X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureTypeSettings.java;h=0dd0f1fac020178b4795632409e08fd0fe64a09a;hb=9fcb12165750b20f8a73d0bb976b22be5fda94a2;hp=e280091dd3b434204f739449301fad74d9b70fe2;hpb=e16e9699b56f3db4e42dc694aaafad76dae66c4b;p=jalview.git diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java index e280091..0dd0f1f 100644 --- a/src/jalview/gui/FeatureTypeSettings.java +++ b/src/jalview/gui/FeatureTypeSettings.java @@ -25,20 +25,22 @@ import jalview.api.FeatureColourI; import jalview.datamodel.GraphLine; import jalview.datamodel.features.FeatureAttributes; import jalview.datamodel.features.FeatureAttributes.Datatype; +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; import jalview.util.matcher.Condition; -import jalview.util.matcher.KeyedMatcher; -import jalview.util.matcher.KeyedMatcherI; -import jalview.util.matcher.KeyedMatcherSet; -import jalview.util.matcher.KeyedMatcherSetI; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.FlowLayout; -import java.awt.LayoutManager; +import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; @@ -47,8 +49,13 @@ import java.awt.event.ItemEvent; import java.awt.event.ItemListener; 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; @@ -61,7 +68,6 @@ import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.JSlider; -import javax.swing.JTabbedPane; import javax.swing.JTextField; import javax.swing.SwingConstants; import javax.swing.border.LineBorder; @@ -78,6 +84,12 @@ import javax.swing.plaf.basic.BasicArrowButton; */ public class FeatureTypeSettings extends JalviewDialog { + private final static String LABEL_18N = MessageManager + .getString("label.label"); + + private final static String SCORE_18N = MessageManager + .getString("label.score"); + private static final int RADIO_WIDTH = 130; private static final String COLON = ":"; @@ -94,10 +106,14 @@ public class FeatureTypeSettings extends JalviewDialog private static final int BELOW_THRESHOLD_OPTION = 2; + private static final DecimalFormat DECFMT_2_2 = new DecimalFormat( + "##.##"); + /* * FeatureRenderer holds colour scheme and filters for feature types */ - private final FeatureRenderer fr; // todo refactor to allow interface type here + private final FeatureRenderer fr; // todo refactor to allow interface type + // here /* * the view panel to update when settings change @@ -108,10 +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 KeyedMatcherSetI originalFilter; + private Map originalFilters; /* * set flag to true when setting values programmatically, @@ -119,10 +136,20 @@ public class FeatureTypeSettings extends JalviewDialog */ private boolean adjusting = false; + /* + * minimum of the value range for graduated colour + * (may be for feature score or for a numeric attribute) + */ private float min; + /* + * maximum of the value range for graduated colour + */ private float max; + /* + * scale factor for conversion between absolute min-max and slider + */ private float scaleFactor; /* @@ -135,7 +162,12 @@ public class FeatureTypeSettings extends JalviewDialog private JRadioButton graduatedColour = new JRadioButton(); - private JPanel singleColour = new JPanel(); + /** + * colours and filters are shown in tabbed view or single content pane + */ + JPanel coloursPanel, filtersPanel; + + JPanel singleColour = new JPanel(); private JPanel minColour = new JPanel(); @@ -177,42 +209,57 @@ public class FeatureTypeSettings extends JalviewDialog /* * filters for the currently selected feature type */ - private List filters; - - // set white normally, black to debug layout - private Color debugBorderColour = Color.white; + private List filters; private JPanel chooseFiltersPanel; - private JTabbedPane tabbedPane; + /* + * the root Sequence Ontology terms (if any) that is a parent of + * the current feature type + */ + private String rootSOTerm; - /** - * Constructor - * - * @param frender - * @param theType + /* + * feature types present in Feature Renderer which have the same Sequence + * Ontology root parent as the one this editor is acting on */ - public FeatureTypeSettings(FeatureRenderer frender, String theType) - { - this(frender, false, theType); - } + 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, with option to make a blocking dialog (has to complete in the - * AWT event queue thread). Currently this option is always set to false. + * Constructor * * @param frender - * @param blocking * @param theType */ - FeatureTypeSettings(FeatureRenderer frender, boolean blocking, - String theType) + public FeatureTypeSettings(FeatureRenderer frender, String theType) { 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; @@ -236,12 +283,50 @@ public class FeatureTypeSettings extends JalviewDialog String title = MessageManager .formatMessage("label.display_settings_for", new String[] { theType }); - initDialogFrame(this, true, blocking, title, 600, 360); - + 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 */ @@ -260,9 +345,9 @@ public class FeatureTypeSettings extends JalviewDialog */ if (fc.isSimpleColour()) { - simpleColour.setSelected(true); singleColour.setBackground(fc.getColour()); singleColour.setForeground(fc.getColour()); + simpleColour.setSelected(true); } /* @@ -275,13 +360,12 @@ public class FeatureTypeSettings extends JalviewDialog if (fc.isColourByAttribute()) { String[] attributeName = fc.getAttributeName(); - colourByTextCombo - .setSelectedItem(toAttributeDisplayName(attributeName)); + colourByTextCombo.setSelectedItem( + FeatureMatcher.toAttributeDisplayName(attributeName)); } else { - colourByTextCombo - .setSelectedItem(MessageManager.getString("label.label")); + colourByTextCombo.setSelectedItem(LABEL_18N); } } else @@ -306,6 +390,7 @@ public class FeatureTypeSettings extends JalviewDialog * Graduated colour, by score or attribute value range */ graduatedColour.setSelected(true); + updateColourMinMax(); // ensure min, max are set colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1); minColour.setEnabled(true); maxColour.setEnabled(true); @@ -317,13 +402,12 @@ public class FeatureTypeSettings extends JalviewDialog if (fc.isColourByAttribute()) { String[] attributeName = fc.getAttributeName(); - colourByRangeCombo - .setSelectedItem(toAttributeDisplayName(attributeName)); + colourByRangeCombo.setSelectedItem( + FeatureMatcher.toAttributeDisplayName(attributeName)); } else { - colourByRangeCombo - .setSelectedItem(MessageManager.getString("label.score")); + colourByRangeCombo.setSelectedItem(SCORE_18N); } Color noColour = fc.getNoColour(); if (noColour == null) @@ -361,7 +445,7 @@ public class FeatureTypeSettings extends JalviewDialog : BELOW_THRESHOLD_OPTION); slider.setEnabled(true); slider.setValue((int) (fc.getThreshold() * scaleFactor)); - thresholdValue.setText(String.valueOf(getRoundedSliderValue())); + thresholdValue.setText(String.valueOf(fc.getThreshold())); thresholdValue.setEnabled(true); thresholdIsMin.setEnabled(true); } @@ -384,8 +468,6 @@ public class FeatureTypeSettings extends JalviewDialog private void initialise() { this.setLayout(new BorderLayout()); - tabbedPane = new JTabbedPane(); - this.add(tabbedPane, BorderLayout.CENTER); /* * an ActionListener that applies colour changes @@ -400,18 +482,16 @@ public class FeatureTypeSettings extends JalviewDialog }; /* - * first tab: colour options + * first panel/tab: colour options */ JPanel coloursPanel = initialiseColoursPanel(); - tabbedPane.addTab(MessageManager.getString("action.colour"), - coloursPanel); + this.add(coloursPanel, BorderLayout.NORTH); /* - * second tab: filter options + * second panel/tab: filter options */ JPanel filtersPanel = initialiseFiltersPanel(); - tabbedPane.addTab(MessageManager.getString("label.filters"), - filtersPanel); + this.add(filtersPanel, BorderLayout.CENTER); JPanel okCancelPanel = initialiseOkCancelPanel(); @@ -422,32 +502,47 @@ public class FeatureTypeSettings extends JalviewDialog * Updates the min-max range if Colour By selected item is Score, or an * attribute, with a min-max range */ - protected void updateMinMax() + protected void updateColourMinMax() { if (!graduatedColour.isSelected()) { return; } - float[] minMax = null; String colourBy = (String) colourByRangeCombo.getSelectedItem(); - if (MessageManager.getString("label.score").equals(colourBy)) + float[] minMax = getMinMax(colourBy); + + if (minMax != null) + { + min = minMax[0]; + max = minMax[1]; + } + } + + /** + * Retrieves the min-max range: + *
    + *
  • of feature score, if colour or filter is by Score
    • + *
  • else of the selected attribute
    • + *
+ * + * @param attName + * @return + */ + private float[] getMinMax(String attName) + { + float[] minMax = null; + if (SCORE_18N.equals(attName)) { minMax = fr.getMinMax().get(featureType)[0]; } else { // colour by attribute range - String[] attNames = fromAttributeDisplayName(colourBy); minMax = FeatureAttributes.getInstance().getMinMax(featureType, - attNames); - } - - if (minMax != null) - { - min = minMax[0]; - max = minMax[1]; + FeatureMatcher.fromAttributeDisplayName(attName)); } + return minMax; } /** @@ -547,14 +642,21 @@ public class FeatureTypeSettings extends JalviewDialog maxColour.setBorder(new LineBorder(Color.black)); /* - * default max colour to current colour (if a plain colour), - * or to Black if colour by label; 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.isSimpleColour() ? fc.getColour() : Color.BLACK; - 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")); @@ -637,6 +739,7 @@ public class FeatureTypeSettings extends JalviewDialog { thresholdValue .setText(String.valueOf(slider.getValue() / scaleFactor)); + thresholdValue.setBackground(Color.white); // to reset red for invalid sliderValueChanged(); } } @@ -702,15 +805,25 @@ public class FeatureTypeSettings extends JalviewDialog private JPanel initialiseColoursPanel() { JPanel colourByPanel = new JPanel(); + colourByPanel.setBackground(Color.white); colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS)); + JvSwingUtils.createTitledBorder(colourByPanel, + 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)); simpleColourPanel.setBackground(Color.white); - JvSwingUtils.createTitledBorder(simpleColourPanel, - MessageManager.getString("label.simple"), true); colourByPanel.add(simpleColourPanel); simpleColour = new JRadioButton( @@ -723,15 +836,18 @@ public class FeatureTypeSettings extends JalviewDialog { if (simpleColour.isSelected() && !adjusting) { - showColourChooser(singleColour, "label.select_colour"); + colourChanged(true); } } - }); - + singleColour.setFont(JvSwingUtils.getLabelFont()); singleColour.setBorder(BorderFactory.createLineBorder(Color.black)); singleColour.setPreferredSize(new Dimension(40, 20)); + FeatureColourI originalColour = originalColours.get(featureType); + singleColour.setBackground(originalColour.getColour()); + singleColour.setForeground(originalColour.getColour()); + singleColour.addMouseListener(new MouseAdapter() { @Override @@ -801,6 +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, @@ -815,9 +971,9 @@ public class FeatureTypeSettings extends JalviewDialog } /** - * Constructs and sets the selected colour options as the colour for the feature - * type, and repaints the alignment, and optionally the Overview and/or - * structure viewer if open + * Constructs and sets the selected colour options as the colour for the + * feature type, and repaints the alignment, and optionally the Overview + * and/or structure viewer if open * * @param updateStructsAndOverview */ @@ -835,14 +991,22 @@ public class FeatureTypeSettings extends JalviewDialog * ensure min-max range is for the latest choice of * 'graduated colour by' */ - updateMinMax(); + updateColourMinMax(); 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(); @@ -856,41 +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 = this.getBackground(); - FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f); - fc.setColourByLabel(true); - String byWhat = (String) colourByTextCombo.getSelectedItem(); - if (!MessageManager.getString("label.label").equals(byWhat)) - { - fc.setAttributeName(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 @@ -900,11 +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(); @@ -918,20 +1045,56 @@ 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(); - if (!MessageManager.getString("label.score").equals(byWhat)) + if (!SCORE_18N.equals(byWhat)) { - fc.setAttributeName(fromAttributeDisplayName(byWhat)); + fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat)); } /* @@ -956,36 +1119,17 @@ public class FeatureTypeSettings extends JalviewDialog return fc; } - /** - * A helper method that converts a 'compound' attribute name from its display - * form, e.g. CSQ:PolyPhen to array form, e.g. { "CSQ", "PolyPhen" } - * - * @param attribute - * @return - */ - private String[] fromAttributeDisplayName(String attribute) - { - return attribute == null ? null : attribute.split(COLON); - } - - /** - * A helper method that converts a 'compound' attribute name to its display - * form, e.g. CSQ:PolyPhen from its array form, e.g. { "CSQ", "PolyPhen" } - * - * @param attName - * @return - */ - private String toAttributeDisplayName(String[] attName) + @Override + protected void raiseClosed() { - return attName == null ? "" : String.join(COLON, attName); + refreshFeatureSettings(); } - @Override - protected void raiseClosed() + protected void refreshFeatureSettings() { if (this.featureSettings != null) { - featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED")); + featureSettings.actionPerformed(new ActionEvent(this, 0, "REFRESH")); } } @@ -1000,16 +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 */ @@ -1017,21 +1179,23 @@ public class FeatureTypeSettings extends JalviewDialog { try { + /* + * set 'adjusting' flag while moving the slider, so it + * doesn't then in turn change the value (with rounding) + */ adjusting = true; float f = Float.parseFloat(thresholdValue.getText()); + f = Float.max(f, this.min); + f = Float.min(f, this.max); + thresholdValue.setText(String.valueOf(f)); slider.setValue((int) (f * scaleFactor)); threshline.value = f; thresholdValue.setBackground(Color.white); // ok - - /* - * force repaint of any Overview window or structure - */ - ap.paintAlignment(true, true); + adjusting = false; + colourChanged(true); } catch (NumberFormatException ex) { thresholdValue.setBackground(Color.red); // not ok - } finally - { adjusting = false; } } @@ -1054,8 +1218,8 @@ public class FeatureTypeSettings extends JalviewDialog /** * Converts the slider value to its absolute value by dividing by the - * scaleFactor. Rounding errors are squashed by forcing min/max of slider range - * to the actual min/max of feature score range + * scaleFactor. Rounding errors are squashed by forcing min/max of slider + * range to the actual min/max of feature score range * * @return */ @@ -1078,11 +1242,11 @@ public class FeatureTypeSettings extends JalviewDialog } /** - * A helper method to build the drop-down choice of attributes for a feature. If - * 'withRange' is true, then Score, and any attributes with a min-max range, are - * added. If 'withText' is true, Label and any known attributes are added. This - * allows 'categorical numerical' attributes e.g. codon position to be coloured - * by text. + * A helper method to build the drop-down choice of attributes for a feature. + * If 'withRange' is true, then Score, and any attributes with a min-max + * range, are added. If 'withText' is true, Label and any known attributes are + * added. This allows 'categorical numerical' attributes e.g. codon position + * to be coloured by text. *

* Where metadata is available with a description for an attribute, that is * added as a tooltip. @@ -1104,7 +1268,7 @@ public class FeatureTypeSettings extends JalviewDialog if (withText) { - displayAtts.add(MessageManager.getString("label.label")); + displayAtts.add(LABEL_18N); tooltips.add(MessageManager.getString("label.description")); } if (withRange) @@ -1112,8 +1276,8 @@ public class FeatureTypeSettings extends JalviewDialog float[][] minMax = fr.getMinMax().get(featureType); if (minMax != null && minMax[0][0] != minMax[0][1]) { - displayAtts.add(MessageManager.getString("label.score")); - tooltips.add(MessageManager.getString("label.score")); + displayAtts.add(SCORE_18N); + tooltips.add(SCORE_18N); } } @@ -1126,7 +1290,7 @@ public class FeatureTypeSettings extends JalviewDialog { continue; } - displayAtts.add(toAttributeDisplayName(attName)); + displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName)); String desc = fa.getDescription(featureType, attName); if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH) { @@ -1148,24 +1312,38 @@ 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); /* - * panel with filters - populated by refreshFiltersDisplay + * panel with filters - populated by refreshFiltersDisplay, + * which also sets the layout manager */ chooseFiltersPanel = new JPanel(); - LayoutManager box = new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS); - chooseFiltersPanel.setLayout(box); + chooseFiltersPanel.setBackground(Color.white); filtersPanel.add(chooseFiltersPanel); - return filtersPanel; + return outerPanel; } /** @@ -1175,9 +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); - andOrPanel.setBorder(BorderFactory.createLineBorder(debugBorderColour)); + andFilters = new JRadioButton(MessageManager.getString("label.and")); orFilters = new JRadioButton(MessageManager.getString("label.or")); ActionListener actionListener = new ActionListener() @@ -1198,10 +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 @@ -1224,7 +1421,7 @@ public class FeatureTypeSettings extends JalviewDialog /* * if this feature type has filters set, load them first */ - KeyedMatcherSetI featureFilters = fr.getFeatureFilter(featureType); + FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType); if (featureFilters != null) { if (!featureFilters.isAnded()) @@ -1237,22 +1434,29 @@ public class FeatureTypeSettings extends JalviewDialog /* * and an empty filter for the user to populate (add) */ - KeyedMatcherI noFilter = new KeyedMatcher(Condition.values()[0], "", - (String) null); - filters.add(noFilter); + filters.add(FeatureMatcher.NULL_MATCHER); + + /* + * use GridLayout to 'justify' rows to the top of the panel, until + * there are too many to fit in, then fall back on BoxLayout + */ + if (filters.size() <= 5) + { + chooseFiltersPanel.setLayout(new GridLayout(5, 1)); + } + else + { + chooseFiltersPanel.setLayout( + new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS)); + } /* * render the conditions in rows, each in its own JPanel */ int filterIndex = 0; - for (KeyedMatcherI filter : filters) + for (FeatureMatcherI filter : filters) { - String[] attName = filter.getKey(); - Condition condition = filter.getMatcher().getCondition(); - String pattern = filter.getMatcher().getPattern(); - JPanel row = addFilter(attName, attNames, condition, pattern, - filterIndex); - row.setBorder(BorderFactory.createLineBorder(debugBorderColour)); + JPanel row = addFilter(filter, attNames, filterIndex); chooseFiltersPanel.add(row); filterIndex++; } @@ -1264,25 +1468,37 @@ public class FeatureTypeSettings extends JalviewDialog /** * A helper method that constructs a row (panel) with one filter condition: *

    - *
  • a drop-down list of attribute names to choose from
    • + *
  • a drop-down list of Label, Score and attribute names to choose + * from
    • *
  • a drop-down list of conditions to choose from
    • *
  • a text field for input of a match pattern
    • *
  • optionally, a 'remove' button
    • *
- * If attribute, condition or pattern are not null, they are set as defaults for - * the input fields. The 'remove' button is added unless the pattern is null or - * empty (incomplete filter condition). + * The filter values are set as defaults for the input fields. The 'remove' + * button is added unless the pattern is empty (incomplete filter condition). + *

+ * Action handlers on these fields provide for + *

    + *
  • validate pattern field - should be numeric if condition is numeric
    • + *
  • save filters and refresh display on any (valid) change
    • + *
  • remove filter and refresh on 'Remove'
    • + *
  • update conditions list on change of Label/Score/Attribute
    • + *
  • refresh value field tooltip with min-max range on change of + * attribute
    • + *
* - * @param attName + * @param filter * @param attNames - * @param cond - * @param pattern * @param filterIndex * @return */ - protected JPanel addFilter(String[] attName, List attNames, - Condition cond, String pattern, int filterIndex) + protected JPanel addFilter(FeatureMatcherI filter, + List attNames, int filterIndex) { + String[] attName = filter.getAttribute(); + Condition cond = filter.getMatcher().getCondition(); + String pattern = filter.getMatcher().getPattern(); + JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT)); filterRow.setBackground(Color.white); @@ -1292,8 +1508,12 @@ public class FeatureTypeSettings extends JalviewDialog */ final JComboBox attCombo = populateAttributesDropdown(attNames, true, true); + String filterBy = setSelectedAttribute(attCombo, filter); + JComboBox condCombo = new JComboBox<>(); + JTextField patternField = new JTextField(8); + patternField.setText(pattern); /* * action handlers that validate and (if valid) apply changes @@ -1303,11 +1523,10 @@ public class FeatureTypeSettings extends JalviewDialog @Override public void actionPerformed(ActionEvent e) { - if (attCombo.getSelectedItem() != null) + if (validateFilter(patternField, condCombo)) { - if (validateFilter(patternField, condCombo)) + if (updateFilter(attCombo, condCombo, patternField, filterIndex)) { - updateFilter(attCombo, condCombo, patternField, filterIndex); filtersChanged(); } } @@ -1322,30 +1541,44 @@ public class FeatureTypeSettings extends JalviewDialog } }; - if (attName == null) // the 'add a condition' row + if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row { attCombo.setSelectedIndex(0); } else { - attCombo.setSelectedItem(toAttributeDisplayName(attName)); + attCombo.setSelectedItem( + FeatureMatcher.toAttributeDisplayName(attName)); } - attCombo.addItemListener(itemListener); + attCombo.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + /* + * on change of attribute, refresh the conditions list to + * ensure it is appropriate for the attribute datatype + */ + populateConditions((String) attCombo.getSelectedItem(), + (Condition) condCombo.getSelectedItem(), condCombo, + patternField); + actionListener.actionPerformed(null); + } + }); filterRow.add(attCombo); /* * drop-down choice of test condition */ - populateConditions((String) attCombo.getSelectedItem(), cond, - condCombo); + populateConditions(filterBy, cond, condCombo, patternField); + condCombo.setPreferredSize(new Dimension(150, 20)); condCombo.addItemListener(itemListener); filterRow.add(condCombo); /* * pattern to match against */ - patternField.setText(pattern); patternField.addActionListener(actionListener); patternField.addFocusListener(new FocusAdapter() { @@ -1358,9 +1591,22 @@ public class FeatureTypeSettings extends JalviewDialog filterRow.add(patternField); /* + * disable pattern field for condition 'Present / NotPresent' + */ + Condition selectedCondition = (Condition) condCombo.getSelectedItem(); + patternField.setEnabled(selectedCondition.needsAPattern()); + + /* + * if a numeric condition is selected, show the value range + * as a tooltip on the value input field + */ + setNumericHints(filterBy, selectedCondition, patternField); + + /* * add remove button if filter is populated (non-empty pattern) */ - if (pattern != null && pattern.trim().length() > 0) + if (!patternField.isEnabled() + || (pattern != null && pattern.trim().length() > 0)) { // todo: gif for button drawing '-' or 'x' JButton removeCondition = new BasicArrowButton(SwingConstants.WEST); @@ -1382,54 +1628,169 @@ public class FeatureTypeSettings extends JalviewDialog } /** - * Populates the drop-down list of comparison conditions for the given attribute - * name. The conditions added depend on the datatype of the attribute values. - * The supplied condition is set as the selected item in the list, provided it - * is in the list. + * Sets the selected item in the Label/Score/Attribute drop-down to match the + * filter + * + * @param attCombo + * @param filter + */ + private String setSelectedAttribute(JComboBox attCombo, + FeatureMatcherI filter) + { + String item = null; + if (filter.isByScore()) + { + item = SCORE_18N; + } + else if (filter.isByLabel()) + { + item = LABEL_18N; + } + else + { + item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute()); + } + attCombo.setSelectedItem(item); + return item; + } + + /** + * If a numeric comparison condition is selected, retrieves the min-max range + * for the value (score or attribute), and sets it as a tooltip on the value + * field. If the field is currently empty, then pre-populates it with + *
    + *
  • the minimum value, if condition is > or >=
    • + *
  • the maximum value, if condition is < or <=
    • + *
+ * + * @param attName + * @param selectedCondition + * @param patternField + */ + private void setNumericHints(String attName, Condition selectedCondition, + JTextField patternField) + { + patternField.setToolTipText(""); + + if (selectedCondition.isNumeric()) + { + float[] minMax = getMinMax(attName); + if (minMax != null) + { + String minFormatted = DECFMT_2_2.format(minMax[0]); + String maxFormatted = DECFMT_2_2.format(minMax[1]); + String tip = String.format("(%s - %s)", minFormatted, maxFormatted); + patternField.setToolTipText(tip); + if (patternField.getText().isEmpty()) + { + if (selectedCondition == Condition.GE + || selectedCondition == Condition.GT) + { + patternField.setText(minFormatted); + } + else + { + if (selectedCondition == Condition.LE + || selectedCondition == Condition.LT) + { + patternField.setText(maxFormatted); + } + } + } + } + } + } + + /** + * Populates the drop-down list of comparison conditions for the given + * attribute name. The conditions added depend on the datatype of the + * attribute values. The supplied condition is set as the selected item in the + * list, provided it is in the list. If the pattern is now invalid + * (non-numeric pattern for a numeric condition), it is cleared. * * @param attName * @param cond * @param condCombo + * @param patternField */ private void populateConditions(String attName, Condition cond, - JComboBox condCombo) + JComboBox condCombo, JTextField patternField) { Datatype type = FeatureAttributes.getInstance().getDatatype(featureType, - attName); - if (MessageManager.getString("label.label").equals(attName)) + FeatureMatcher.fromAttributeDisplayName(attName)); + if (LABEL_18N.equals(attName)) { type = Datatype.Character; } - else if (MessageManager.getString("label.score").equals(attName)) + else if (SCORE_18N.equals(attName)) { type = Datatype.Number; } + /* + * remove itemListener before starting + */ + ItemListener listener = condCombo.getItemListeners()[0]; + condCombo.removeItemListener(listener); + boolean condIsValid = false; + + condCombo.removeAllItems(); for (Condition c : Condition.values()) { - if ((c.isNumeric() && type != Datatype.Character) + if ((c.isNumeric() && type == Datatype.Number) || (!c.isNumeric() && type != Datatype.Number)) { condCombo.addItem(c); + if (c == cond) + { + condIsValid = true; + } } } /* * set the selected condition (does nothing if not in the list) */ - if (cond != null) + if (condIsValid) { condCombo.setSelectedItem(cond); } + else + { + condCombo.setSelectedIndex(0); + } + + /* + * clear pattern if it is now invalid for condition + */ + if (((Condition) condCombo.getSelectedItem()).isNumeric()) + { + try + { + String pattern = patternField.getText().trim(); + if (pattern.length() > 0) + { + Float.valueOf(pattern); + } + } catch (NumberFormatException e) + { + patternField.setText(""); + } + } + + /* + * restore the listener + */ + condCombo.addItemListener(listener); } /** - * Answers true unless a numeric condition has been selected with a non-numeric - * value. Sets the value field to RED with a tooltip if in error. + * Answers true unless a numeric condition has been selected with a + * non-numeric value. Sets the value field to RED with a tooltip if in error. *

- * If the pattern entered is empty, this method returns false, but does not mark - * the field as invalid. This supports selecting an attribute for a new - * condition before a match pattern has been entered. + * If the pattern is expected but is empty, this method returns false, but + * does not mark the field as invalid. This supports selecting an attribute + * for a new condition before a match pattern has been entered. * * @param value * @param condCombo @@ -1443,15 +1804,20 @@ public class FeatureTypeSettings extends JalviewDialog } Condition cond = (Condition) condCombo.getSelectedItem(); + if (!cond.needsAPattern()) + { + return true; + } + value.setBackground(Color.white); value.setToolTipText(""); String v1 = value.getText().trim(); if (v1.length() == 0) { - return false; + // return false; } - if (cond.isNumeric()) + if (cond.isNumeric() && v1.length() > 0) { try { @@ -1470,35 +1836,59 @@ public class FeatureTypeSettings extends JalviewDialog /** * Constructs a filter condition from the given input fields, and replaces the - * condition at filterIndex with the new one + * condition at filterIndex with the new one. Does nothing if the pattern + * field is blank (unless the match condition is one that doesn't require a + * pattern, e.g. 'Is present'). Answers true if the filter was updated, else + * false. + *

+ * This method may update the tooltip on the filter value field to show the + * value range, if a numeric condition is selected. This ensures the tooltip + * is updated when a numeric valued attribute is chosen on the last 'add a + * filter' row. * * @param attCombo * @param condCombo * @param valueField * @param filterIndex */ - protected void updateFilter(JComboBox attCombo, + protected boolean updateFilter(JComboBox attCombo, JComboBox condCombo, JTextField valueField, int filterIndex) { String attName = (String) attCombo.getSelectedItem(); Condition cond = (Condition) condCombo.getSelectedItem(); - String pattern = valueField.getText(); - KeyedMatcherI km = new KeyedMatcher(cond, pattern, - fromAttributeDisplayName(attName)); + String pattern = valueField.getText().trim(); + + setNumericHints(attName, cond, valueField); + + if (pattern.length() == 0 && cond.needsAPattern()) + { + valueField.setEnabled(true); // ensure pattern field is enabled! + return false; + } + + /* + * Construct a matcher that operates on Label, Score, + * or named attribute + */ + FeatureMatcherI km = null; + if (LABEL_18N.equals(attName)) + { + km = FeatureMatcher.byLabel(cond, pattern); + } + else if (SCORE_18N.equals(attName)) + { + km = FeatureMatcher.byScore(cond, pattern); + } + else + { + km = FeatureMatcher.byAttribute(cond, pattern, + FeatureMatcher.fromAttributeDisplayName(attName)); + } filters.set(filterIndex, km); - } - /** - * Makes the dialog visible, at the Feature Colour tab or at the Filters tab - * - * @param coloursTab - */ - public void showTab(boolean coloursTab) - { - setVisible(true); - tabbedPane.setSelectedIndex(coloursTab ? 0 : 1); + return true; } /** @@ -1509,8 +1899,8 @@ public class FeatureTypeSettings extends JalviewDialog *

  • change of match pattern
    • *
  • removal of a condition
    • * - * The inputs are parsed into a combined filter and this is set for the feature - * type, and the alignment redrawn. + * The inputs are parsed into a combined filter and this is set for the + * feature type, and the alignment redrawn. */ protected void filtersChanged() { @@ -1518,12 +1908,13 @@ public class FeatureTypeSettings extends JalviewDialog * update the filter conditions for the feature type */ boolean anded = andFilters.isSelected(); - KeyedMatcherSetI combined = new KeyedMatcherSet(); + FeatureMatcherSetI combined = new FeatureMatcherSet(); - for (KeyedMatcherI filter : filters) + for (FeatureMatcherI filter : filters) { String pattern = filter.getMatcher().getPattern(); - if (pattern.trim().length() > 0) + Condition condition = filter.getMatcher().getCondition(); + if (pattern.trim().length() > 0 || !condition.needsAPattern()) { if (anded) { @@ -1541,6 +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();