*/
package jalview.gui;
+import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
+import jalview.api.ViewStyleI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcher;
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;
private static final int MIN_HEIGHT = 400;
- private final static String BASE_TOOLTIP = "Click to edit, right-click for menu";
+ private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit");
final FeatureRenderer fr;
private float originalTransparency;
+ private ViewStyleI originalViewStyle;
+
private Map<String, FeatureMatcherSetI> originalFilters;
final JInternalFrame frame;
transparency.setMaximum(100 - originalTransparencyAsPercent);
originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
+ originalViewStyle = new ViewStyle(af.viewport.getViewStyle());
try
{
table = new JTable()
{
- static final String tt = "Click to edit, right-click for menu"; // todo i18n
-
@Override
public String getToolTipText(MouseEvent e)
{
case COLOUR_COLUMN:
FeatureColourI colour = (FeatureColourI) table.getValueAt(row,
column);
- tip = getColorTooltip(colour);
+ tip = getColorTooltip(colour, true);
break;
case FILTER_COLUMN:
FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
default:
break;
}
+
return tip;
}
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());
boolean extendSelection = evt.isShiftDown();
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
invertSelection, extendSelection, toggleSelection, type);
+ fr.ap.av.sendSelection();
}
}
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);
{
fr.setGroupVisibility(check.getText(), check.isSelected());
resetTable(new String[] { grp });
- af.alignPanel.paintAlignment(true, true);
+ refreshDisplay();
}
});
groupPanel.add(check);
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);
}
if (fr.setFeaturePriority(rowData, visibleNew))
{
- af.alignPanel.paintAlignment(true, true);
+ refreshDisplay();
}
}
}
}
});
- 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();
}
});
if (!inConstruction)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
- af.alignPanel.paintAlignment(true, true);
+ refreshDisplay();
}
}
});
transparency.setToolTipText(
MessageManager.getString("label.transparency_tip"));
- JPanel transPanel = new JPanel(new GridLayout(1, 2));
- bigPanel.add(transPanel, BorderLayout.SOUTH);
+ boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+ 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()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ af.getViewport()
+ .setShowComplementFeatures(showComplement.isSelected());
+ refreshDisplay();
+ }
+ });
+
+ 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();
+ }
+ });
+
+ JPanel lowerPanel = new JPanel(new GridLayout(1, 2));
+ bigPanel.add(lowerPanel, BorderLayout.SOUTH);
JPanel transbuttons = new JPanel(new GridLayout(5, 1));
transbuttons.add(optimizeOrder);
transbuttons.add(sortByScore);
transbuttons.add(sortByDens);
transbuttons.add(help);
- transPanel.add(transparency);
- transPanel.add(transbuttons);
+
+ boolean hasComplement = af.getViewport().getCodingComplement() != null;
+ JPanel transPanelLeft = new JPanel(
+ new GridLayout(hasComplement ? 3 : 2, 1));
+ transPanelLeft.add(new JLabel(" Colour transparency" + ":"));
+ transPanelLeft.add(transparency);
+ if (hasComplement)
+ {
+ JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ cp.add(showComplement);
+ cp.add(showComplementOnTop);
+ transPanelLeft.add(cp);
+ }
+ lowerPanel.add(transPanelLeft);
+ lowerPanel.add(transbuttons);
JPanel buttonPanel = new JPanel();
buttonPanel.add(ok);
}
/**
+ * Repaints alignment, structure and overview (if shown). If there is a
+ * complementary view which is showing this view's features, then also
+ * repaints that.
+ */
+ void refreshDisplay()
+ {
+ af.alignPanel.paintAlignment(true, true);
+ AlignViewportI complement = af.getViewport().getCodingComplement();
+ if (complement != null && complement.isShowComplementFeatures())
+ {
+ AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+ af2.alignPanel.paintAlignment(true, true);
+ }
+ }
+
+ /**
* 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)
+ public static String getColorTooltip(FeatureColourI fcol,
+ boolean withHint)
{
if (fcol == null)
{
}
if (fcol.isSimpleColour())
{
- return BASE_TOOLTIP;
+ return withHint ? BASE_TOOLTIP : null;
}
String description = fcol.getDescription();
description = description.replaceAll("<", "<");
description = description.replaceAll(">", ">");
StringBuilder tt = new StringBuilder(description);
- tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
+ if (withHint)
+ {
+ tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
+ }
return JvSwingUtils.wrapTooltip(true, tt.toString());
}
}
/**
- * 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
git://source.jalview.org / jalview.git / blobdiff