*/
package jalview.gui;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
+import jalview.bin.Console;
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.gui.JalviewColourChooser.ColourChooserListener;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.event.ItemListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.math.BigDecimal;
+import java.math.MathContext;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.List;
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.JTextField;
-import javax.swing.SwingConstants;
+import javax.swing.border.EmptyBorder;
import javax.swing.border.LineBorder;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
-import javax.swing.plaf.basic.BasicArrowButton;
/**
* A dialog where the user can configure colour scheme, and any filters, for one
*/
public class FeatureTypeSettings extends JalviewDialog
{
+ private final static MathContext FOUR_SIG_FIG = new MathContext(4);
+
private final static String LABEL_18N = MessageManager
.getString("label.label");
/*
* 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
* 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
private float max;
/*
- * scale factor for conversion between absolute min-max and slider
- */
- private 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();
- /**
- * colours and filters are shown in tabbed view or single content pane
- */
- JPanel coloursPanel, filtersPanel;
+ JPanel coloursPanel;
+
+ JPanel filtersPanel;
JPanel singleColour = new JPanel();
- private JPanel minColour = new JPanel();
+ JPanel minColour = new JPanel();
- private JPanel maxColour = new JPanel();
+ JPanel maxColour = new JPanel();
- private JComboBox<String> threshold = new JComboBox<>();
+ private JComboBox<Object> threshold = new JComboBox<>();
- private JSlider slider = new JSlider();
+ private Slider slider;
- private JTextField thresholdValue = new JTextField(20);
+ JTextField thresholdValue = new JTextField(20);
private JCheckBox thresholdIsMin = new JCheckBox();
/*
* 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;
/*
* filters for the currently selected feature type
*/
- private List<FeatureMatcherI> filters;
+ List<FeatureMatcherI> filters;
private JPanel chooseFiltersPanel;
ap = fr.ap;
originalFilter = fr.getFeatureFilter(theType);
originalColour = fr.getFeatureColours().get(theType);
-
+
adjusting = true;
-
+
try
{
initialise();
ex.printStackTrace();
return;
}
-
- updateColoursTab();
-
- updateFiltersTab();
-
+
+ updateColoursPanel();
+
+ updateFiltersPanel();
+
adjusting = false;
-
+
colourChanged(false);
-
+
String title = MessageManager
.formatMessage("label.display_settings_for", new String[]
{ theType });
}
/**
- * Configures the widgets on the Colours tab according to the current feature
- * colour scheme
+ * 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);
* update min-max scaling if there is a range to work with,
* else disable the widgets (this shouldn't happen if only
* valid options are offered in the combo box)
+ * offset slider to have only non-negative values if necessary (JAL-2983)
*/
- scaleFactor = (max == min) ? 1f : 100f / (max - min);
- float range = (max - min) * scaleFactor;
- slider.setMinimum((int) (min * scaleFactor));
- slider.setMaximum((int) (max * scaleFactor));
- slider.setMajorTickSpacing((int) (range / 10f));
+ slider.setSliderModel(min, max, min);
+ slider.setMajorTickSpacing(
+ (int) ((slider.getMaximum() - slider.getMinimum()) / 10f));
threshline = new GraphLine((max - min) / 2f, "Threshold",
Color.black);
fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
: BELOW_THRESHOLD_OPTION);
slider.setEnabled(true);
- slider.setValue((int) (fc.getThreshold() * scaleFactor));
- thresholdValue.setText(String.valueOf(fc.getThreshold()));
+ slider.setSliderValue(fc.getThreshold());
+ setThresholdValueText(fc.getThreshold());
thresholdValue.setEnabled(true);
thresholdIsMin.setEnabled(true);
}
};
/*
- * first panel/tab: colour options
+ * first panel: colour options
*/
JPanel coloursPanel = initialiseColoursPanel();
this.add(coloursPanel, BorderLayout.NORTH);
/*
- * second panel/tab: filter options
+ * second panel: filter options
*/
JPanel filtersPanel = initialiseFiltersPanel();
this.add(filtersPanel, BorderLayout.CENTER);
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
{
if (minColour.isEnabled())
{
- showColourChooser(minColour, "label.select_colour_minimum_value");
+ String ttl = MessageManager
+ .getString("label.select_colour_minimum_value");
+ showColourChooser(minColour, ttl);
}
}
});
{
if (maxColour.isEnabled())
{
- showColourChooser(maxColour, "label.select_colour_maximum_value");
+ String ttl = MessageManager
+ .getString("label.select_colour_maximum_value");
+ showColourChooser(maxColour, ttl);
}
}
});
thresholdValue_actionPerformed();
}
});
+ slider = new Slider(0f, 100f, 50f);
slider.setPaintLabels(false);
slider.setPaintTicks(true);
slider.setBackground(Color.white);
{
if (!adjusting)
{
- thresholdValue
- .setText(String.valueOf(slider.getValue() / scaleFactor));
+ setThresholdValueText(slider.getSliderValue());
thresholdValue.setBackground(Color.white); // to reset red for invalid
sliderValueChanged();
}
*/
if (ap != null)
{
- ap.paintAlignment(true, true);
+ refreshDisplay(true);
}
}
});
simpleColour = new JRadioButton(
MessageManager.getString("label.simple_colour"));
simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
+ simpleColour.setOpaque(false);
simpleColour.addItemListener(new ItemListener()
{
@Override
// }
// else
// {
- singleColour.setBackground(originalColour.getColour());
- singleColour.setForeground(originalColour.getColour());
+ singleColour.setBackground(originalColour.getColour());
+ singleColour.setForeground(originalColour.getColour());
// }
singleColour.addMouseListener(new MouseAdapter()
{
{
if (simpleColour.isSelected())
{
- showColourChooser(singleColour, "label.select_colour");
+ String ttl = MessageManager
+ .formatMessage("label.select_colour_for", featureType);
+ showColourChooser(singleColour, ttl);
}
}
});
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
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);
}
/**
* save the colour, and repaint stuff
*/
fr.setColour(featureType, acg);
- ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
+ refreshDisplay(updateStructsAndOverview);
- updateColoursTab();
+ updateColoursPanel();
}
/**
}
float minValue = min;
float maxValue = max;
- final int thresholdOption = threshold.getSelectedIndex();
+ int thresholdOption = threshold.getSelectedIndex();
if (thresholdIsMin.isSelected()
&& thresholdOption == ABOVE_THRESHOLD_OPTION)
{
{
fr.setColour(featureType, originalColour);
fr.setFeatureFilter(featureType, originalFilter);
- ap.paintAlignment(true, true);
+ refreshDisplay(true);
}
/**
*/
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));
+ setThresholdValueText(f);
+ slider.setSliderValue(f);
threshline.value = f;
thresholdValue.setBackground(Color.white); // ok
adjusting = false;
}
/**
+ * Sets the text field for threshold value, rounded to four significant
+ * figures
+ *
+ * @param f
+ */
+ void setThresholdValueText(float f)
+ {
+ BigDecimal formatted = new BigDecimal(f).round(FOUR_SIG_FIG)
+ .stripTrailingZeros();
+ thresholdValue.setText(formatted.toPlainString());
+ }
+
+ /**
* Action on change of threshold slider value. This may be done interactively
* (by moving the slider), or programmatically (to update the slider after
* manual input of a threshold value).
*/
protected void sliderValueChanged()
{
- threshline.value = getRoundedSliderValue();
+ threshline.value = slider.getSliderValue();
/*
* repaint alignment, but not Overview or structure,
colourChanged(false);
}
- /**
- * 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
- *
- * @return
- */
- private float getRoundedSliderValue()
- {
- int value = slider.getValue();
- float f = value == slider.getMaximum() ? max
- : (value == slider.getMinimum() ? min : value / scaleFactor);
- return f;
- }
-
void addActionListener(ActionListener listener)
{
if (featureSettings != null)
* @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;
}
andOrPanel.setBackground(Color.white);
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
* 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
{
orFilters.setSelected(true);
}
- featureFilters.getMatchers().forEach(matcher -> filters.add(matcher));
+ // avoid use of lambda expression to keep SwingJS happy
+ // featureFilters.getMatchers().forEach(item -> filters.add(item));
+ for (FeatureMatcherI matcher : featureFilters.getMatchers())
+ {
+ filters.add(matcher);
+ }
}
/*
* 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);
if (!patternField.isEnabled()
|| (pattern != null && pattern.trim().length() > 0))
{
- // todo: gif for button drawing '-' or 'x'
- JButton removeCondition = new BasicArrowButton(SwingConstants.WEST);
+ 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_condition"));
removeCondition.addActionListener(new ActionListener()
* @param attCombo
* @param filter
*/
- private String setSelectedAttribute(JComboBox<String> attCombo,
+ private String setSelectedAttribute(JComboBox<Object> attCombo,
FeatureMatcherI filter)
{
String item = null;
* @param condCombo
* @param patternField
*/
- private void populateConditions(String attName, Condition cond,
+ void populateConditions(String attName, Condition cond,
JComboBox<Condition> condCombo, JTextField patternField)
{
Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
* @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)
+ {
+ Console.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);
- ap.paintAlignment(true, true);
+ refreshDisplay(true);
- updateFiltersTab();
+ updateFiltersPanel();
+ }
+
+ /**
+ * Repaints alignment, structure and overview (if shown). If there is a
+ * complementary view which is showing this view's features, then also
+ * repaints that.
+ *
+ * @param updateStructsAndOverview
+ */
+ void refreshDisplay(boolean updateStructsAndOverview)
+ {
+ ap.paintAlignment(true, updateStructsAndOverview);
+ AlignViewportI complement = ap.getAlignViewport().getCodingComplement();
+ if (complement != null && complement.isShowComplementFeatures())
+ {
+ AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+ af2.alignPanel.paintAlignment(true, updateStructsAndOverview);
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff