import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
import jalview.util.MessageManager;
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;
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;
/*
* 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
/*
* the colour and filters to reset to on Cancel
+ * (including feature sub-types if modified)
*/
- private final FeatureColourI originalColour;
+ private Map<String, FeatureColourI> originalColours;
- private final FeatureMatcherSetI originalFilter;
+ private Map<String, FeatureMatcherSetI> originalFilters;
/*
* set flag to true when setting values programmatically,
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();
*/
private List<FeatureMatcherI> filters;
- // set white normally, black to debug layout
- private Color debugBorderColour = Color.white;
-
private JPanel chooseFiltersPanel;
- private JTabbedPane tabbedPane;
+ /*
+ * feature types present in Feature Renderer which are
+ * sub-types of the one this editor is acting on
+ */
+ private final List<String> subTypes;
- /**
- * Constructor
- *
- * @param frender
- * @param theType
+ /*
+ * if true, filter or colour settings are also applied to
+ * any feature sub-types in the Sequence Ontology
*/
- public FeatureTypeSettings(FeatureRenderer frender, String theType)
- {
- this(frender, false, theType);
- }
+ 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);
- adjusting = true;
+ /*
+ * determine sub-types (if any) of this feature type
+ */
+ List<String> types = fr.getRenderOrder();
+ subTypes = SequenceOntologyFactory.getInstance()
+ .getChildTerms(this.featureType, types);
+ Collections.sort(subTypes); // sort for ease of reading in tooltip
+ /*
+ * 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 : subTypes)
+ {
+ originalFilters.put(child, fr.getFeatureFilter(child));
+ originalColours.put(child, fr.getFeatureColours().get(child));
+ }
+
+ adjusting = true;
+
try
{
initialise();
ex.printStackTrace();
return;
}
-
+
updateColoursTab();
-
+
updateFiltersTab();
-
+
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, 500, 500);
+
waitForInput();
}
*/
if (fc.isSimpleColour())
{
- simpleColour.setSelected(true);
singleColour.setBackground(fc.getColour());
singleColour.setForeground(fc.getColour());
+ simpleColour.setSelected(true);
}
/*
private void initialise()
{
this.setLayout(new BorderLayout());
- tabbedPane = new JTabbedPane();
- this.add(tabbedPane, BorderLayout.CENTER);
/*
* an ActionListener that applies colour changes
};
/*
- * 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();
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
+ * default max colour to last plain colour;
+ * make min colour a pale version of max colour
*/
FeatureColourI fc = fr.getFeatureColours().get(featureType);
- Color bg = fc.isSimpleColour() ? fc.getColour() : Color.BLACK;
+ Color bg = fc.getColour() == null ? Color.BLACK : fc.getColour();
maxColour.setBackground(bg);
minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
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 sub-types as well (if there are any)
+ */
+ if (!subTypes.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(
{
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
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", featureType));
+ 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,
}
/**
- * 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
*/
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 : subTypes)
+ {
+ fr.setColour(child, acg);
+ }
+ }
+ refreshFeatureSettings();
ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
updateColoursTab();
*/
if (byCategory.isSelected())
{
- Color c = this.getBackground();
- FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f);
+ Color c = singleColour.getBackground();
+ FeatureColourI fc = new FeatureColour(c);
fc.setColourByLabel(true);
String byWhat = (String) colourByTextCombo.getSelectedItem();
if (!LABEL_18N.equals(byWhat))
@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"));
}
}
/**
* 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<String, FeatureMatcherSetI> entry : originalFilters
+ .entrySet())
+ {
+ fr.setFeatureFilter(entry.getKey(), entry.getValue());
+ }
+ }
+
+ protected void restoreOriginalColours()
+ {
+ for (Entry<String, FeatureColourI> entry : originalColours.entrySet())
+ {
+ fr.setColour(entry.getKey(), entry.getValue());
+ }
+ }
+
/**
* Action on text entry of a threshold value
*/
/**
* 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
*/
}
/**
- * 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.
* <p>
* Where metadata is available with a description for an attribute, that is
* added as a tooltip.
{
filters = new ArrayList<>();
+ JPanel outerPanel = new JPanel();
+ outerPanel.setLayout(new BoxLayout(outerPanel, BoxLayout.Y_AXIS));
+ outerPanel.setBackground(Color.white);
+
+ /*
+ * option to apply colour to sub-types as well (if there are any)
+ */
+ if (!subTypes.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);
chooseFiltersPanel.setBackground(Color.white);
filtersPanel.add(chooseFiltersPanel);
- return filtersPanel;
+ return outerPanel;
}
/**
*/
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));
+
+// JPanel panel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
+// andOrPanel.add(panel1, BorderLayout.WEST);
+// panel1.setBackground(Color.white);
+// panel1.setBorder(BorderFactory.createLineBorder(debugBorderColour));
andFilters = new JRadioButton(MessageManager.getString("label.and"));
orFilters = new JRadioButton(MessageManager.getString("label.or"));
ActionListener actionListener = new ActionListener()
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 * subTypes.size());
+ sb.append(MessageManager.getString("label.apply_also_to"));
+ for (String child : subTypes)
+ {
+ sb.append("<br>").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
for (FeatureMatcherI filter : filters)
{
JPanel row = addFilter(filter, attNames, filterIndex);
- row.setBorder(BorderFactory.createLineBorder(debugBorderColour));
chooseFiltersPanel.add(row);
filterIndex++;
}
/**
* A helper method that constructs a row (panel) with one filter condition:
* <ul>
- * <li>a drop-down list of Label, Score and attribute names to choose from</li>
+ * <li>a drop-down list of Label, Score and attribute names to choose
+ * from</li>
* <li>a drop-down list of conditions to choose from</li>
* <li>a text field for input of a match pattern</li>
* <li>optionally, a 'remove' button</li>
* disable pattern field for condition 'Present / NotPresent'
*/
Condition selectedCondition = (Condition) condCombo.getSelectedItem();
- if (!selectedCondition.needsAPattern())
- {
- patternField.setEnabled(false);
- }
+ patternField.setEnabled(selectedCondition.needsAPattern());
/*
* if a numeric condition is selected, show the value range
* as a tooltip on the value input field
*/
- setPatternTooltip(filterBy, selectedCondition, patternField);
+ setNumericHints(filterBy, selectedCondition, patternField);
/*
* add remove button if filter is populated (non-empty pattern)
}
/**
- * If a numeric comparison condition is selected, retrieve the min-max range for
- * the value (score or attribute), and set it as a tooltip on the value file
+ * 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
+ * <ul>
+ * <li>the minimum value, if condition is > or >=</li>
+ * <li>the maximum value, if condition is < or <=</li>
+ * </ul>
*
* @param attName
* @param selectedCondition
* @param patternField
*/
- private void setPatternTooltip(String attName,
- Condition selectedCondition, JTextField patternField)
+ private void setNumericHints(String attName, Condition selectedCondition,
+ JTextField patternField)
{
patternField.setToolTipText("");
float[] minMax = getMinMax(attName);
if (minMax != null)
{
- String tip = String.format("(%s - %s)",
- DECFMT_2_2.format(minMax[0]), DECFMT_2_2.format(minMax[1]));
+ 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.
+ * 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
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);
condCombo.setSelectedIndex(0);
}
- condCombo.addItemListener(listener);
-
/*
* clear pattern if it is now invalid for condition
*/
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.
* <p>
- * 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
/**
* 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.
* <p>
* 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
Condition cond = (Condition) condCombo.getSelectedItem();
String pattern = valueField.getText().trim();
- setPatternTooltip(attName, cond, valueField);
+ setNumericHints(attName, cond, valueField);
if (pattern.length() == 0 && cond.needsAPattern())
{
+ valueField.setEnabled(true); // ensure pattern field is enabled!
return false;
}
}
/**
- * 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
* <ul>
* <li>change of selected attribute</li>
* <li>change of match pattern</li>
* <li>removal of a condition</li>
* </ul>
- * 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()
{
* (note this might now be an empty filter with no conditions)
*/
fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
+ if (applyFiltersToSubtypes)
+ {
+ for (String child : subTypes)
+ {
+ fr.setFeatureFilter(child, combined.isEmpty() ? null : combined);
+ }
+ }
+
+ refreshFeatureSettings();
ap.paintAlignment(true, true);
updateFiltersTab();
git://source.jalview.org / jalview.git / blobdiff