*/
package jalview.gui;
+import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
+import jalview.api.SplitContainerI;
+import jalview.api.ViewStyleI;
+import jalview.controller.FeatureSettingsControllerGuiI;
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.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+import jalview.viewmodel.styles.ViewStyle;
import jalview.xml.binding.jalview.JalviewUserColours;
import jalview.xml.binding.jalview.JalviewUserColours.Colour;
import jalview.xml.binding.jalview.JalviewUserColours.Filter;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
+import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.GridLayout;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
+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.stream.XMLStreamReader;
public class FeatureSettings extends JPanel
- implements FeatureSettingsControllerI
+ implements FeatureSettingsControllerI, FeatureSettingsControllerGuiI
{
private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
.getString("label.sequence_feature_colours");
private static final int MIN_HEIGHT = 400;
+ private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit");
+
final FeatureRenderer fr;
public final AlignFrame af;
private float originalTransparency;
+ private ViewStyleI originalViewStyle;
+
private Map<String, FeatureMatcherSetI> originalFilters;
final JInternalFrame frame;
JSlider transparency = new JSlider();
- JCheckBox showComplement;
-
/*
* when true, constructor is still executing - so ignore UI events
*/
int selectedRow = -1;
- JButton fetchDAS = new JButton();
-
- JButton saveDAS = new JButton();
-
- JButton cancelDAS = new JButton();
-
boolean resettingTable = false;
/*
transparency.setMaximum(100 - originalTransparencyAsPercent);
originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
+ originalViewStyle = new ViewStyle(af.viewport.getViewStyle());
try
{
{
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());
FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
column);
tip = o.isEmpty()
default:
break;
}
+
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(Color.class, new ColorEditor(this));
- //
table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
@Override
public void mousePressed(MouseEvent evt)
{
- selectedRow = table.rowAtPoint(evt.getPoint());
+ Point pt = evt.getPoint();
+ selectedRow = table.rowAtPoint(pt);
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
if (evt.isPopupTrigger())
{
popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
evt.getY());
}
- else if (evt.getClickCount() == 2)
+ else if (evt.getClickCount() == 2
+ && table.columnAtPoint(pt) == TYPE_COLUMN)
{
boolean invertSelection = evt.isAltDown();
boolean toggleSelection = Platform.isControlDown(evt);
boolean extendSelection = evt.isShiftDown();
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
invertSelection, extendSelection, toggleSelection, type);
+ fr.ap.av.sendSelection();
}
}
}
discoverAllFeatureData();
- final PropertyChangeListener change;
final FeatureSettings fs = this;
fr.addPropertyChangeListener(change = new PropertyChangeListener()
{
}
});
-
- frame = new JInternalFrame();
- frame.setContentPane(this);
- if (Platform.isAMac())
+ SplitContainerI splitframe = af.getSplitViewContainer();
+ if (splitframe != null)
{
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 480);
+ frame = null; // keeps eclipse happy
+ splitframe.addFeatureSettingsUI(this);
}
else
{
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 450);
- }
- frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (Platform.isAMac())
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, 480);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, 450);
+ }
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
- frame.addInternalFrameListener(
- new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
{
- fr.removePropertyChangeListener(change);
- };
- });
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ featureSettings_isClosed();
+ };
+ });
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
inConstruction = false;
}
+ PropertyChangeListener change;
+
+ @Override
+ public AlignViewControllerGuiI getAlignframe()
+ {
+ return af;
+ }
+
+ @Override
+ public void featureSettings_isClosed()
+ {
+ fr.removePropertyChangeListener(change);
+ change = null;
+ }
+
protected void popupSort(final int rowSelected, final String type,
final Object typeCol, final Map<String, float[][]> minmax, int x,
int y)
{
- final FeatureColourI featureColour = (FeatureColourI) typeCol;
-
JPopupMenu men = new JPopupMenu(MessageManager
.formatMessage("label.settings_for_param", new String[]
{ type }));
{
fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
false, type);
+ fr.ap.av.sendSelection();
}
});
JMenuItem clearCols = new JMenuItem(MessageManager
{
fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
false, type);
+ fr.ap.av.sendSelection();
}
});
JMenuItem hideCols = new JMenuItem(
public void actionPerformed(ActionEvent arg0)
{
fr.ap.alignFrame.hideFeatureColumns(type, true);
+ fr.ap.av.sendSelection();
}
});
JMenuItem hideOtherCols = new JMenuItem(
public void actionPerformed(ActionEvent arg0)
{
fr.ap.alignFrame.hideFeatureColumns(type, false);
+ fr.ap.av.sendSelection();
}
});
men.add(selCols);
data[dataIndex][FILTER_COLUMN] = featureFilter == null
? new FeatureMatcherSet()
: featureFilter;
- data[dataIndex][SHOW_COLUMN] = new Boolean(
+ data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(
af.getViewport().getFeaturesDisplayed().isVisible(type));
dataIndex++;
displayableTypes.remove(type);
data[dataIndex][FILTER_COLUMN] = featureFilter == null
? new FeatureMatcherSet()
: featureFilter;
- data[dataIndex][SHOW_COLUMN] = new Boolean(true);
+ data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(true);
dataIndex++;
displayableTypes.remove(type);
}
{
try
{
- frame.setClosed(true);
+ if (frame != null)
+ {
+ frame.setClosed(true);
+ }
+ else
+ {
+ SplitContainerI sc = af.getSplitViewContainer();
+ sc.closeFeatureSettings(this);
+ af.featureSettings = null;
+ }
} catch (Exception exe)
{
}
}
}
});
- help.setFont(JvSwingUtils.getLabelFont());
- help.setText(MessageManager.getString("action.help"));
- help.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- Help.showHelpWindow(HelpId.SequenceFeatureSettings);
- } catch (HelpSetException e1)
- {
- e1.printStackTrace();
- }
- }
- });
JButton cancel = new JButton(MessageManager.getString("action.cancel"));
cancel.setFont(JvSwingUtils.getLabelFont());
fr.setTransparency(originalTransparency);
fr.setFeatureFilters(originalFilters);
updateFeatureRenderer(originalData);
+ af.getViewport().setViewStyle(originalViewStyle);
close();
}
});
MessageManager.getString("label.transparency_tip"));
boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
- showComplement = new JCheckBox(
- "Show " + (nucleotide ? "protein" : "CDS") + " features");
+ String text = MessageManager.formatMessage("label.show_linked_features",
+ nucleotide
+ ? MessageManager.getString("label.protein")
+ .toLowerCase()
+ : "CDS");
+ JCheckBox showComplement = new JCheckBox(text);
showComplement.setSelected(af.getViewport().isShowComplementFeatures());
showComplement.addActionListener(new ActionListener()
{
}
});
- JPanel transPanel = new JPanel(new GridLayout(1, 2));
- bigPanel.add(transPanel, BorderLayout.SOUTH);
+ JCheckBox showComplementOnTop = new JCheckBox(
+ MessageManager.getString("label.on_top"));
+ showComplementOnTop
+ .setSelected(af.getViewport().isShowComplementFeaturesOnTop());
+ showComplementOnTop.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ af.getViewport().setShowComplementFeaturesOnTop(
+ showComplementOnTop.isSelected());
+ refreshDisplay();
+ }
+ });
+ // JButton viewComplementSettings = new JButton(MessageManager
+ // .formatMessage("label.show_linked_feature_settings",
+ // nucleotide
+ // ? MessageManager.getString("label.protein")
+ // .toLowerCase()
+ // : "CDS"));
+ // viewComplementSettings.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // AlignViewControllerGuiI complAf = af.getSplitViewContainer()
+ // .getComplementAlignFrame(af);
+ // FeatureSettings complFeatureSettings = (FeatureSettings) complAf
+ // .getFeatureSettingsUI();
+ // if (complFeatureSettings != null)
+ // {
+ // complFeatureSettings.frame.setVisible(true);
+ // try
+ // {
+ // complFeatureSettings.frame.setSelected(true);
+ // return;
+ // } catch (Exception q)
+ // {
+ // }
+ // }
+ // {
+ // complAf.showFeatureSettingsUI();
+ // }
+ // }
+ // });
+ JPanel lowerPanel = new JPanel(new GridLayout(1, 2));
+ bigPanel.add(lowerPanel, BorderLayout.SOUTH);
JPanel transbuttons = new JPanel(new GridLayout(5, 1));
transbuttons.add(optimizeOrder);
boolean hasComplement = af.getViewport().getCodingComplement() != null;
JPanel transPanelLeft = new JPanel(
- new GridLayout(hasComplement ? 2 : 1, 1));
+ new GridLayout(hasComplement ? 4 : 2, 1));
+ transPanelLeft.add(new JLabel(" Colour transparency" + ":"));
transPanelLeft.add(transparency);
if (hasComplement)
{
- transPanelLeft.add(showComplement);
+ JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ cp.add(showComplement);
+ cp.add(showComplementOnTop);
+ transPanelLeft.add(cp);
}
- transPanel.add(transPanelLeft);
- transPanel.add(transbuttons);
+ lowerPanel.add(transPanelLeft);
+ lowerPanel.add(transbuttons);
JPanel buttonPanel = new JPanel();
buttonPanel.add(ok);
}
}
+ /**
+ * Answers a suitable tooltip to show on the colour cell of the table
+ *
+ * @param fcol
+ * @param withHint
+ * if true include 'click to edit' and similar text
+ * @return
+ */
+ public static String getColorTooltip(FeatureColourI fcol,
+ boolean withHint)
+ {
+ if (fcol == null)
+ {
+ return null;
+ }
+ if (fcol.isSimpleColour())
+ {
+ return withHint ? BASE_TOOLTIP : null;
+ }
+ String description = fcol.getDescription();
+ description = description.replaceAll("<", "<");
+ description = description.replaceAll(">", ">");
+ StringBuilder tt = new StringBuilder(description);
+ if (withHint)
+ {
+ tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
+ }
+ return JvSwingUtils.wrapTooltip(true, tt.toString());
+ }
+
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
+ int w, int h)
+ {
+ boolean thr = false;
+ StringBuilder tx = new StringBuilder();
+
+ if (gcol.isColourByAttribute())
+ {
+ tx.append(FeatureMatcher
+ .toAttributeDisplayName(gcol.getAttributeName()));
+ }
+ else if (!gcol.isColourByLabel())
+ {
+ 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)
+ {
+ 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());
+ }
+
// ///////////////////////////////////////////////////////////////////////
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
// ///////////////////////////////////////////////////////////////////////
}
/**
- * Answers the class of the object in column c of the first row of the table
+ * Answers the class of column c of the table
*/
@Override
public Class<?> getColumnClass(int c)
{
- Object v = getValueAt(0, c);
- return v == null ? null : v.getClass();
+ switch (c)
+ {
+ case TYPE_COLUMN:
+ return String.class;
+ case COLOUR_COLUMN:
+ return FeatureColour.class;
+ case FILTER_COLUMN:
+ return FeatureMatcherSet.class;
+ default:
+ return Boolean.class;
+ }
}
@Override
class ColorRenderer extends JLabel implements TableCellRenderer
{
- javax.swing.border.Border unselectedBorder = null;
-
- javax.swing.border.Border selectedBorder = null;
+ Border unselectedBorder = 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())
{
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
{
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