/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
+import jalview.api.FeatureSettingsControllerI;
import jalview.bin.Cache;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import java.awt.BorderLayout;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
-public class FeatureSettings extends JPanel
+public class FeatureSettings extends JPanel implements
+ FeatureSettingsControllerI
{
DasSourceBrowser dassourceBrowser;
this.af = af;
fr = af.getFeatureRenderer();
// allow transparency to be recovered
- transparency.setMaximum(100 - (int) ((originalTransparency=fr.getTransparency()) * 100));
+ transparency.setMaximum(100 - (int) ((originalTransparency = fr
+ .getTransparency()) * 100));
try
{
ex.printStackTrace();
}
- table = new JTable() {
+ table = new JTable()
+ {
@Override
- public String getToolTipText(MouseEvent e) {
- if (table.columnAtPoint(e.getPoint()) == 0) {
+ public String getToolTipText(MouseEvent e)
+ {
+ if (table.columnAtPoint(e.getPoint()) == 0)
+ {
/*
* Tooltip for feature name only
*/
- return JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.feature_settings_click_drag"));
+ return JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.feature_settings_click_drag"));
}
return null;
}
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
table.getValueAt(selectedRow, 1), fr.getMinMax(),
- evt.getX(),
- evt.getY());
+ evt.getX(), evt.getY());
}
}
});
}
}
});
-// table.setToolTipText(JvSwingUtils.wrapTooltip(true,
-// MessageManager.getString("label.feature_settings_click_drag")));
+ // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ // MessageManager.getString("label.feature_settings_click_drag")));
scrollPane.setViewportView(table);
dassourceBrowser = new DasSourceBrowser(this);
fr.findAllFeatures(true); // display everything!
}
- setTableData();
+ discoverAllFeatureData();
final PropertyChangeListener change;
final FeatureSettings fs = this;
fr.addPropertyChangeListener(change = new PropertyChangeListener()
final Object typeCol, final Hashtable minmax, int x, int y)
{
JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
- "label.settings_for_param", new String[]
- { type }));
+ "label.settings_for_param", new String[] { type }));
JMenuItem scr = new JMenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
public void actionPerformed(ActionEvent e)
{
- me.af.avc.sortAlignmentByFeatureScore(new String[]
- { type });
+ me.af.avc.sortAlignmentByFeatureScore(new String[] { type });
}
});
public void actionPerformed(ActionEvent e)
{
- me.af.avc.sortAlignmentByFeatureDensity(new String[]
- { type });
+ me.af.avc.sortAlignmentByFeatureDensity(new String[] { type });
}
});
*/
Hashtable typeWidth = null;
- synchronized public void setTableData()
+ @Override
+ synchronized public void discoverAllFeatureData()
{
Vector allFeatures = new Vector();
Vector allGroups = new Vector();
String group;
for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- if (af.getViewport().getAlignment().getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures() == null)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
+ .getSequenceFeatures();
+ if (tmpfeatures == null)
{
continue;
}
- tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures();
-
int index = 0;
while (index < tmpfeatures.length)
{
af.alignPanel.overviewPanel.updateOverviewImage();
}
- resetTable(new String[]
- { grp });
+ resetTable(new String[] { grp });
}
});
groupPanel.add(check);
{
tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures();
+ .getSequenceFeatures();
if (tmpfeatures == null)
{
continue;
void load()
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "fc" }, new String[]
- { "Sequence Feature Colours" }, "Sequence Feature Colours");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "fc" },
+ new String[] { "Sequence Feature Colours" },
+ "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.load_feature_colours"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
file), "UTF-8");
jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
- jucs = jucs
- .unmarshal(in);
+ jucs = jucs.unmarshal(in);
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
void save()
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "fc" }, new String[]
- { "Sequence Feature Colours" }, "Sequence Feature Colours");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "fc" },
+ new String[] { "Sequence Feature Colours" },
+ "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_feature_colours"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
}
}
if (sort)
- {
+ {
jalview.util.QuickSort.sort(width, data);
- // update global priority order
+ // update global priority order
}
updateFeatureRenderer(data, false);
}
});
this.add(tabbedPane, java.awt.BorderLayout.CENTER);
- tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane);
- tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane);
+ tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
+ settingsPane);
+ tabbedPane.addTab(MessageManager.getString("label.das_settings"),
+ dasSettingsPane);
bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
transbuttons.add(optimizeOrder);
transbuttons.add(invert);
{
SequenceI[] dataset, seqs;
int iSize;
- AlignViewport vp = af.getViewport();
+ AlignmentViewport vp = af.getViewport();
if (vp.getSelectionGroup() != null
&& vp.getSelectionGroup().getSize() > 0)
{
this.data = data;
}
- private String[] columnNames =
- { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") };
+ private String[] columnNames = {
+ MessageManager.getString("label.feature_type"),
+ MessageManager.getString("action.colour"),
+ MessageManager.getString("label.display") };
private Object[][] data;