X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureTypeSettings.java;h=735e514530d60344e4581bbf8327faae8afc0929;hb=f887a21118fae5bc1f2cadcd4f36ffed4554edc8;hp=b9737084b45c4f333f1bac06ce6d4a078d429c5e;hpb=0b0d8f48a1dc4e18bfa4d1a03f017ec3253e3247;p=jalview.git diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java index b973708..735e514 100644 --- a/src/jalview/gui/FeatureTypeSettings.java +++ b/src/jalview/gui/FeatureTypeSettings.java @@ -29,6 +29,7 @@ import jalview.datamodel.features.FeatureMatcher; import jalview.datamodel.features.FeatureMatcherI; import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; +import jalview.gui.JalviewColourChooser.ColourChooserListener; import jalview.schemes.FeatureColour; import jalview.util.ColorUtils; import jalview.util.MessageManager; @@ -56,14 +57,13 @@ import javax.swing.BoxLayout; import javax.swing.ButtonGroup; import javax.swing.JButton; import javax.swing.JCheckBox; -import javax.swing.JColorChooser; import javax.swing.JComboBox; 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.border.EmptyBorder; import javax.swing.border.LineBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; @@ -105,14 +105,15 @@ public class FeatureTypeSettings extends JalviewDialog /* * 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 */ - private final AlignmentViewPanel ap; + final AlignmentViewPanel ap; - private final String featureType; + final String featureType; /* * the colour and filters to reset to on Cancel @@ -125,7 +126,7 @@ public class FeatureTypeSettings extends JalviewDialog * set flag to true when setting values programmatically, * to avoid invocation of action handlers */ - private boolean adjusting = false; + boolean adjusting = false; /* * minimum of the value range for graduated colour @@ -141,29 +142,33 @@ public class FeatureTypeSettings extends JalviewDialog /* * scale factor for conversion between absolute min-max and slider */ - private float scaleFactor; + float scaleFactor; /* * radio button group, to select what to colour by: * simple colour, by category (text), or graduated */ - private JRadioButton simpleColour = new JRadioButton(); + JRadioButton simpleColour = new JRadioButton(); - private JRadioButton byCategory = new JRadioButton(); + JRadioButton byCategory = new JRadioButton(); - private JRadioButton graduatedColour = new JRadioButton(); + JRadioButton graduatedColour = new JRadioButton(); - private JPanel singleColour = new JPanel(); + JPanel coloursPanel; + + JPanel filtersPanel; - private JPanel minColour = new JPanel(); + JPanel singleColour = new JPanel(); - private JPanel maxColour = new JPanel(); + JPanel minColour = new JPanel(); + + JPanel maxColour = new JPanel(); private JComboBox threshold = new JComboBox<>(); - private JSlider slider = new JSlider(); + JSlider slider = new JSlider(); - private JTextField thresholdValue = new JTextField(20); + JTextField thresholdValue = new JTextField(20); private JCheckBox thresholdIsMin = new JCheckBox(); @@ -195,15 +200,10 @@ 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; + List filters; private JPanel chooseFiltersPanel; - private JTabbedPane tabbedPane; - /** * Constructor * @@ -212,28 +212,14 @@ public class FeatureTypeSettings extends JalviewDialog */ public FeatureTypeSettings(FeatureRenderer frender, String theType) { - this(frender, false, theType); - } - - /** - * 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. - * - * @param frender - * @param blocking - * @param theType - */ - FeatureTypeSettings(FeatureRenderer frender, boolean blocking, - String theType) - { this.fr = frender; this.featureType = theType; ap = fr.ap; originalFilter = fr.getFeatureFilter(theType); originalColour = fr.getFeatureColours().get(theType); - + adjusting = true; - + try { initialise(); @@ -242,28 +228,27 @@ public class FeatureTypeSettings extends JalviewDialog ex.printStackTrace(); return; } - - updateColoursTab(); - - updateFiltersTab(); - + + updateColoursPanel(); + + updateFiltersPanel(); + adjusting = false; - + colourChanged(false); - + 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(); } /** - * Configures the widgets on the Colours tab according to the current feature + * Configures the widgets on the Colours panel according to the current feature * colour scheme */ - private void updateColoursTab() + private void updateColoursPanel() { FeatureColourI fc = fr.getFeatureColours().get(featureType); @@ -278,9 +263,9 @@ public class FeatureTypeSettings extends JalviewDialog */ if (fc.isSimpleColour()) { - simpleColour.setSelected(true); singleColour.setBackground(fc.getColour()); singleColour.setForeground(fc.getColour()); + simpleColour.setSelected(true); } /* @@ -378,7 +363,7 @@ 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); } @@ -401,8 +386,6 @@ 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 @@ -417,18 +400,16 @@ public class FeatureTypeSettings extends JalviewDialog }; /* - * first tab: colour options + * first panel: colour options */ JPanel coloursPanel = initialiseColoursPanel(); - tabbedPane.addTab(MessageManager.getString("action.colour"), - coloursPanel); + this.add(coloursPanel, BorderLayout.NORTH); /* - * second tab: filter options + * second panel: filter options */ JPanel filtersPanel = initialiseFiltersPanel(); - tabbedPane.addTab(MessageManager.getString("label.filters"), - filtersPanel); + this.add(filtersPanel, BorderLayout.CENTER); JPanel okCancelPanel = initialiseOkCancelPanel(); @@ -505,6 +486,7 @@ public class FeatureTypeSettings extends JalviewDialog graduatedColour = new JRadioButton( MessageManager.getString("label.by_range_of") + COLON); graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20)); + graduatedColour.setOpaque(false); graduatedColour.addItemListener(new ItemListener() { @Override @@ -556,7 +538,8 @@ public class FeatureTypeSettings extends JalviewDialog { if (minColour.isEnabled()) { - showColourChooser(minColour, "label.select_colour_minimum_value"); + String ttl = MessageManager.getString("label.select_colour_minimum_value"); + showColourChooser(minColour, ttl); } } }); @@ -572,21 +555,28 @@ public class FeatureTypeSettings extends JalviewDialog { if (maxColour.isEnabled()) { - showColourChooser(maxColour, "label.select_colour_maximum_value"); + String ttl = MessageManager.getString("label.select_colour_maximum_value"); + showColourChooser(maxColour, ttl); } } }); 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)); + 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")); @@ -669,6 +659,7 @@ public class FeatureTypeSettings extends JalviewDialog { thresholdValue .setText(String.valueOf(slider.getValue() / scaleFactor)); + thresholdValue.setBackground(Color.white); // to reset red for invalid sliderValueChanged(); } } @@ -734,20 +725,22 @@ 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); /* * 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( MessageManager.getString("label.simple_colour")); simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20)); + simpleColour.setOpaque(false); simpleColour.addItemListener(new ItemListener() { @Override @@ -755,15 +748,24 @@ 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)); + // if (originalColour.isGraduatedColour()) + // { + // singleColour.setBackground(originalColour.getMaxColour()); + // singleColour.setForeground(originalColour.getMaxColour()); + // } + // else + // { + singleColour.setBackground(originalColour.getColour()); + singleColour.setForeground(originalColour.getColour()); + // } singleColour.addMouseListener(new MouseAdapter() { @Override @@ -771,7 +773,8 @@ public class FeatureTypeSettings extends JalviewDialog { if (simpleColour.isSelected()) { - showColourChooser(singleColour, "label.select_colour"); + String ttl = MessageManager.formatMessage("label.select_colour_for", featureType); + showColourChooser(singleColour, ttl); } } }); @@ -789,6 +792,7 @@ public class FeatureTypeSettings extends JalviewDialog byCategory = new JRadioButton( MessageManager.getString("label.by_text_of") + COLON); byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20)); + byCategory.setOpaque(false); byCategory.addItemListener(new ItemListener() { @Override @@ -833,23 +837,35 @@ public class FeatureTypeSettings extends JalviewDialog return colourByPanel; } - private void showColourChooser(JPanel colourPanel, String key) + /** + * Shows a colour chooser dialog, and if a selection is made, updates the + * colour of the given panel + * + * @param colourPanel + * the panel whose background colour is being picked + * @param title + */ + void showColourChooser(JPanel colourPanel, String title) { - Color col = JColorChooser.showDialog(this, - MessageManager.getString(key), colourPanel.getBackground()); - if (col != null) + ColourChooserListener listener = new ColourChooserListener() { - colourPanel.setBackground(col); - colourPanel.setForeground(col); - } - colourPanel.repaint(); - colourChanged(true); + @Override + public void colourSelected(Color col) + { + colourPanel.setBackground(col); + colourPanel.setForeground(col); + colourPanel.repaint(); + colourChanged(true); + } + }; + JalviewColourChooser.showColourChooser(this, title, + colourPanel.getBackground(), listener); } /** - * 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 */ @@ -877,7 +893,7 @@ public class FeatureTypeSettings extends JalviewDialog fr.setColour(featureType, acg); ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview); - updateColoursTab(); + updateColoursPanel(); } /** @@ -888,42 +904,9 @@ 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 (!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 @@ -933,14 +916,9 @@ 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(); + int thresholdOption = threshold.getSelectedIndex(); if (thresholdIsMin.isSelected() && thresholdOption == ABOVE_THRESHOLD_OPTION) { @@ -951,14 +929,50 @@ 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(); + } /* - * make the graduated colour + * construct a colour that 'remembers' all the options, including + * those not currently selected */ - FeatureColourI fc = new FeatureColour(minColour.getBackground(), - maxColour.getBackground(), noColour, minValue, maxValue); + FeatureColourI fc = new FeatureColour(singleColour.getBackground(), + minColour.getBackground(), maxColour.getBackground(), noColour, + minValue, maxValue); /* + * easiest case - a single colour + */ + 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(); @@ -1026,21 +1040,23 @@ 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; } } @@ -1063,8 +1079,8 @@ 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 */ @@ -1087,11 +1103,11 @@ 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. @@ -1186,9 +1202,10 @@ public class FeatureTypeSettings extends JalviewDialog { JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); andOrPanel.setBackground(Color.white); - andOrPanel.setBorder(BorderFactory.createLineBorder(debugBorderColour)); andFilters = new JRadioButton(MessageManager.getString("label.and")); orFilters = new JRadioButton(MessageManager.getString("label.or")); + andFilters.setOpaque(false); + orFilters.setOpaque(false); ActionListener actionListener = new ActionListener() { @Override @@ -1216,7 +1233,7 @@ public class FeatureTypeSettings extends JalviewDialog * for adding a condition. This should be called after a filter has been * removed, added or amended. */ - private void updateFiltersTab() + private void updateFiltersPanel() { /* * clear the panel and list of filter conditions @@ -1274,7 +1291,6 @@ public class FeatureTypeSettings extends JalviewDialog for (FeatureMatcherI filter : filters) { JPanel row = addFilter(filter, attNames, filterIndex); - row.setBorder(BorderFactory.createLineBorder(debugBorderColour)); chooseFiltersPanel.add(row); filterIndex++; } @@ -1286,7 +1302,8 @@ public class FeatureTypeSettings extends JalviewDialog /** * A helper method that constructs a row (panel) with one filter condition: *

    - *
  • a drop-down list of Label, Score and 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
    • @@ -1323,8 +1340,8 @@ public class FeatureTypeSettings extends JalviewDialog * drop-down choice of attribute, with description as a tooltip * if we can obtain it */ - final JComboBox attCombo = populateAttributesDropdown(attNames, - true, true); + JComboBox attCombo = populateAttributesDropdown(attNames, true, + true); String filterBy = setSelectedAttribute(attCombo, filter); JComboBox condCombo = new JComboBox<>(); @@ -1426,6 +1443,8 @@ public class FeatureTypeSettings extends JalviewDialog || (pattern != null && pattern.trim().length() > 0)) { JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x + removeCondition.setBorder(new EmptyBorder(0, 0, 0, 0)); + removeCondition.setBackground(Color.WHITE); removeCondition.setPreferredSize(new Dimension(23, 17)); removeCondition .setToolTipText(MessageManager.getString("label.delete_row")); @@ -1484,8 +1503,8 @@ public class FeatureTypeSettings extends JalviewDialog * @param selectedCondition * @param patternField */ - private void setNumericHints(String attName, - Condition selectedCondition, JTextField patternField) + private void setNumericHints(String attName, Condition selectedCondition, + JTextField patternField) { patternField.setToolTipText(""); @@ -1519,18 +1538,18 @@ 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. If the pattern is now invalid (non-numeric pattern for a - * numeric condition), it is cleared. + * 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, + void populateConditions(String attName, Condition cond, JComboBox condCombo, JTextField patternField) { Datatype type = FeatureAttributes.getInstance().getDatatype(featureType, @@ -1602,12 +1621,12 @@ public class FeatureTypeSettings extends JalviewDialog } /** - * 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 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. + * 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 @@ -1653,14 +1672,15 @@ public class FeatureTypeSettings extends JalviewDialog /** * Constructs a filter condition from the given input fields, and replaces the - * 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. + * 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. + * 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 @@ -1708,17 +1728,6 @@ public class FeatureTypeSettings extends JalviewDialog } /** - * 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); - } - - /** * Action on any change to feature filtering, namely *

      *
    • change of selected attribute
      • @@ -1726,8 +1735,8 @@ 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() { @@ -1761,6 +1770,6 @@ public class FeatureTypeSettings extends JalviewDialog fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined); ap.paintAlignment(true, true); - updateFiltersTab(); + updateFiltersPanel(); } }