import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
+ import jalview.bin.Cache;
import jalview.datamodel.GraphLine;
import jalview.datamodel.features.FeatureAttributes;
import jalview.datamodel.features.FeatureAttributes.Datatype;
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 java.awt.event.MouseEvent;
import java.text.DecimalFormat;
import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+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;
/*
* 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 JPanel maxColour = new JPanel();
- private JComboBox<String> threshold = new JComboBox<>();
+ private JComboBox<Object> threshold = new JComboBox<>();
private JSlider slider = new JSlider();
/*
* choice of option for 'colour for no value'
*/
- private JComboBox<String> noValueCombo;
+ private JComboBox<Object> noValueCombo;
/*
* choice of what to colour by text (Label or attribute)
*/
- private JComboBox<String> colourByTextCombo;
+ private JComboBox<Object> colourByTextCombo;
/*
* choice of what to colour by range (Score or attribute)
*/
- private JComboBox<String> colourByRangeCombo;
+ private JComboBox<Object> colourByRangeCombo;
private JRadioButton andFilters;
private JPanel chooseFiltersPanel;
+ /*
+ * the root Sequence Ontology terms (if any) that is a parent of
+ * the current feature type
+ */
+ private String rootSOTerm;
+
+ /*
+ * a map whose keys are Sequence Ontology terms - selected from the
+ * current term and its parents in the SO - whose subterms include
+ * additional feature types; the map entry is the list of additional
+ * feature types that match the key or have it as a parent term; in
+ * other words, distinct 'aggregations' that include the current feature type
+ */
+ private final Map<String, List<String>> relatedSoTerms;
+
+ /*
+ * if true, filter or colour settings are also applied to
+ * any sub-types of parentTerm in the Sequence Ontology
+ */
+ private boolean applyFiltersToSubtypes;
+
+ private boolean applyColourToSubtypes;
+
+ private String parentSOTerm;
+
/**
* Constructor
*
this.fr = frender;
this.featureType = theType;
ap = fr.ap;
- originalFilter = fr.getFeatureFilter(theType);
- originalColour = fr.getFeatureColours().get(theType);
-
+
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ relatedSoTerms = so.findSequenceOntologyGroupings(
+ this.featureType, fr.getRenderOrder());
+
+ /*
+ * save original colours and filters for this feature type,
+ * and any related 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 (List<String> related : relatedSoTerms.values())
+ {
+ for (String type : related)
+ {
+ originalFilters.put(type, fr.getFeatureFilter(type));
+ originalColours.put(type, fr.getFeatureColours().get(type));
+ }
+ }
+
adjusting = true;
-
+
try
{
initialise();
ex.printStackTrace();
return;
}
-
+
updateColoursTab();
-
+
updateFiltersTab();
-
+
adjusting = false;
-
+
colourChanged(false);
-
+
String title = MessageManager
.formatMessage("label.display_settings_for", new String[]
{ theType });
}
/**
+ * Answers a (possibly empty) map of any Sequence Ontology terms (the current
+ * feature type and its parents) which incorporate additional known feature
+ * types (the map entry).
+ * <p>
+ * For example if {@code stop_gained} and {@code stop_lost} are known feature
+ * types, then SO term {@ nonsynonymous_variant} is the first common parent of
+ * both terms
+ *
+ * @param featureType
+ * the current feature type being configured
+ * @param featureTypes
+ * all known feature types on the alignment
+ * @return
+ */
+ protected static Map<String, List<String>> findSequenceOntologyGroupings(
+ String featureType, List<String> featureTypes)
+ {
+ List<String> sortedTypes = new ArrayList<>(featureTypes);
+ Collections.sort(sortedTypes);
+
+ Map<String, List<String>> parents = new HashMap<>();
+
+ /*
+ * method:
+ * walk up featureType and all of its parents
+ * find other feature types which are subsumed by each term
+ * add each distinct aggregation of included feature types to the map
+ */
+ List<String> candidates = new ArrayList<>();
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ candidates.add(featureType);
+ while (!candidates.isEmpty())
+ {
+ String term = candidates.remove(0);
+ List<String> includedFeatures = new ArrayList<>();
+ for (String type : sortedTypes)
+ {
+ if (!type.equals(featureType) && so.isA(type, term))
+ {
+ includedFeatures.add(type);
+ }
+ }
+ if (!includedFeatures.isEmpty()
+ && !parents.containsValue(includedFeatures))
+ {
+ parents.put(term, includedFeatures);
+ }
+ candidates.addAll(so.getParents(term));
+ }
+
+ return parents;
+ }
+
+ /**
* Configures the widgets on the Colours tab according to the current feature
* colour scheme
*/
* if not set, default max colour to last plain colour,
* and make min colour a pale version of max colour
*/
+ FeatureColourI originalColour = originalColours.get(featureType);
Color max = originalColour.getMaxColour();
if (max == null)
{
MessageManager.getString("action.colour"), true);
/*
+ * option to apply colour to other selected types as well
+ */
+ if (!relatedSoTerms.isEmpty())
+ {
+ applyColourToSubtypes = false;
+ colourByPanel.add(initSubtypesPanel(false));
+ }
+
+ /*
* simple colour radio button and colour picker
*/
JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
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
return colourByPanel;
}
+ /**
+ * Constructs and returns a panel with the option to apply any changes also to
+ * sub-types of SO terms at or above the feature type
+ *
+ * @return
+ */
+ protected JPanel initSubtypesPanel(final boolean forFilters)
+ {
+ JPanel toSubtypes = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ toSubtypes.setBackground(Color.WHITE);
+
+ /*
+ * checkbox 'apply to sub-types of...'
+ */
+ JCheckBox applyToSubtypesCB = new JCheckBox(MessageManager
+ .formatMessage("label.apply_to_subtypes", rootSOTerm));
+ toSubtypes.add(applyToSubtypesCB);
+ toSubtypes
+ .setToolTipText(MessageManager.getString("label.group_by_so"));
+
+ /*
+ * combobox to choose 'parent' of sub-types
+ */
+ List<String> soTerms = new ArrayList<>();
+ for (String term : relatedSoTerms.keySet())
+ {
+ soTerms.add(term);
+ }
+ // sort from most restrictive to most inclusive
+ Collections.sort(soTerms, new Comparator<String>()
+ {
+ @Override
+ public int compare(String o1, String o2)
+ {
+ return Integer.compare(relatedSoTerms.get(o1).size(),
+ relatedSoTerms.get(o2).size());
+ }
+ });
+ List<String> tooltips = new ArrayList<>();
+ for (String term : soTerms)
+ {
+ tooltips.add(getSOTermsTooltip(relatedSoTerms.get(term)));
+ }
+ JComboBox<String> parentType = JvSwingUtils
+ .buildComboWithTooltips(soTerms, tooltips);
+ toSubtypes.add(parentType);
+
+ /*
+ * on toggle of checkbox, or change of parent SO term,
+ * reset and then reapply filters to the selected scope
+ */
+ final ActionListener action = new ActionListener()
+ {
+ /*
+ * reset and reapply settings on toggle of checkbox
+ */
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ parentSOTerm = (String) parentType.getSelectedItem();
+ if (forFilters)
+ {
+ applyFiltersToSubtypes = applyToSubtypesCB.isSelected();
+ restoreOriginalFilters();
+ filtersChanged();
+ }
+ else
+ {
+ applyColourToSubtypes = applyToSubtypesCB.isSelected();
+ restoreOriginalColours();
+ colourChanged(true);
+ }
+ }
+ };
+ applyToSubtypesCB.addActionListener(action);
+ parentType.addActionListener(action);
+
+ return toSubtypes;
+ }
+
private void showColourChooser(JPanel colourPanel, String key)
{
Color col = JColorChooser.showDialog(this,
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 : relatedSoTerms.get(parentSOTerm))
+ {
+ fr.setColour(child, acg);
+ }
+ }
+ refreshFeatureSettings();
ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
updateColoursTab();
@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);
}
/**
+ * Restores filters for all feature types to their values when the dialog was
+ * opened
+ */
+ protected void restoreOriginalFilters()
+ {
+ for (Entry<String, FeatureMatcherSetI> entry : originalFilters
+ .entrySet())
+ {
+ fr.setFeatureFilter(entry.getKey(), entry.getValue());
+ }
+ }
+
+ /**
+ * Restores colours for all feature types to their values when the dialog was
+ * opened
+ */
+ protected void restoreOriginalColours()
+ {
+ for (Entry<String, FeatureColourI> entry : originalColours.entrySet())
+ {
+ fr.setColour(entry.getKey(), entry.getValue());
+ }
+ }
+
+ /**
* Action on text entry of a threshold value
*/
protected void thresholdValue_actionPerformed()
*/
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));
* @param withRange
* @param withText
*/
- protected JComboBox<String> populateAttributesDropdown(
+ protected JComboBox<Object> populateAttributesDropdown(
List<String[]> attNames, boolean withRange, boolean withText)
{
List<String> displayAtts = new ArrayList<>();
tooltips.add(desc == null ? "" : desc);
}
- JComboBox<String> attCombo = JvSwingUtils
- .buildComboWithTooltips(displayAtts, tooltips);
-
+ // now convert String List to Object List for buildComboWithTooltips
+ List<Object> displayAttsObjects = new ArrayList<>(displayAtts);
+ JComboBox<Object> attCombo = JvSwingUtils
+ .buildComboWithTooltips(displayAttsObjects, tooltips);
+
return attCombo;
}
{
filters = new ArrayList<>();
+ JPanel outerPanel = new JPanel();
+ outerPanel.setLayout(new BoxLayout(outerPanel, BoxLayout.Y_AXIS));
+ outerPanel.setBackground(Color.white);
+
+ /*
+ * option to apply colour to other selected types as well
+ */
+ if (!relatedSoTerms.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);
+
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 also to...' combobox with a list of known
+ * feature types (excluding the current type) which are sub-types of the
+ * selected Sequence Ontology term
+ *
+ * @param
+ * @return
+ */
+ protected String getSOTermsTooltip(List<String> list)
+ {
+ StringBuilder sb = new StringBuilder(20 * relatedSoTerms.size());
+ sb.append(MessageManager.getString("label.apply_also_to"));
+ for (String child : list)
+ {
+ 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
* drop-down choice of attribute, with description as a tooltip
* if we can obtain it
*/
- final JComboBox<String> attCombo = populateAttributesDropdown(attNames,
+ final JComboBox<Object> attCombo = populateAttributesDropdown(attNames,
true, true);
String filterBy = setSelectedAttribute(attCombo, filter);
* @param attCombo
* @param filter
*/
- private String setSelectedAttribute(JComboBox<String> attCombo,
+ private String setSelectedAttribute(JComboBox<Object> attCombo,
FeatureMatcherI filter)
{
String item = null;
* @param valueField
* @param filterIndex
*/
- protected boolean updateFilter(JComboBox<String> attCombo,
+ protected boolean updateFilter(JComboBox<Object> attCombo,
JComboBox<Condition> condCombo, JTextField valueField,
int filterIndex)
{
- String attName = (String) attCombo.getSelectedItem();
+ String attName;
+ try
+ {
+ attName = (String) attCombo.getSelectedItem();
+ } catch (Exception e)
+ {
+ Cache.log.error("Problem casting Combo box entry to String");
+ attName = attCombo.getSelectedItem().toString();
+ }
Condition cond = (Condition) condCombo.getSelectedItem();
String pattern = valueField.getText().trim();
* (note this might now be an empty filter with no conditions)
*/
fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
+ if (applyFiltersToSubtypes)
+ {
+ for (String child : relatedSoTerms.get(parentSOTerm))
+ {
+ fr.setFeatureFilter(child, combined.isEmpty() ? null : combined);
+ }
+ }
+
+ refreshFeatureSettings();
ap.paintAlignment(true, true);
updateFiltersTab();
git://source.jalview.org / jalview.git / commitdiff