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;
private JPanel chooseFiltersPanel;
/*
- * feature types present in Feature Renderer which are
- * sub-types of the one this editor is acting on
+ * the root Sequence Ontology terms (if any) that is a parent of
+ * the current feature type
*/
- private final List<String> subTypes;
+ private String rootSOTerm;
+
+ /*
+ * feature types present in Feature Renderer which have the same Sequence
+ * Ontology root parent as the one this editor is acting on
+ */
+ private final List<String> peerSoTerms;
/*
* if true, filter or colour settings are also applied to
- * any feature sub-types in the Sequence Ontology
+ * any sub-types of rootSOTerm in the Sequence Ontology
*/
private boolean applyFiltersToSubtypes;
*/
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;
- /*
- * 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
+ peerSoTerms = findSequenceOntologyPeers(this.featureType);
/*
* save original colours and filters for this feature type
originalFilters.put(theType, fr.getFeatureFilter(theType));
originalColours = new HashMap<>();
originalColours.put(theType, fr.getFeatureColours().get(theType));
- for (String child : subTypes)
+ for (String child : peerSoTerms)
{
originalFilters.put(child, fr.getFeatureFilter(child));
originalColours.put(child, fr.getFeatureColours().get(child));
String title = MessageManager
.formatMessage("label.display_settings_for", new String[]
{ theType });
- initDialogFrame(this, true, blocking, title, 500, 500);
-
+ initDialogFrame(this, true, false, title, 580, 500);
waitForInput();
}
/**
+ * Answers a (possibly empty) list of feature types known to the Feature
+ * Renderer which share a top level Sequence Ontology parent with the current
+ * feature type. The current type is not included.
+ *
+ * @return
+ */
+ protected List<String> findSequenceOntologyPeers(String featureType)
+ {
+ List<String> peers = new ArrayList<>();
+
+ /*
+ * first find the SO term (if any) that is the root
+ * parent of the current type
+ */
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ List<String> 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<String> 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
*/
*/
if (fc.isSimpleColour())
{
- simpleColour.setSelected(true);
singleColour.setBackground(fc.getColour());
singleColour.setForeground(fc.getColour());
+ simpleColour.setSelected(true);
}
/*
: 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);
}
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"));
{
thresholdValue
.setText(String.valueOf(slider.getValue() / scaleFactor));
+ thresholdValue.setBackground(Color.white); // to reset red for invalid
sliderValueChanged();
}
}
MessageManager.getString("action.colour"), true);
/*
- * option to apply colour to sub-types as well (if there are any)
+ * option to apply colour to peer types as well (if there are any)
*/
- if (!subTypes.isEmpty())
+ if (!peerSoTerms.isEmpty())
{
applyColourToSubtypes = false;
colourByPanel.add(initSubtypesPanel(false));
*/
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));
+ FeatureColourI originalColour = originalColours.get(featureType);
+ singleColour.setBackground(originalColour.getColour());
+ singleColour.setForeground(originalColour.getColour());
+
singleColour.addMouseListener(new MouseAdapter()
{
@Override
JPanel toSubtypes = new JPanel(new FlowLayout(FlowLayout.LEFT));
toSubtypes.setBackground(Color.WHITE);
JCheckBox applyToSubtypesCB = new JCheckBox(MessageManager
- .formatMessage("label.apply_to_subtypes", featureType));
+ .formatMessage("label.apply_to_subtypes", rootSOTerm));
applyToSubtypesCB.setToolTipText(getSubtypesTooltip());
applyToSubtypesCB.addActionListener(new ActionListener()
{
fr.setColour(featureType, acg);
if (applyColourToSubtypes)
{
- for (String child : subTypes)
+ for (String child : peerSoTerms)
{
fr.setColour(child, acg);
}
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
{
// 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();
{
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();
{
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;
}
}
outerPanel.setBackground(Color.white);
/*
- * option to apply colour to sub-types as well (if there are any)
+ * option to apply colour to peer types as well (if there are any)
*/
- if (!subTypes.isEmpty())
+ if (!peerSoTerms.isEmpty())
{
applyFiltersToSubtypes = false;
outerPanel.add(initSubtypesPanel(true));
{
JPanel andOrPanel = new JPanel(new BorderLayout());
andOrPanel.setBackground(Color.white);
-//<<<<<<< HEAD
-// JPanel panel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
-// andOrPanel.add(panel1, BorderLayout.WEST);
-// panel1.setBackground(Color.white);
-// panel1.setBorder(BorderFactory.createLineBorder(debugBorderColour));
-//=======
-//>>>>>>> refs/heads/develop
+
andFilters = new JRadioButton(MessageManager.getString("label.and"));
orFilters = new JRadioButton(MessageManager.getString("label.or"));
ActionListener actionListener = new ActionListener()
*/
protected String getSubtypesTooltip()
{
- StringBuilder sb = new StringBuilder(20 * subTypes.size());
+ StringBuilder sb = new StringBuilder(20 * peerSoTerms.size());
sb.append(MessageManager.getString("label.apply_also_to"));
- for (String child : subTypes)
+ for (String child : peerSoTerms)
{
sb.append("<br>").append(child);
}
fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
if (applyFiltersToSubtypes)
{
- for (String child : subTypes)
+ for (String child : peerSoTerms)
{
fr.setFeatureFilter(child, combined.isEmpty() ? null : combined);
}
git://source.jalview.org / jalview.git / blobdiff