*/
package jalview.gui;
-import static jalview.gui.FeatureSettings.FeatureTableModel.COLOUR_COLUMN;
-import static jalview.gui.FeatureSettings.FeatureTableModel.FILTER_COLUMN;
-import static jalview.gui.FeatureSettings.FeatureTableModel.SHOW_COLUMN;
-import static jalview.gui.FeatureSettings.FeatureTableModel.TYPE_COLUMN;
-
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
-import jalview.schemabinding.version2.JalviewUserColours;
import jalview.schemes.FeatureColour;
-import jalview.util.Format;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.util.QuickSort;
-import jalview.util.matcher.KeyedMatcherSet;
-import jalview.util.matcher.KeyedMatcherSetI;
-import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
-import jalview.ws.DasSequenceFeatureFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.JalviewUserColours.Filter;
+import jalview.xml.binding.jalview.ObjectFactory;
import java.awt.BorderLayout;
import java.awt.Color;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.util.Arrays;
+import java.util.Comparator;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import java.util.Vector;
import javax.help.HelpSetException;
import javax.swing.AbstractCellEditor;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JDialog;
import javax.swing.JInternalFrame;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
+import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.table.AbstractTableModel;
+import javax.swing.table.JTableHeader;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI
{
+ private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
+ .getString("label.sequence_feature_colours");
+
+ /*
+ * column indices of fields in Feature Settings table
+ */
+ static final int TYPE_COLUMN = 0;
+
+ static final int COLOUR_COLUMN = 1;
+
+ static final int FILTER_COLUMN = 2;
+
+ static final int SHOW_COLUMN = 3;
+
private static final int COLUMN_COUNT = 4;
private static final int MIN_WIDTH = 400;
private static final int MIN_HEIGHT = 400;
- DasSourceBrowser dassourceBrowser;
-
- DasSequenceFeatureFetcher dasFeatureFetcher;
-
- JPanel dasSettingsPane = new JPanel();
+ private final static String BASE_TOOLTIP = "Click to edit, right-click for menu";
final FeatureRenderer fr;
private float originalTransparency;
- private Map<String, KeyedMatcherSetI> originalFilters;
+ private Map<String, FeatureMatcherSetI> originalFilters;
final JInternalFrame frame;
int selectedRow = -1;
- JButton fetchDAS = new JButton();
-
- JButton saveDAS = new JButton();
-
- JButton cancelDAS = new JButton();
-
boolean resettingTable = false;
/*
int originalTransparencyAsPercent = (int) (originalTransparency * 100);
transparency.setMaximum(100 - originalTransparencyAsPercent);
- originalFilters = fr.getFeatureFilters();
+ originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
try
{
table = new JTable()
{
+ static final String tt = "Click to edit, right-click for menu"; // todo i18n
+
@Override
public String getToolTipText(MouseEvent e)
{
String tip = null;
int column = table.columnAtPoint(e.getPoint());
+ int row = table.rowAtPoint(e.getPoint());
+
switch (column)
{
case TYPE_COLUMN:
tip = JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.feature_settings_click_drag"));
break;
+ case COLOUR_COLUMN:
+ FeatureColourI colour = (FeatureColourI) table.getValueAt(row,
+ column);
+ tip = getColorTooltip(colour, true);
+ break;
case FILTER_COLUMN:
- int row = table.rowAtPoint(e.getPoint());
- KeyedMatcherSet o = (KeyedMatcherSet) table.getValueAt(row,
+ FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
column);
tip = o.isEmpty()
- ? MessageManager.getString("label.filters_tooltip")
+ ? MessageManager
+ .getString("label.configure_feature_tooltip")
: o.toString();
break;
default:
}
return tip;
}
+
+ /**
+ * Position the tooltip near the bottom edge of, and half way across, the
+ * current cell
+ */
+ @Override
+ public Point getToolTipLocation(MouseEvent e)
+ {
+ Point point = e.getPoint();
+ int column = table.columnAtPoint(point);
+ int row = table.rowAtPoint(point);
+ Rectangle r = getCellRect(row, column, false);
+ Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3);
+ return loc;
+ }
};
- table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
+ JTableHeader tableHeader = table.getTableHeader();
+ tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12));
+ tableHeader.setReorderingAllowed(false);
table.setFont(new Font("Verdana", Font.PLAIN, 12));
// table.setDefaultRenderer(Color.class, new ColorRenderer());
table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
- table.setDefaultEditor(KeyedMatcherSet.class, new FilterEditor(this));
- table.setDefaultRenderer(KeyedMatcherSet.class, new FilterRenderer());
+ table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this));
+ table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer());
TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
new ColorRenderer(), new ColorEditor(this));
// MessageManager.getString("label.feature_settings_click_drag")));
scrollPane.setViewportView(table);
- dassourceBrowser = new DasSourceBrowser(this);
- dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
-
if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
{
fr.findAllFeatures(true); // display everything!
javax.swing.event.InternalFrameEvent evt)
{
fr.removePropertyChangeListener(change);
- dassourceBrowser.fs = null;
};
});
frame.setLayer(JLayeredPane.PALETTE_LAYER);
});
men.add(dens);
- /*
- * variable colour options include colour by label, by score,
- * by selected attribute text, or attribute value
- */
- final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
- MessageManager.getString("label.variable_colour"));
- mxcol.setSelected(!featureColour.isSimpleColour());
- men.add(mxcol);
- mxcol.addActionListener(new ActionListener()
- {
- JColorChooser colorChooser;
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (e.getSource() == mxcol)
- {
- if (featureColour.isSimpleColour())
- {
- FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
- fc.addActionListener(this);
- }
- else
- {
- // bring up simple color chooser
- colorChooser = new JColorChooser();
- String title = MessageManager
- .getString("label.select_colour");
- JDialog dialog = JColorChooser.createDialog(me,
- title, true, // modal
- colorChooser, this, // OK button handler
- null); // no CANCEL button handler
- colorChooser.setColor(featureColour.getMaxColour());
- dialog.setVisible(true);
- }
- }
- else
- {
- if (e.getSource() instanceof FeatureTypeSettings)
- {
- /*
- * update after OK in feature colour dialog; the updated
- * colour will have already been set in the FeatureRenderer
- */
- FeatureColourI fci = fr.getFeatureColours().get(type);
- table.setValueAt(fci, rowSelected, 1);
- table.validate();
- }
- else
- {
- // probably the color chooser!
- table.setValueAt(new FeatureColour(colorChooser.getColor()),
- rowSelected, 1);
- table.validate();
- me.updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(),
- false);
- }
- }
- }
-
- });
-
JMenuItem selCols = new JMenuItem(
MessageManager.getString("label.select_columns_containing"));
selCols.addActionListener(new ActionListener()
}
}
- int columnCount = COLUMN_COUNT;
- Object[][] data = new Object[displayableTypes.size()][columnCount];
+ Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT];
int dataIndex = 0;
if (fr.hasRenderOrder())
data[dataIndex][TYPE_COLUMN] = type;
data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
- KeyedMatcherSetI featureFilter = fr.getFeatureFilter(type);
+ FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type);
data[dataIndex][FILTER_COLUMN] = featureFilter == null
- ? new KeyedMatcherSet()
+ ? new FeatureMatcherSet()
: featureFilter;
data[dataIndex][SHOW_COLUMN] = new Boolean(
af.getViewport().getFeaturesDisplayed().isVisible(type));
fr.clearRenderOrder();
return;
}
- KeyedMatcherSetI featureFilter = fr.getFeatureFilter(type);
+ FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type);
data[dataIndex][FILTER_COLUMN] = featureFilter == null
- ? new KeyedMatcherSet()
+ ? new FeatureMatcherSet()
: featureFilter;
data[dataIndex][SHOW_COLUMN] = new Boolean(true);
dataIndex++;
if (originalData == null)
{
- int size = data[0].length;
- originalData = new Object[data.length][size];
+ originalData = new Object[data.length][COLUMN_COUNT];
for (int i = 0; i < data.length; i++)
{
- System.arraycopy(data[i], 0, originalData[i], 0, size);
+ System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT);
}
}
else
/*
* new feature detected - add to original data (on top)
*/
- int size = currentData[0].length;
- Object[][] newData = new Object[originalData.length + 1][size];
+ Object[][] newData = new Object[originalData.length
+ + 1][COLUMN_COUNT];
for (int i = 0; i < originalData.length; i++)
{
- System.arraycopy(originalData[i], 0, newData[i + 1], 0, size);
+ System.arraycopy(originalData[i], 0, newData[i + 1], 0,
+ COLUMN_COUNT);
}
newData[0] = row;
originalData = newData;
}
}
+ /**
+ * Offers a file chooser dialog, and then loads the feature colours and
+ * filters from file in XML format and unmarshals to Jalview feature settings
+ */
void load()
{
JalviewFileChooser chooser = new JalviewFileChooser("fc",
- "Sequence Feature Colours");
+ SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.load_feature_colours"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
File file = chooser.getSelectedFile();
+ load(file);
+ }
+ }
- try
- {
- InputStreamReader in = new InputStreamReader(
- new FileInputStream(file), "UTF-8");
+ /**
+ * Loads feature colours and filters from XML stored in the given file
+ *
+ * @param file
+ */
+ void load(File file)
+ {
+ try
+ {
+ InputStreamReader in = new InputStreamReader(
+ new FileInputStream(file), "UTF-8");
- JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(in);
+ JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+ JalviewUserColours.class);
+ JalviewUserColours jucs = jbe.getValue();
- for (int i = jucs.getColourCount() - 1; i >= 0; i--)
- {
- String name;
- jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- if (newcol.hasMax())
- {
- Color mincol = null, maxcol = null;
- try
- {
- mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
- maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
+ // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
- } catch (Exception e)
- {
- Cache.log.warn("Couldn't parse out graduated feature color.",
- e);
- }
- FeatureColourI gcol = new FeatureColour(mincol, maxcol,
- newcol.getMin(), newcol.getMax());
- if (newcol.hasAutoScale())
- {
- gcol.setAutoScaled(newcol.getAutoScale());
- }
- if (newcol.hasColourByLabel())
- {
- gcol.setColourByLabel(newcol.getColourByLabel());
- }
- if (newcol.hasThreshold())
- {
- gcol.setThreshold(newcol.getThreshold());
- }
- if (newcol.getThreshType().length() > 0)
- {
- String ttyp = newcol.getThreshType();
- if (ttyp.equalsIgnoreCase("ABOVE"))
- {
- gcol.setAboveThreshold(true);
- }
- if (ttyp.equalsIgnoreCase("BELOW"))
- {
- gcol.setBelowThreshold(true);
- }
- }
- fr.setColour(name = newcol.getName(), gcol);
- }
- else
- {
- Color color = new Color(
- Integer.parseInt(jucs.getColour(i).getRGB(), 16));
- fr.setColour(name = jucs.getColour(i).getName(),
- new FeatureColour(color));
- }
- fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
- }
- if (table != null)
+ /*
+ * load feature colours
+ */
+ for (int i = jucs.getColour().size() - 1; i >= 0; i--)
+ {
+ Colour newcol = jucs.getColour().get(i);
+ FeatureColourI colour = jalview.project.Jalview2XML
+ .parseColour(newcol);
+ fr.setColour(newcol.getName(), colour);
+ fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
+ }
+
+ /*
+ * load feature filters; loaded filters will replace any that are
+ * currently defined, other defined filters are left unchanged
+ */
+ for (int i = 0; i < jucs.getFilter().size(); i++)
+ {
+ Filter filterModel = jucs.getFilter().get(i);
+ String featureType = filterModel.getFeatureType();
+ FeatureMatcherSetI filter = jalview.project.Jalview2XML
+ .parseFilter(featureType, filterModel.getMatcherSet());
+ if (!filter.isEmpty())
{
- resetTable(null);
- Object[][] data = ((FeatureTableModel) table.getModel())
- .getData();
- ensureOrder(data);
- updateFeatureRenderer(data, false);
- table.repaint();
+ fr.setFeatureFilter(featureType, filter);
}
- } catch (Exception ex)
+ }
+
+ /*
+ * update feature settings table
+ */
+ if (table != null)
{
- System.out.println("Error loading User Colour File\n" + ex);
+ resetTable(null);
+ Object[][] data = ((FeatureTableModel) table.getModel())
+ .getData();
+ ensureOrder(data);
+ updateFeatureRenderer(data, false);
+ table.repaint();
}
+ } catch (Exception ex)
+ {
+ System.out.println("Error loading User Colour File\n" + ex);
}
}
+ /**
+ * Offers a file chooser dialog, and then saves the current feature colours
+ * and any filters to the selected file in XML format
+ */
void save()
{
JalviewFileChooser chooser = new JalviewFileChooser("fc",
- "Sequence Feature Colours");
+ SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_feature_colours"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
- ucs.setSchemeName("Sequence Features");
- try
- {
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(choice), "UTF-8"));
+ save(chooser.getSelectedFile());
+ }
+ }
+
+ /**
+ * Saves feature colours and filters to the given file
+ *
+ * @param file
+ */
+ void save(File file)
+ {
+ JalviewUserColours ucs = new JalviewUserColours();
+ ucs.setSchemeName("Sequence Features");
+ try
+ {
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(file), "UTF-8"));
- Set<String> fr_colours = fr.getAllFeatureColours();
- Iterator<String> e = fr_colours.iterator();
- float[] sortOrder = new float[fr_colours.size()];
- String[] sortTypes = new String[fr_colours.size()];
- int i = 0;
- while (e.hasNext())
+ /*
+ * sort feature types by colour order, from 0 (highest)
+ * to 1 (lowest)
+ */
+ Set<String> fr_colours = fr.getAllFeatureColours();
+ String[] sortedTypes = fr_colours
+ .toArray(new String[fr_colours.size()]);
+ Arrays.sort(sortedTypes, new Comparator<String>()
+ {
+ @Override
+ public int compare(String type1, String type2)
{
- sortTypes[i] = e.next();
- sortOrder[i] = fr.getOrder(sortTypes[i]);
- i++;
+ return Float.compare(fr.getOrder(type1), fr.getOrder(type2));
}
- QuickSort.sort(sortOrder, sortTypes);
- sortOrder = null;
- for (i = 0; i < sortTypes.length; i++)
+ });
+
+ /*
+ * save feature colours
+ */
+ for (String featureType : sortedTypes)
+ {
+ FeatureColourI fcol = fr.getFeatureStyle(featureType);
+ Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+ fcol);
+ ucs.getColour().add(col);
+ }
+
+ /*
+ * save any feature filters
+ */
+ for (String featureType : sortedTypes)
+ {
+ FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
+ if (filter != null && !filter.isEmpty())
{
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
- col.setName(sortTypes[i]);
- FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
- if (fcol.isSimpleColour())
- {
- col.setRGB(Format.getHexString(fcol.getColour()));
- }
- else
- {
- col.setRGB(Format.getHexString(fcol.getMaxColour()));
- col.setMin(fcol.getMin());
- col.setMax(fcol.getMax());
- col.setMinRGB(
- jalview.util.Format.getHexString(fcol.getMinColour()));
- col.setAutoScale(fcol.isAutoScaled());
- col.setThreshold(fcol.getThreshold());
- col.setColourByLabel(fcol.isColourByLabel());
- col.setThreshType(fcol.isAboveThreshold() ? "ABOVE"
- : (fcol.isBelowThreshold() ? "BELOW" : "NONE"));
- }
- ucs.addColour(col);
+ Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
+ FeatureMatcherI firstMatcher = iterator.next();
+ jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
+ .marshalFilter(firstMatcher, iterator,
+ filter.isAnded());
+ Filter filterModel = new Filter();
+ filterModel.setFeatureType(featureType);
+ filterModel.setMatcherSet(ms);
+ ucs.getFilter().add(filterModel);
}
- ucs.marshal(out);
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
}
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewUserColours.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewUserColours(ucs), out);
+
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
+ out.flush();
+
+ // ucs.marshal(out);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
}
public void invertSelection()
{
- for (int i = 0; i < table.getRowCount(); i++)
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ for (int i = 0; i < data.length; i++)
{
- Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN);
-
- table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN);
+ data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN];
}
+ updateFeatureRenderer(data, true);
+ table.repaint();
}
public void orderByAvWidth()
{
String type = (String) data[i][TYPE_COLUMN];
FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN];
- KeyedMatcherSetI theFilter = (KeyedMatcherSetI) data[i][FILTER_COLUMN];
+ FeatureMatcherSetI theFilter = (FeatureMatcherSetI) data[i][FILTER_COLUMN];
Boolean isShown = (Boolean) data[i][SHOW_COLUMN];
rowData[i] = new FeatureSettingsBean(type, colour, theFilter,
isShown);
JPanel settingsPane = new JPanel();
settingsPane.setLayout(new BorderLayout());
- dasSettingsPane.setLayout(new BorderLayout());
-
JPanel bigPanel = new JPanel();
bigPanel.setLayout(new BorderLayout());
JButton loadColours = new JButton(
MessageManager.getString("label.load_colours"));
loadColours.setFont(JvSwingUtils.getLabelFont());
+ loadColours.setToolTipText(
+ MessageManager.getString("label.load_colours_tooltip"));
loadColours.addActionListener(new ActionListener()
{
@Override
JButton saveColours = new JButton(
MessageManager.getString("label.save_colours"));
saveColours.setFont(JvSwingUtils.getLabelFont());
+ saveColours.setToolTipText(
+ MessageManager.getString("label.save_colours_tooltip"));
saveColours.addActionListener(new ActionListener()
{
@Override
transparency.setMaximum(70);
transparency.setToolTipText(
MessageManager.getString("label.transparency_tip"));
- fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
- fetchDAS.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- fetchDAS_actionPerformed(e);
- }
- });
- saveDAS.setText(MessageManager.getString("action.save_as_default"));
- saveDAS.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- saveDAS_actionPerformed(e);
- }
- });
-
- JPanel dasButtonPanel = new JPanel();
- dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
- dasSettingsPane.setBorder(null);
- cancelDAS.setEnabled(false);
- cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
- cancelDAS.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancelDAS_actionPerformed(e);
- }
- });
JPanel transPanel = new JPanel(new GridLayout(1, 2));
bigPanel.add(transPanel, BorderLayout.SOUTH);
buttonPanel.add(loadColours);
buttonPanel.add(saveColours);
bigPanel.add(scrollPane, BorderLayout.CENTER);
- dasSettingsPane.add(dasButtonPanel, BorderLayout.SOUTH);
- dasButtonPanel.add(fetchDAS);
- dasButtonPanel.add(cancelDAS);
- dasButtonPanel.add(saveDAS);
settingsPane.add(bigPanel, BorderLayout.CENTER);
settingsPane.add(buttonPanel, BorderLayout.SOUTH);
this.add(settingsPane);
}
- public void fetchDAS_actionPerformed(ActionEvent e)
- {
- fetchDAS.setEnabled(false);
- cancelDAS.setEnabled(true);
- dassourceBrowser.setGuiEnabled(false);
- Vector<jalviewSourceI> selectedSources = dassourceBrowser
- .getSelectedSources();
- doDasFeatureFetch(selectedSources, true, true);
- }
-
/**
- * get the features from selectedSources for all or the current selection
+ * Answers a suitable tooltip to show on the colour cell of the table
*
- * @param selectedSources
- * @param checkDbRefs
- * @param promptFetchDbRefs
+ * @param fcol
+ * @param withHint
+ * if true include 'click to edit' and similar text
+ * @return
*/
- private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
- boolean checkDbRefs, boolean promptFetchDbRefs)
+ public static String getColorTooltip(FeatureColourI fcol,
+ boolean withHint)
{
- SequenceI[] dataset, seqs;
- int iSize;
- AlignmentViewport vp = af.getViewport();
- if (vp.getSelectionGroup() != null
- && vp.getSelectionGroup().getSize() > 0)
+ if (fcol == null)
{
- iSize = vp.getSelectionGroup().getSize();
- dataset = new SequenceI[iSize];
- seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
+ return null;
}
- else
+ if (fcol.isSimpleColour())
{
- iSize = vp.getAlignment().getHeight();
- seqs = vp.getAlignment().getSequencesArray();
+ return withHint ? BASE_TOOLTIP : null;
}
-
- dataset = new SequenceI[iSize];
- for (int i = 0; i < iSize; i++)
+ String description = fcol.getDescription();
+ description = description.replaceAll("<", "<");
+ description = description.replaceAll(">", ">");
+ StringBuilder tt = new StringBuilder(description);
+ if (withHint)
{
- dataset[i] = seqs[i].getDatasetSequence();
+ tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
}
-
- cancelDAS.setEnabled(true);
- dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
- this, selectedSources, checkDbRefs, promptFetchDbRefs);
- af.getViewport().setShowSequenceFeatures(true);
- af.showSeqFeatures.setSelected(true);
- }
-
- /**
- * blocking call to initialise the das source browser
- */
- public void initDasSources()
- {
- dassourceBrowser.initDasSources();
- }
-
- /**
- * examine the current list of das sources and return any matching the given
- * nicknames in sources
- *
- * @param sources
- * Vector of Strings to resolve to DAS source nicknames.
- * @return sources that are present in source list.
- */
- public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
- {
- return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
- }
-
- /**
- * get currently selected das sources. ensure you have called initDasSources
- * before calling this.
- *
- * @return vector of selected das source nicknames
- */
- public Vector<jalviewSourceI> getSelectedSources()
- {
- return dassourceBrowser.getSelectedSources();
+ return JvSwingUtils.wrapTooltip(true, tt.toString());
}
- /**
- * properly initialise DAS fetcher and then initiate a new thread to fetch
- * features from the named sources (rather than any turned on by default)
- *
- * @param sources
- * @param block
- * if true then runs in same thread, otherwise passes to the Swing
- * executor
- */
- public void fetchDasFeatures(Vector<String> sources, boolean block)
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
+ int w, int h)
{
- initDasSources();
- List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
- .resolveSourceNicknames(sources);
- if (resolved.size() == 0)
+ boolean thr = false;
+ StringBuilder tx = new StringBuilder();
+
+ if (gcol.isColourByAttribute())
{
- resolved = dassourceBrowser.getSelectedSources();
+ tx.append(FeatureMatcher
+ .toAttributeDisplayName(gcol.getAttributeName()));
}
- if (resolved.size() > 0)
+ else if (!gcol.isColourByLabel())
{
- final List<jalviewSourceI> dassources = resolved;
- fetchDAS.setEnabled(false);
- // cancelDAS.setEnabled(true); doDasFetch does this.
- Runnable fetcher = new Runnable()
- {
-
- @Override
- public void run()
- {
- doDasFeatureFetch(dassources, true, false);
-
- }
- };
- if (block)
+ tx.append(MessageManager.getString("label.score"));
+ }
+ tx.append(" ");
+ if (gcol.isAboveThreshold())
+ {
+ thr = true;
+ tx.append(">");
+ }
+ if (gcol.isBelowThreshold())
+ {
+ thr = true;
+ tx.append("<");
+ }
+ if (gcol.isColourByLabel())
+ {
+ if (thr)
{
- fetcher.run();
+ tx.append(" ");
}
- else
+ if (!gcol.isColourByAttribute())
{
- SwingUtilities.invokeLater(fetcher);
+ tx.append("Label");
}
+ comp.setIcon(null);
}
- }
-
- public void saveDAS_actionPerformed(ActionEvent e)
- {
- dassourceBrowser
- .saveProperties(jalview.bin.Cache.applicationProperties);
- }
-
- public void complete()
- {
- fetchDAS.setEnabled(true);
- cancelDAS.setEnabled(false);
- dassourceBrowser.setGuiEnabled(true);
-
- }
-
- public void cancelDAS_actionPerformed(ActionEvent e)
- {
- if (dasFeatureFetcher != null)
+ else
{
- dasFeatureFetcher.cancel();
+ Color newColor = gcol.getMaxColour();
+ comp.setBackground(newColor);
+ // System.err.println("Width is " + w / 2);
+ Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
+ comp.setIcon(ficon);
+ // tt+="RGB value: Max (" + newColor.getRed() + ", "
+ // + newColor.getGreen() + ", " + newColor.getBlue()
+ // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
+ // + ", " + minCol.getBlue() + ")");
}
- complete();
- }
-
- public void noDasSourceActive()
- {
- complete();
- JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.getString("label.no_das_sources_selected_warn"),
- MessageManager.getString("label.no_das_sources_selected_title"),
- JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
+ comp.setHorizontalAlignment(SwingConstants.CENTER);
+ comp.setText(tx.toString());
}
// ///////////////////////////////////////////////////////////////////////
// ///////////////////////////////////////////////////////////////////////
class FeatureTableModel extends AbstractTableModel
{
- /*
- * column indices of fields in Feature Settings table
- */
- static final int TYPE_COLUMN = 0;
-
- static final int COLOUR_COLUMN = 1;
-
- static final int FILTER_COLUMN = 2;
-
- static final int SHOW_COLUMN = 3;
-
private String[] columnNames = {
MessageManager.getString("label.feature_type"),
MessageManager.getString("action.colour"),
- MessageManager.getString("label.filter"),
+ MessageManager.getString("label.configuration"),
MessageManager.getString("label.show") };
private Object[][] data;
class ColorRenderer extends JLabel implements TableCellRenderer
{
- javax.swing.border.Border unselectedBorder = null;
+ Border unselectedBorder = null;
- javax.swing.border.Border selectedBorder = null;
-
- final String baseTT = "Click to edit, right/apple click for menu.";
+ Border selectedBorder = null;
public ColorRenderer()
{
{
FeatureColourI cellColour = (FeatureColourI) color;
setOpaque(true);
- setToolTipText(baseTT);
setBackground(tbl.getBackground());
if (!cellColour.isSimpleColour())
{
Object filter, boolean isSelected, boolean hasFocus, int row,
int column)
{
- KeyedMatcherSetI theFilter = (KeyedMatcherSetI) filter;
+ FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter;
setOpaque(true);
String asText = theFilter.toString();
setBackground(tbl.getBackground());
renderGraduatedColor(comp, gcol, w, h);
}
- public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
- int w, int h)
- {
- boolean thr = false;
- StringBuilder tt = new StringBuilder();
- StringBuilder tx = new StringBuilder();
-
- if (gcol.isColourByAttribute())
- {
- tx.append(String.join(":", gcol.getAttributeName()));
- }
- else if (!gcol.isColourByLabel())
- {
- tx.append(MessageManager.getString("label.score"));
- }
- tx.append(" ");
- if (gcol.isAboveThreshold())
- {
- thr = true;
- tx.append(">");
- tt.append("Thresholded (Above ").append(gcol.getThreshold())
- .append(") ");
- }
- if (gcol.isBelowThreshold())
- {
- thr = true;
- tx.append("<");
- tt.append("Thresholded (Below ").append(gcol.getThreshold())
- .append(") ");
- }
- if (gcol.isColourByLabel())
- {
- tt.append("Coloured by label text. ").append(tt);
- if (thr)
- {
- tx.append(" ");
- }
- if (!gcol.isColourByAttribute())
- {
- tx.append("Label");
- }
- comp.setIcon(null);
- }
- else
- {
- Color newColor = gcol.getMaxColour();
- comp.setBackground(newColor);
- // System.err.println("Width is " + w / 2);
- Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
- comp.setIcon(ficon);
- // tt+="RGB value: Max (" + newColor.getRed() + ", "
- // + newColor.getGreen() + ", " + newColor.getBlue()
- // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
- // + ", " + minCol.getBlue() + ")");
- }
- comp.setHorizontalAlignment(SwingConstants.CENTER);
- comp.setText(tx.toString());
- if (tt.length() > 0)
- {
- if (comp.getToolTipText() == null)
- {
- comp.setToolTipText(tt.toString());
- }
- else
- {
- comp.setToolTipText(
- tt.append(" ").append(comp.getToolTipText()).toString());
- }
- }
- }
-
class ColorEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
{
// bring up graduated chooser.
chooser = new FeatureTypeSettings(me.fr, type);
- chooser.setRequestFocusEnabled(true);
- chooser.requestFocus();
+ /**
+ * @j2sNative
+ */
+ {
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
+ }
chooser.addActionListener(this);
- chooser.showTab(true);
+ // Make the renderer reappear.
+ fireEditingStopped();
}
- // Make the renderer reappear.
- fireEditingStopped();
-
}
else
{
* update table data without triggering updateFeatureRenderer
*/
currentColor = fr.getFeatureColours().get(type);
- KeyedMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
+ FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
if (currentFilter == null)
{
- currentFilter = new KeyedMatcherSet();
+ currentFilter = new FeatureMatcherSet();
}
Object[] data = ((FeatureTableModel) table.getModel())
.getData()[rowSelected];
{
FeatureSettings me;
- KeyedMatcherSetI currentFilter;
+ FeatureMatcherSetI currentFilter;
Point lastLocation;
chooser.getWidth(), chooser.getHeight());
chooser.validate();
}
- chooser.showTab(false);
fireEditingStopped();
}
else if (e.getSource() instanceof Component)
currentFilter = me.fr.getFeatureFilter(type);
if (currentFilter == null)
{
- currentFilter = new KeyedMatcherSet();
+ currentFilter = new FeatureMatcherSet();
}
Object[] data = ((FeatureTableModel) table.getModel())
.getData()[rowSelected];
public Component getTableCellEditorComponent(JTable theTable, Object value,
boolean isSelected, int row, int column)
{
- currentFilter = (KeyedMatcherSetI) value;
+ currentFilter = (FeatureMatcherSetI) value;
this.rowSelected = row;
type = me.table.getValueAt(row, TYPE_COLUMN).toString();
button.setOpaque(true);
button.setBackground(me.getBackground());
button.setText(currentFilter.toString());
- button.setToolTipText(currentFilter.toString());
button.setIcon(null);
return button;
}
git://source.jalview.org / jalview.git / blobdiff