e)
644 thresholdValue_actionPerformed();
647 thresholdValue.addFocusListener(new FocusAdapter()
650 public void focusLost(FocusEvent e)
652 thresholdValue_actionPerformed();
655 slider.setPaintLabels(false);
656 slider.setPaintTicks(true);
657 slider.setBackground(Color.white);
658 slider.setEnabled(false);
659 slider.setOpaque(false);
660 slider.setPreferredSize(new Dimension(100, 32));
661 slider.setToolTipText(
662 MessageManager.getString("label.adjust_threshold"));
664 slider.addChangeListener(new ChangeListener()
667 public void stateChanged(ChangeEvent evt)
672 .setText(String.valueOf(slider.getValue() / scaleFactor));
673 sliderValueChanged();
677 slider.addMouseListener(new MouseAdapter()
680 public void mouseReleased(MouseEvent evt)
683 * only update Overview and/or structure colouring
684 * when threshold slider drag ends (mouse up)
688 ap.paintAlignment(true, true);
693 thresholdValue.setEnabled(false);
694 thresholdValue.setColumns(7);
696 thresholdPanel.add(threshold);
697 thresholdPanel.add(slider);
698 thresholdPanel.add(thresholdValue);
700 thresholdIsMin.setBackground(Color.white);
702 .setText(MessageManager.getString("label.threshold_minmax"));
703 thresholdIsMin.setToolTipText(MessageManager
704 .getString("label.toggle_absolute_relative_display_threshold"));
705 thresholdIsMin.addActionListener(changeColourAction);
706 thresholdPanel.add(thresholdIsMin);
708 return graduatedColourPanel;
712 * Lay out OK and Cancel buttons
716 private JPanel initialiseOkCancelPanel()
718 JPanel okCancelPanel = new JPanel();
719 // okCancelPanel.setBackground(Color.white);
720 okCancelPanel.add(ok);
721 okCancelPanel.add(cancel);
722 return okCancelPanel;
726 * Lay out Colour options panel, containing
728 * <li>plain colour, with colour picker</li>
729 * <li>colour by text, with choice of Label or other attribute</li>
730 * <li>colour by range, of score or other attribute, when available</li>
735 private JPanel initialiseColoursPanel()
737 JPanel colourByPanel = new JPanel();
738 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
741 * simple colour radio button and colour picker
743 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
744 simpleColourPanel.setBackground(Color.white);
745 JvSwingUtils.createTitledBorder(simpleColourPanel,
746 MessageManager.getString("label.simple"), true);
747 colourByPanel.add(simpleColourPanel);
749 simpleColour = new JRadioButton(
750 MessageManager.getString("label.simple_colour"));
751 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
752 simpleColour.addItemListener(new ItemListener()
755 public void itemStateChanged(ItemEvent e)
757 if (simpleColour.isSelected() && !adjusting)
759 showColourChooser(singleColour, "label.select_colour");
765 singleColour.setFont(JvSwingUtils.getLabelFont());
766 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
767 singleColour.setPreferredSize(new Dimension(40, 20));
768 singleColour.addMouseListener(new MouseAdapter()
771 public void mousePressed(MouseEvent e)
773 if (simpleColour.isSelected())
775 showColourChooser(singleColour, "label.select_colour");
779 simpleColourPanel.add(simpleColour); // radio button
780 simpleColourPanel.add(singleColour); // colour picker button
783 * colour by text (category) radio button and drop-down choice list
785 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
786 byTextPanel.setBackground(Color.white);
787 JvSwingUtils.createTitledBorder(byTextPanel,
788 MessageManager.getString("label.colour_by_text"), true);
789 colourByPanel.add(byTextPanel);
790 byCategory = new JRadioButton(
791 MessageManager.getString("label.by_text_of") + COLON);
792 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
793 byCategory.addItemListener(new ItemListener()
796 public void itemStateChanged(ItemEvent e)
798 if (byCategory.isSelected())
804 byTextPanel.add(byCategory);
806 List<String[]> attNames = FeatureAttributes.getInstance()
807 .getAttributes(featureType);
808 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
809 colourByTextCombo.addItemListener(new ItemListener()
812 public void itemStateChanged(ItemEvent e)
817 byTextPanel.add(colourByTextCombo);
820 * graduated colour panel
822 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
823 colourByPanel.add(graduatedColourPanel);
826 * 3 radio buttons select between simple colour,
827 * by category (text), or graduated
829 ButtonGroup bg = new ButtonGroup();
830 bg.add(simpleColour);
832 bg.add(graduatedColour);
834 return colourByPanel;
837 private void showColourChooser(JPanel colourPanel, String key)
839 Color col = JColorChooser.showDialog(this,
840 MessageManager.getString(key), colourPanel.getBackground());
843 colourPanel.setBackground(col);
844 colourPanel.setForeground(col);
846 colourPanel.repaint();
851 * Constructs and sets the selected colour options as the colour for the feature
852 * type, and repaints the alignment, and optionally the Overview and/or
853 * structure viewer if open
855 * @param updateStructsAndOverview
857 void colourChanged(boolean updateStructsAndOverview)
862 * ignore action handlers while setting values programmatically
868 * ensure min-max range is for the latest choice of
869 * 'graduated colour by'
871 updateColourMinMax();
873 FeatureColourI acg = makeColourFromInputs();
876 * save the colour, and repaint stuff
878 fr.setColour(featureType, acg);
879 ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
885 * Converts the input values into an instance of FeatureColour
889 private FeatureColourI makeColourFromInputs()
892 * easiest case - a single colour
894 if (simpleColour.isSelected())
896 return new FeatureColour(singleColour.getBackground());
900 * next easiest case - colour by Label, or attribute text
902 if (byCategory.isSelected())
904 Color c = this.getBackground();
905 FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f);
906 fc.setColourByLabel(true);
907 String byWhat = (String) colourByTextCombo.getSelectedItem();
908 if (!LABEL_18N.equals(byWhat))
910 fc.setAttributeName(fromAttributeDisplayName(byWhat));
916 * remaining case - graduated colour by score, or attribute value
918 Color noColour = null;
919 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
921 noColour = minColour.getBackground();
923 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
925 noColour = maxColour.getBackground();
931 thresh = Float.valueOf(thresholdValue.getText());
932 } catch (NumberFormatException e)
934 // invalid inputs are already handled on entry
938 * min-max range is to (or from) threshold value if
939 * 'threshold is min/max' is selected
941 float minValue = min;
942 float maxValue = max;
943 final int thresholdOption = threshold.getSelectedIndex();
944 if (thresholdIsMin.isSelected()
945 && thresholdOption == ABOVE_THRESHOLD_OPTION)
949 if (thresholdIsMin.isSelected()
950 && thresholdOption == BELOW_THRESHOLD_OPTION)
956 * make the graduated colour
958 FeatureColourI fc = new FeatureColour(minColour.getBackground(),
959 maxColour.getBackground(), noColour, minValue, maxValue);
962 * set attribute to colour by if selected
964 String byWhat = (String) colourByRangeCombo.getSelectedItem();
965 if (!SCORE_18N.equals(byWhat))
967 fc.setAttributeName(fromAttributeDisplayName(byWhat));
971 * set threshold options and 'autoscaled' which is
972 * false if 'threshold is min/max' is selected
973 * else true (colour range is on actual range of values)
975 fc.setThreshold(thresh);
976 fc.setAutoScaled(!thresholdIsMin.isSelected());
977 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
978 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
980 if (threshline == null)
983 * todo not yet implemented: visual indication of feature threshold
985 threshline = new GraphLine((max - min) / 2f, "Threshold",
993 * A helper method that converts a 'compound' attribute name from its display
994 * form, e.g. CSQ:PolyPhen to array form, e.g. { "CSQ", "PolyPhen" }
999 private String[] fromAttributeDisplayName(String attribute)
1001 return attribute == null ? null : attribute.split(COLON);
1005 * A helper method that converts a 'compound' attribute name to its display
1006 * form, e.g. CSQ:PolyPhen from its array form, e.g. { "CSQ", "PolyPhen" }
1011 private String toAttributeDisplayName(String[] attName)
1013 return attName == null ? "" : String.join(COLON, attName);
1017 protected void raiseClosed()
1019 if (this.featureSettings != null)
1021 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
1026 * Action on OK is just to dismiss the dialog - any changes have already been
1030 public void okPressed()
1035 * Action on Cancel is to restore colour scheme and filters as they were when
1036 * the dialog was opened
1039 public void cancelPressed()
1041 fr.setColour(featureType, originalColour);
1042 fr.setFeatureFilter(featureType, originalFilter);
1043 ap.paintAlignment(true, true);
1047 * Action on text entry of a threshold value
1049 protected void thresholdValue_actionPerformed()
1054 float f = Float.parseFloat(thresholdValue.getText());
1055 slider.setValue((int) (f * scaleFactor));
1056 threshline.value = f;
1057 thresholdValue.setBackground(Color.white); // ok
1060 * force repaint of any Overview window or structure
1062 ap.paintAlignment(true, true);
1063 } catch (NumberFormatException ex)
1065 thresholdValue.setBackground(Color.red); // not ok
1073 * Action on change of threshold slider value. This may be done interactively
1074 * (by moving the slider), or programmatically (to update the slider after
1075 * manual input of a threshold value).
1077 protected void sliderValueChanged()
1079 threshline.value = getRoundedSliderValue();
1082 * repaint alignment, but not Overview or structure,
1083 * to avoid overload while dragging the slider
1085 colourChanged(false);
1089 * Converts the slider value to its absolute value by dividing by the
1090 * scaleFactor. Rounding errors are squashed by forcing min/max of slider range
1091 * to the actual min/max of feature score range
1095 private float getRoundedSliderValue()
1097 int value = slider.getValue();
1098 float f = value == slider.getMaximum() ? max
1099 : (value == slider.getMinimum() ? min : value / scaleFactor);
1103 void addActionListener(ActionListener listener)
1105 if (featureSettings != null)
1108 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1110 featureSettings = listener;
1114 * A helper method to build the drop-down choice of attributes for a feature. If
1115 * 'withRange' is true, then Score, and any attributes with a min-max range, are
1116 * added. If 'withText' is true, Label and any known attributes are added. This
1117 * allows 'categorical numerical' attributes e.g. codon position to be coloured
1120 * Where metadata is available with a description for an attribute, that is
1121 * added as a tooltip.
1123 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1124 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1126 * This method does not add any ActionListener to the JComboBox.
1132 protected JComboBox<String> populateAttributesDropdown(
1133 List<String[]> attNames, boolean withRange, boolean withText)
1135 List<String> displayAtts = new ArrayList<>();
1136 List<String> tooltips = new ArrayList<>();
1140 displayAtts.add(LABEL_18N);
1141 tooltips.add(MessageManager.getString("label.description"));
1145 float[][] minMax = fr.getMinMax().get(featureType);
1146 if (minMax != null && minMax[0][0] != minMax[0][1])
1148 displayAtts.add(SCORE_18N);
1149 tooltips.add(SCORE_18N);
1153 FeatureAttributes fa = FeatureAttributes.getInstance();
1154 for (String[] attName : attNames)
1156 float[] minMax = fa.getMinMax(featureType, attName);
1157 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1158 if (!withText && !hasRange)
1162 displayAtts.add(toAttributeDisplayName(attName));
1163 String desc = fa.getDescription(featureType, attName);
1164 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1166 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1168 tooltips.add(desc == null ? "" : desc);
1171 JComboBox<String> attCombo = JvSwingUtils
1172 .buildComboWithTooltips(displayAtts, tooltips);
1178 * Populates initial layout of the feature attribute filters panel
1180 private JPanel initialiseFiltersPanel()
1182 filters = new ArrayList<>();
1184 JPanel filtersPanel = new JPanel();
1185 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1186 filtersPanel.setBackground(Color.white);
1187 JvSwingUtils.createTitledBorder(filtersPanel,
1188 MessageManager.getString("label.filters"), true);
1190 JPanel andOrPanel = initialiseAndOrPanel();
1191 filtersPanel.add(andOrPanel);
1194 * panel with filters - populated by refreshFiltersDisplay,
1195 * which also sets the layout manager
1197 chooseFiltersPanel = new JPanel();
1198 chooseFiltersPanel.setBackground(Color.white);
1199 filtersPanel.add(chooseFiltersPanel);
1201 return filtersPanel;
1205 * Lays out the panel with radio buttons to AND or OR filter conditions
1209 private JPanel initialiseAndOrPanel()
1211 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1212 andOrPanel.setBackground(Color.white);
1213 andOrPanel.setBorder(BorderFactory.createLineBorder(debugBorderColour));
1214 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1215 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1216 ActionListener actionListener = new ActionListener()
1219 public void actionPerformed(ActionEvent e)
1224 andFilters.addActionListener(actionListener);
1225 orFilters.addActionListener(actionListener);
1226 ButtonGroup andOr = new ButtonGroup();
1227 andOr.add(andFilters);
1228 andOr.add(orFilters);
1229 andFilters.setSelected(true);
1231 new JLabel(MessageManager.getString("label.join_conditions")));
1232 andOrPanel.add(andFilters);
1233 andOrPanel.add(orFilters);
1238 * Refreshes the display to show any filters currently configured for the
1239 * selected feature type (editable, with 'remove' option), plus one extra row
1240 * for adding a condition. This should be called after a filter has been
1241 * removed, added or amended.
1243 private void updateFiltersTab()
1246 * clear the panel and list of filter conditions
1248 chooseFiltersPanel.removeAll();
1252 * look up attributes known for feature type
1254 List<String[]> attNames = FeatureAttributes.getInstance()
1255 .getAttributes(featureType);
1258 * if this feature type has filters set, load them first
1260 FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
1261 if (featureFilters != null)
1263 if (!featureFilters.isAnded())
1265 orFilters.setSelected(true);
1267 featureFilters.getMatchers().forEach(matcher -> filters.add(matcher));
1271 * and an empty filter for the user to populate (add)
1273 filters.add(FeatureMatcher.NULL_MATCHER);
1276 * use GridLayout to 'justify' rows to the top of the panel, until
1277 * there are too many to fit in, then fall back on BoxLayout
1279 if (filters.size() <= 5)
1281 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1285 chooseFiltersPanel.setLayout(
1286 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1290 * render the conditions in rows, each in its own JPanel
1292 int filterIndex = 0;
1293 for (FeatureMatcherI filter : filters)
1295 JPanel row = addFilter(filter, attNames, filterIndex);
1296 row.setBorder(BorderFactory.createLineBorder(debugBorderColour));
1297 chooseFiltersPanel.add(row);
1306 * A helper method that constructs a row (panel) with one filter condition:
1308 * <li>a drop-down list of Label, Score and attribute names to choose from</li>
1309 * <li>a drop-down list of conditions to choose from</li>
1310 * <li>a text field for input of a match pattern</li>
1311 * <li>optionally, a 'remove' button</li>
1313 * The filter values are set as defaults for the input fields. The 'remove'
1314 * button is added unless the pattern is empty (incomplete filter condition).
1316 * Action handlers on these fields provide for
1318 * <li>validate pattern field - should be numeric if condition is numeric</li>
1319 * <li>save filters and refresh display on any (valid) change</li>
1320 * <li>remove filter and refresh on 'Remove'</li>
1321 * <li>update conditions list on change of Label/Score/Attribute</li>
1322 * <li>refresh value field tooltip with min-max range on change of
1328 * @param filterIndex
1331 protected JPanel addFilter(FeatureMatcherI filter,
1332 List<String[]> attNames, int filterIndex)
1334 String[] attName = filter.getAttribute();
1335 Condition cond = filter.getMatcher().getCondition();
1336 String pattern = filter.getMatcher().getPattern();
1338 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1339 filterRow.setBackground(Color.white);
1342 * drop-down choice of attribute, with description as a tooltip
1343 * if we can obtain it
1345 final JComboBox<String> attCombo = populateAttributesDropdown(attNames,
1347 String filterBy = setSelectedAttribute(attCombo, filter);
1349 JComboBox<Condition> condCombo = new JComboBox<>();
1351 JTextField patternField = new JTextField(8);
1352 patternField.setText(pattern);
1355 * action handlers that validate and (if valid) apply changes
1357 ActionListener actionListener = new ActionListener()
1360 public void actionPerformed(ActionEvent e)
1362 if (validateFilter(patternField, condCombo))
1364 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1371 ItemListener itemListener = new ItemListener()
1374 public void itemStateChanged(ItemEvent e)
1376 actionListener.actionPerformed(null);
1380 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1382 attCombo.setSelectedIndex(0);
1386 attCombo.setSelectedItem(toAttributeDisplayName(attName));
1388 attCombo.addItemListener(new ItemListener()
1391 public void itemStateChanged(ItemEvent e)
1394 * on change of attribute, refresh the conditions list to
1395 * ensure it is appropriate for the attribute datatype
1397 populateConditions((String) attCombo.getSelectedItem(),
1398 (Condition) condCombo.getSelectedItem(), condCombo,
1400 actionListener.actionPerformed(null);
1404 filterRow.add(attCombo);
1407 * drop-down choice of test condition
1409 populateConditions(filterBy, cond, condCombo, patternField);
1410 condCombo.setPreferredSize(new Dimension(150, 20));
1411 condCombo.addItemListener(itemListener);
1412 filterRow.add(condCombo);
1415 * pattern to match against
1417 patternField.addActionListener(actionListener);
1418 patternField.addFocusListener(new FocusAdapter()
1421 public void focusLost(FocusEvent e)
1423 actionListener.actionPerformed(null);
1426 filterRow.add(patternField);
1429 * disable pattern field for condition 'Present / NotPresent'
1431 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1432 if (!selectedCondition.needsAPattern())
1434 patternField.setEnabled(false);
1438 * if a numeric condition is selected, show the value range
1439 * as a tooltip on the value input field
1441 setPatternTooltip(filterBy, selectedCondition, patternField);
1444 * add remove button if filter is populated (non-empty pattern)
1446 if (!patternField.isEnabled()
1447 || (pattern != null && pattern.trim().length() > 0))
1449 // todo: gif for button drawing '-' or 'x'
1450 JButton removeCondition = new BasicArrowButton(SwingConstants.WEST);
1452 .setToolTipText(MessageManager.getString("label.delete_row"));
1453 removeCondition.addActionListener(new ActionListener()
1456 public void actionPerformed(ActionEvent e)
1458 filters.remove(filterIndex);
1462 filterRow.add(removeCondition);
1469 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1475 private String setSelectedAttribute(JComboBox<String> attCombo,
1476 FeatureMatcherI filter)
1479 if (filter.isByScore())
1483 else if (filter.isByLabel())
1489 item = toAttributeDisplayName(filter.getAttribute());
1491 attCombo.setSelectedItem(item);
1496 * If a numeric comparison condition is selected, retrieve the min-max range for
1497 * the value (score or attribute), and set it as a tooltip on the value file
1500 * @param selectedCondition
1501 * @param patternField
1503 private void setPatternTooltip(String attName,
1504 Condition selectedCondition, JTextField patternField)
1506 patternField.setToolTipText("");
1508 if (selectedCondition.isNumeric())
1510 float[] minMax = getMinMax(attName);
1513 String tip = String.format("(%s - %s)",
1514 DECFMT_2_2.format(minMax[0]), DECFMT_2_2.format(minMax[1]));
1515 patternField.setToolTipText(tip);
1521 * Populates the drop-down list of comparison conditions for the given attribute
1522 * name. The conditions added depend on the datatype of the attribute values.
1523 * The supplied condition is set as the selected item in the list, provided it
1524 * is in the list. If the pattern is now invalid (non-numeric pattern for a
1525 * numeric condition), it is cleared.
1530 * @param patternField
1532 private void populateConditions(String attName, Condition cond,
1533 JComboBox<Condition> condCombo, JTextField patternField)
1535 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1536 fromAttributeDisplayName(attName));
1537 if (LABEL_18N.equals(attName))
1539 type = Datatype.Character;
1541 else if (SCORE_18N.equals(attName))
1543 type = Datatype.Number;
1547 * remove itemListener before starting
1549 ItemListener listener = condCombo.getItemListeners()[0];
1550 condCombo.removeItemListener(listener);
1551 boolean condIsValid = false;
1552 condCombo.removeAllItems();
1553 for (Condition c : Condition.values())
1555 if ((c.isNumeric() && type != Datatype.Character)
1556 || (!c.isNumeric() && type != Datatype.Number))
1558 condCombo.addItem(c);
1567 * set the selected condition (does nothing if not in the list)
1571 condCombo.setSelectedItem(cond);
1575 condCombo.setSelectedIndex(0);
1578 condCombo.addItemListener(listener);
1581 * clear pattern if it is now invalid for condition
1583 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1587 String pattern = patternField.getText().trim();
1588 if (pattern.length() > 0)
1590 Float.valueOf(pattern);
1592 } catch (NumberFormatException e)
1594 patternField.setText("");
1600 * Answers true unless a numeric condition has been selected with a non-numeric
1601 * value. Sets the value field to RED with a tooltip if in error.
1603 * If the pattern is expected but is empty, this method returns false, but does
1604 * not mark the field as invalid. This supports selecting an attribute for a new
1605 * condition before a match pattern has been entered.
1610 protected boolean validateFilter(JTextField value,
1611 JComboBox<Condition> condCombo)
1613 if (value == null || condCombo == null)
1615 return true; // fields not populated
1618 Condition cond = (Condition) condCombo.getSelectedItem();
1619 if (!cond.needsAPattern())
1624 value.setBackground(Color.white);
1625 value.setToolTipText("");
1626 String v1 = value.getText().trim();
1627 if (v1.length() == 0)
1632 if (cond.isNumeric() && v1.length() > 0)
1637 } catch (NumberFormatException e)
1639 value.setBackground(Color.red);
1640 value.setToolTipText(
1641 MessageManager.getString("label.numeric_required"));
1650 * Constructs a filter condition from the given input fields, and replaces the
1651 * condition at filterIndex with the new one. Does nothing if the pattern field
1652 * is blank (unless the match condition is one that doesn't require a pattern,
1653 * e.g. 'Is present'). Answers true if the filter was updated, else false.
1655 * This method may update the tooltip on the filter value field to show the
1656 * value range, if a numeric condition is selected. This ensures the tooltip is
1657 * updated when a numeric valued attribute is chosen on the last 'add a filter'
1663 * @param filterIndex
1665 protected boolean updateFilter(JComboBox<String> attCombo,
1666 JComboBox<Condition> condCombo, JTextField valueField,
1669 String attName = (String) attCombo.getSelectedItem();
1670 Condition cond = (Condition) condCombo.getSelectedItem();
1671 String pattern = valueField.getText().trim();
1673 setPatternTooltip(attName, cond, valueField);
1675 if (pattern.length() == 0 && cond.needsAPattern())
1681 * Construct a matcher that operates on Label, Score,
1682 * or named attribute
1684 FeatureMatcherI km = null;
1685 if (LABEL_18N.equals(attName))
1687 km = FeatureMatcher.byLabel(cond, pattern);
1689 else if (SCORE_18N.equals(attName))
1691 km = FeatureMatcher.byScore(cond, pattern);
1695 km = FeatureMatcher.byAttribute(cond, pattern,
1696 fromAttributeDisplayName(attName));
1699 filters.set(filterIndex, km);
1705 * Makes the dialog visible, at the Feature Colour tab or at the Filters tab
1709 public void showTab(boolean coloursTab)
1712 tabbedPane.setSelectedIndex(coloursTab ? 0 : 1);
1716 * Action on any change to feature filtering, namely
1718 * <li>change of selected attribute</li>
1719 * <li>change of selected condition</li>
1720 * <li>change of match pattern</li>
1721 * <li>removal of a condition</li>
1723 * The inputs are parsed into a combined filter and this is set for the feature
1724 * type, and the alignment redrawn.
1726 protected void filtersChanged()
1729 * update the filter conditions for the feature type
1731 boolean anded = andFilters.isSelected();
1732 FeatureMatcherSetI combined = new FeatureMatcherSet();
1734 for (FeatureMatcherI filter : filters)
1736 String pattern = filter.getMatcher().getPattern();
1737 Condition condition = filter.getMatcher().getCondition();
1738 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1742 combined.and(filter);
1746 combined.or(filter);
1752 * save the filter conditions in the FeatureRenderer
1753 * (note this might now be an empty filter with no conditions)
1755 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1756 ap.paintAlignment(true, true);