X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureTypeSettings.java;h=0dd0f1fac020178b4795632409e08fd0fe64a09a;hb=9fcb12165750b20f8a73d0bb976b22be5fda94a2;hp=43a9e6a84d03d72235c028bd1f2b885a7f485403;hpb=6bb0b7e5af42a340f9b9778e6f0ebb8b0d04f32e;p=jalview.git diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java index 43a9e6a..0dd0f1f 100644 --- a/src/jalview/gui/FeatureTypeSettings.java +++ b/src/jalview/gui/FeatureTypeSettings.java @@ -29,6 +29,8 @@ import jalview.datamodel.features.FeatureMatcher; import jalview.datamodel.features.FeatureMatcherI; import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; +import jalview.io.gff.SequenceOntologyFactory; +import jalview.io.gff.SequenceOntologyI; import jalview.schemes.FeatureColour; import jalview.util.ColorUtils; import jalview.util.MessageManager; @@ -49,7 +51,11 @@ import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.text.DecimalFormat; import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; import java.util.List; +import java.util.Map; +import java.util.Map.Entry; import javax.swing.BorderFactory; import javax.swing.BoxLayout; @@ -118,10 +124,11 @@ public class FeatureTypeSettings extends JalviewDialog /* * the colour and filters to reset to on Cancel + * (including feature sub-types if modified) */ - private final FeatureColourI originalColour; + private Map originalColours; - private final FeatureMatcherSetI originalFilter; + private Map originalFilters; /* * set flag to true when setting values programmatically, @@ -206,6 +213,26 @@ public class FeatureTypeSettings extends JalviewDialog private JPanel chooseFiltersPanel; + /* + * the root Sequence Ontology terms (if any) that is a parent of + * the current feature type + */ + private String rootSOTerm; + + /* + * feature types present in Feature Renderer which have the same Sequence + * Ontology root parent as the one this editor is acting on + */ + private final List peerSoTerms; + + /* + * if true, filter or colour settings are also applied to + * any sub-types of rootSOTerm in the Sequence Ontology + */ + private boolean applyFiltersToSubtypes; + + private boolean applyColourToSubtypes; + /** * Constructor * @@ -217,11 +244,25 @@ public class FeatureTypeSettings extends JalviewDialog this.fr = frender; this.featureType = theType; ap = fr.ap; - originalFilter = fr.getFeatureFilter(theType); - originalColour = fr.getFeatureColours().get(theType); - + + peerSoTerms = findSequenceOntologyPeers(this.featureType); + + /* + * save original colours and filters for this feature type + * and any sub-types, to restore on Cancel + */ + originalFilters = new HashMap<>(); + originalFilters.put(theType, fr.getFeatureFilter(theType)); + originalColours = new HashMap<>(); + originalColours.put(theType, fr.getFeatureColours().get(theType)); + for (String child : peerSoTerms) + { + originalFilters.put(child, fr.getFeatureFilter(child)); + originalColours.put(child, fr.getFeatureColours().get(child)); + } + adjusting = true; - + try { initialise(); @@ -230,24 +271,62 @@ public class FeatureTypeSettings extends JalviewDialog ex.printStackTrace(); return; } - + updateColoursTab(); - + updateFiltersTab(); - + adjusting = false; - + colourChanged(false); - + String title = MessageManager .formatMessage("label.display_settings_for", new String[] { theType }); - initDialogFrame(this, true, false, title, 500, 500); - + initDialogFrame(this, true, false, title, 580, 500); waitForInput(); } /** + * Answers a (possibly empty) list of feature types known to the Feature + * Renderer which share a top level Sequence Ontology parent with the current + * feature type. The current type is not included. + * + * @return + */ + protected List findSequenceOntologyPeers(String featureType) + { + List peers = new ArrayList<>(); + + /* + * first find the SO term (if any) that is the root + * parent of the current type + */ + SequenceOntologyI so = SequenceOntologyFactory.getInstance(); + List roots = so.getRootParents(featureType); + if (roots == null || roots.size() > 1) + { + /* + * feature type is not an SO term, or has ambiguous root + */ + return peers; + } + rootSOTerm = roots.get(0); + + List types = fr.getRenderOrder(); + for (String type : types) + { + if (!type.equals(featureType) && so.isA(type, rootSOTerm)) + { + peers.add(type); + } + + } + Collections.sort(peers); // sort for ease of reading in tooltip + return peers; + } + + /** * Configures the widgets on the Colours tab according to the current feature * colour scheme */ @@ -366,8 +445,7 @@ public class FeatureTypeSettings extends JalviewDialog : BELOW_THRESHOLD_OPTION); slider.setEnabled(true); slider.setValue((int) (fc.getThreshold() * scaleFactor)); - float roundedSliderValue = getRoundedSliderValue(); - thresholdValue.setText(String.valueOf(fc.getThreshold()));// roundedSliderValue)); + thresholdValue.setText(String.valueOf(fc.getThreshold())); thresholdValue.setEnabled(true); thresholdIsMin.setEnabled(true); } @@ -564,13 +642,21 @@ public class FeatureTypeSettings extends JalviewDialog maxColour.setBorder(new LineBorder(Color.black)); /* - * default max colour to last plain colour; - * make min colour a pale version of max colour + * if not set, default max colour to last plain colour, + * and make min colour a pale version of max colour */ - FeatureColourI fc = fr.getFeatureColours().get(featureType); - Color bg = fc.getColour() == null ? Color.BLACK : fc.getColour(); - maxColour.setBackground(bg); - minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f)); + FeatureColourI originalColour = originalColours.get(featureType); + Color max = originalColour.getMaxColour(); + if (max == null) + { + max = originalColour.getColour(); + minColour.setBackground(ColorUtils.bleachColour(max, 0.9f)); + } + else + { + maxColour.setBackground(max); + minColour.setBackground(originalColour.getMinColour()); + } noValueCombo = new JComboBox<>(); noValueCombo.addItem(MessageManager.getString("label.no_colour")); @@ -653,6 +739,7 @@ public class FeatureTypeSettings extends JalviewDialog { thresholdValue .setText(String.valueOf(slider.getValue() / scaleFactor)); + thresholdValue.setBackground(Color.white); // to reset red for invalid sliderValueChanged(); } } @@ -724,6 +811,15 @@ public class FeatureTypeSettings extends JalviewDialog MessageManager.getString("action.colour"), true); /* + * option to apply colour to peer types as well (if there are any) + */ + if (!peerSoTerms.isEmpty()) + { + applyColourToSubtypes = false; + colourByPanel.add(initSubtypesPanel(false)); + } + + /* * simple colour radio button and colour picker */ JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); @@ -748,16 +844,10 @@ public class FeatureTypeSettings extends JalviewDialog singleColour.setFont(JvSwingUtils.getLabelFont()); singleColour.setBorder(BorderFactory.createLineBorder(Color.black)); singleColour.setPreferredSize(new Dimension(40, 20)); - if (originalColour.isGraduatedColour()) - { - singleColour.setBackground(originalColour.getMaxColour()); - singleColour.setForeground(originalColour.getMaxColour()); - } - else - { - singleColour.setBackground(originalColour.getColour()); - singleColour.setForeground(originalColour.getColour()); - } + FeatureColourI originalColour = originalColours.get(featureType); + singleColour.setBackground(originalColour.getColour()); + singleColour.setForeground(originalColour.getColour()); + singleColour.addMouseListener(new MouseAdapter() { @Override @@ -827,6 +917,46 @@ public class FeatureTypeSettings extends JalviewDialog return colourByPanel; } + /** + * Constructs and returns a panel with a checkbox for the option to apply any + * changes also to sub-types of the feature type + * + * @return + */ + protected JPanel initSubtypesPanel(final boolean forFilters) + { + JPanel toSubtypes = new JPanel(new FlowLayout(FlowLayout.LEFT)); + toSubtypes.setBackground(Color.WHITE); + JCheckBox applyToSubtypesCB = new JCheckBox(MessageManager + .formatMessage("label.apply_to_subtypes", rootSOTerm)); + applyToSubtypesCB.setToolTipText(getSubtypesTooltip()); + applyToSubtypesCB.addActionListener(new ActionListener() + { + /* + * reset and reapply settings on toggle of checkbox + */ + @Override + public void actionPerformed(ActionEvent e) + { + if (forFilters) + { + applyFiltersToSubtypes = applyToSubtypesCB.isSelected(); + restoreOriginalFilters(); + filtersChanged(); + } + else + { + applyColourToSubtypes = applyToSubtypesCB.isSelected(); + restoreOriginalColours(); + colourChanged(true); + } + } + }); + toSubtypes.add(applyToSubtypesCB); + + return toSubtypes; + } + private void showColourChooser(JPanel colourPanel, String key) { Color col = JColorChooser.showDialog(this, @@ -866,9 +996,17 @@ public class FeatureTypeSettings extends JalviewDialog FeatureColourI acg = makeColourFromInputs(); /* - * save the colour, and repaint stuff + * save the colour, and set on subtypes if selected */ fr.setColour(featureType, acg); + if (applyColourToSubtypes) + { + for (String child : peerSoTerms) + { + fr.setColour(child, acg); + } + } + refreshFeatureSettings(); ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview); updateColoursTab(); @@ -882,42 +1020,9 @@ public class FeatureTypeSettings extends JalviewDialog private FeatureColourI makeColourFromInputs() { /* - * easiest case - a single colour - */ - if (simpleColour.isSelected()) - { - return new FeatureColour(singleColour.getBackground()); - } - - /* - * next easiest case - colour by Label, or attribute text - */ - if (byCategory.isSelected()) - { - Color c = singleColour.getBackground(); - FeatureColourI fc = new FeatureColour(c); - fc.setColourByLabel(true); - String byWhat = (String) colourByTextCombo.getSelectedItem(); - if (!LABEL_18N.equals(byWhat)) - { - fc.setAttributeName( - FeatureMatcher.fromAttributeDisplayName(byWhat)); - } - return fc; - } - - /* - * remaining case - graduated colour by score, or attribute value + * min-max range is to (or from) threshold value if + * 'threshold is min/max' is selected */ - Color noColour = null; - if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION) - { - noColour = minColour.getBackground(); - } - else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION) - { - noColour = maxColour.getBackground(); - } float thresh = 0f; try @@ -927,11 +1032,6 @@ public class FeatureTypeSettings extends JalviewDialog { // invalid inputs are already handled on entry } - - /* - * min-max range is to (or from) threshold value if - * 'threshold is min/max' is selected - */ float minValue = min; float maxValue = max; final int thresholdOption = threshold.getSelectedIndex(); @@ -945,14 +1045,50 @@ public class FeatureTypeSettings extends JalviewDialog { maxValue = thresh; } + Color noColour = null; + if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION) + { + noColour = minColour.getBackground(); + } + else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION) + { + noColour = maxColour.getBackground(); + } + + /* + * construct a colour that 'remembers' all the options, including + * those not currently selected + */ + FeatureColourI fc = new FeatureColour(singleColour.getBackground(), + minColour.getBackground(), maxColour.getBackground(), noColour, + minValue, maxValue); /* - * make the graduated colour + * easiest case - a single colour */ - FeatureColourI fc = new FeatureColour(minColour.getBackground(), - maxColour.getBackground(), noColour, minValue, maxValue); + if (simpleColour.isSelected()) + { + ((FeatureColour) fc).setGraduatedColour(false); + return fc; + } /* + * next easiest case - colour by Label, or attribute text + */ + if (byCategory.isSelected()) + { + fc.setColourByLabel(true); + String byWhat = (String) colourByTextCombo.getSelectedItem(); + if (!LABEL_18N.equals(byWhat)) + { + fc.setAttributeName( + FeatureMatcher.fromAttributeDisplayName(byWhat)); + } + return fc; + } + + /* + * remaining case - graduated colour by score, or attribute value; * set attribute to colour by if selected */ String byWhat = (String) colourByRangeCombo.getSelectedItem(); @@ -986,9 +1122,14 @@ public class FeatureTypeSettings extends JalviewDialog @Override protected void raiseClosed() { + refreshFeatureSettings(); + } + + protected void refreshFeatureSettings() + { if (this.featureSettings != null) { - featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED")); + featureSettings.actionPerformed(new ActionEvent(this, 0, "REFRESH")); } } @@ -1003,16 +1144,34 @@ public class FeatureTypeSettings extends JalviewDialog /** * Action on Cancel is to restore colour scheme and filters as they were when - * the dialog was opened + * the dialog was opened (including any feature sub-types that may have been + * changed) */ @Override public void cancelPressed() { - fr.setColour(featureType, originalColour); - fr.setFeatureFilter(featureType, originalFilter); + restoreOriginalColours(); + restoreOriginalFilters(); ap.paintAlignment(true, true); } + protected void restoreOriginalFilters() + { + for (Entry entry : originalFilters + .entrySet()) + { + fr.setFeatureFilter(entry.getKey(), entry.getValue()); + } + } + + protected void restoreOriginalColours() + { + for (Entry entry : originalColours.entrySet()) + { + fr.setColour(entry.getKey(), entry.getValue()); + } + } + /** * Action on text entry of a threshold value */ @@ -1026,7 +1185,7 @@ public class FeatureTypeSettings extends JalviewDialog */ adjusting = true; float f = Float.parseFloat(thresholdValue.getText()); - f = Float.max(f, this.min); + f = Float.max(f, this.min); f = Float.min(f, this.max); thresholdValue.setText(String.valueOf(f)); slider.setValue((int) (f * scaleFactor)); @@ -1153,11 +1312,25 @@ public class FeatureTypeSettings extends JalviewDialog { filters = new ArrayList<>(); + JPanel outerPanel = new JPanel(); + outerPanel.setLayout(new BoxLayout(outerPanel, BoxLayout.Y_AXIS)); + outerPanel.setBackground(Color.white); + + /* + * option to apply colour to peer types as well (if there are any) + */ + if (!peerSoTerms.isEmpty()) + { + applyFiltersToSubtypes = false; + outerPanel.add(initSubtypesPanel(true)); + } + JPanel filtersPanel = new JPanel(); filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS)); filtersPanel.setBackground(Color.white); JvSwingUtils.createTitledBorder(filtersPanel, MessageManager.getString("label.filters"), true); + outerPanel.add(filtersPanel); JPanel andOrPanel = initialiseAndOrPanel(); filtersPanel.add(andOrPanel); @@ -1170,7 +1343,7 @@ public class FeatureTypeSettings extends JalviewDialog chooseFiltersPanel.setBackground(Color.white); filtersPanel.add(chooseFiltersPanel); - return filtersPanel; + return outerPanel; } /** @@ -1180,8 +1353,9 @@ public class FeatureTypeSettings extends JalviewDialog */ private JPanel initialiseAndOrPanel() { - JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + JPanel andOrPanel = new JPanel(new BorderLayout()); andOrPanel.setBackground(Color.white); + andFilters = new JRadioButton(MessageManager.getString("label.and")); orFilters = new JRadioButton(MessageManager.getString("label.or")); ActionListener actionListener = new ActionListener() @@ -1202,10 +1376,29 @@ public class FeatureTypeSettings extends JalviewDialog new JLabel(MessageManager.getString("label.join_conditions"))); andOrPanel.add(andFilters); andOrPanel.add(orFilters); + return andOrPanel; } /** + * Builds a tooltip for the 'Apply to subtypes' checkbox with a list of + * subtypes of this feature type + * + * @return + */ + protected String getSubtypesTooltip() + { + StringBuilder sb = new StringBuilder(20 * peerSoTerms.size()); + sb.append(MessageManager.getString("label.apply_also_to")); + for (String child : peerSoTerms) + { + sb.append("
").append(child); + } + String tooltip = JvSwingUtils.wrapTooltip(true, sb.toString()); + return tooltip; + } + + /** * Refreshes the display to show any filters currently configured for the * selected feature type (editable, with 'remove' option), plus one extra row * for adding a condition. This should be called after a filter has been @@ -1739,6 +1932,15 @@ public class FeatureTypeSettings extends JalviewDialog * (note this might now be an empty filter with no conditions) */ fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined); + if (applyFiltersToSubtypes) + { + for (String child : peerSoTerms) + { + fr.setFeatureFilter(child, combined.isEmpty() ? null : combined); + } + } + + refreshFeatureSettings(); ap.paintAlignment(true, true); updateFiltersTab();