/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import java.io.*;
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-import java.awt.event.*;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-
-import javax.swing.*;
-import javax.swing.event.*;
-import javax.swing.table.*;
-
-import jalview.analysis.AlignmentSorter;
-import jalview.api.FeaturesDisplayedI;
+import jalview.api.FeatureSettingsControllerI;
import jalview.bin.Cache;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Help.HelpId;
+import jalview.io.JalviewFileChooser;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import jalview.ws.dbsources.das.api.jalviewSourceI;
-public class FeatureSettings extends JPanel
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.help.HelpSetException;
+import javax.swing.AbstractCellEditor;
+import javax.swing.BorderFactory;
+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.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.JSlider;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.TableCellEditor;
+import javax.swing.table.TableCellRenderer;
+
+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)
+ {
+ /*
+ * Tooltip for feature name only
+ */
+ return JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.feature_settings_click_drag"));
+ }
+ return null;
+ }
+ };
table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
table.setFont(new Font("Verdana", Font.PLAIN, 12));
table.setDefaultRenderer(Color.class, new ColorRenderer());
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
- if (evt.isPopupTrigger())
+ if (SwingUtilities.isRightMouseButton(evt))
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
table.getValueAt(selectedRow, 1), fr.getMinMax(),
(String) table.getValueAt(selectedRow, 0));
}
}
+
+ // isPopupTrigger fires on mouseReleased on Mac
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ selectedRow = table.rowAtPoint(evt.getPoint());
+ if (evt.isPopupTrigger())
+ {
+ popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
+ table.getValueAt(selectedRow, 1), fr.getMinMax(),
+ evt.getX(), evt.getY());
+ }
+ }
});
table.addMouseMotionListener(new MouseMotionAdapter()
}
}
});
- table.setToolTipText("<html>"
- + JvSwingUtils
- .wrapTooltip("Click/drag feature types up or down to change render order.<br/>Double click to select columns containing feature in alignment/current selection<br/>Pressing Alt will select columns outside features rather than inside<br/>Pressing Shift to modify current selection (rather than clear current selection)<br/>Press CTRL or Command/Meta to toggle columns in/outside features<br/>")
- + "</html>");
+ // 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)
{
public void itemStateChanged(ItemEvent evt)
{
fr.setGroupVisibility(check.getText(), check.isSelected());
- af.alignPanel.seqPanel.seqCanvas.repaint();
+ af.alignPanel.getSeqPanel().seqCanvas.repaint();
if (af.alignPanel.overviewPanel != null)
{
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;
{
order[i] = fr.getOrder(data[i][0].toString());
if (order[i] < 0)
+ {
order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
+ }
if (i > 1)
+ {
sort = sort || order[i - 1] > order[i];
+ }
}
if (sort)
+ {
jalview.util.QuickSort.sort(order, data);
+ }
}
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("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 = (jalview.schemabinding.version2.JalviewUserColours) 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("Save Feature Colour Scheme");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
public void orderByAvWidth()
{
if (table == null || table.getModel() == null)
+ {
return;
+ }
Object[][] data = ((FeatureTableModel) table.getModel()).getData();
float[] width = new float[data.length];
float[] awidth;
width[i] = 0;
}
if (max < width[i])
+ {
max = width[i];
+ }
}
boolean sort = false;
for (int i = 0; i < width.length; i++)
fr.setOrder(data[i][0].toString(), width[i]); // store for later
}
if (i > 0)
+ {
sort = sort || width[i - 1] > width[i];
+ }
}
if (sort)
+ {
jalview.util.QuickSort.sort(width, data);
- // update global priority order
+ // update global priority order
+ }
updateFeatureRenderer(data, false);
table.repaint();
JButton sortByDens = new JButton();
- JPanel transbuttons = new JPanel(new GridLayout(4, 1));
+ JButton help = new JButton();
+
+ JPanel transbuttons = new JPanel(new GridLayout(5, 1));
private void jbInit() throws Exception
{
af.avc.sortAlignmentByFeatureDensity(null);
}
});
+ help.setFont(JvSwingUtils.getLabelFont());
+ help.setText(MessageManager.getString("action.help"));
+ help.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.SequenceFeatureSettings);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ help.setFont(JvSwingUtils.getLabelFont());
+ help.setText(MessageManager.getString("action.help"));
+ help.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.SequenceFeatureSettings);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
cancel.setFont(JvSwingUtils.getLabelFont());
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
public void stateChanged(ChangeEvent evt)
{
- fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
af.alignPanel.paintAlignment(true);
}
});
transparency.setMaximum(70);
+ transparency.setToolTipText(MessageManager
+ .getString("label.transparency_tip"));
fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
fetchDAS.addActionListener(new ActionListener()
{
}
});
this.add(tabbedPane, java.awt.BorderLayout.CENTER);
- tabbedPane.addTab("Feature Settings", settingsPane);
- tabbedPane.addTab("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);
transbuttons.add(sortByScore);
transbuttons.add(sortByDens);
+ transbuttons.add(help);
+ JPanel sliderPanel = new JPanel();
+ sliderPanel.add(transparency);
transPanel.add(transparency);
transPanel.add(transbuttons);
buttonPanel.add(ok);
{
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 =
- { "Feature Type", "Colour", "Display" };
+ private String[] columnNames = {
+ MessageManager.getString("label.feature_type"),
+ MessageManager.getString("action.colour"),
+ MessageManager.getString("label.display") };
private Object[][] data;
git://source.jalview.org / jalview.git / blobdiff