/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
+import java.util.Arrays;
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.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;
}
table.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
table.getValueAt(selectedRow, 1), fr.getMinMax(),
- evt.getX(),
- evt.getY());
+ evt.getX(), evt.getY());
}
}
});
table.addMouseMotionListener(new MouseMotionAdapter()
{
+ @Override
public void mouseDragged(MouseEvent evt)
{
int newRow = table.rowAtPoint(evt.getPoint());
if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
{
- Object[] temp = new Object[3];
- temp[0] = table.getValueAt(selectedRow, 0);
- temp[1] = table.getValueAt(selectedRow, 1);
- temp[2] = table.getValueAt(selectedRow, 2);
-
- table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
- table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
- table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
-
- table.setValueAt(temp[0], newRow, 0);
- table.setValueAt(temp[1], newRow, 1);
- table.setValueAt(temp[2], newRow, 2);
-
+ Object[][] data = ((FeatureTableModel) table.getModel())
+ .getData();
+ Object[] temp = data[selectedRow];
+ data[selectedRow] = data[newRow];
+ data[newRow] = temp;
+ updateFeatureRenderer(data);
+ table.repaint();
selectedRow = newRow;
}
}
});
-// 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()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (!fs.resettingTable && !fs.handlingUpdate)
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
}
protected void popupSort(final int selectedRow, final String type,
- final Object typeCol, final Hashtable minmax, int x, int y)
+ final Object typeCol, final Map<String, float[][]> 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);
scr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- me.af.avc.sortAlignmentByFeatureScore(new String[]
- { type });
+ me.af.avc.sortAlignmentByFeatureScore(Arrays
+ .asList(new String[] { type }));
}
});
dens.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- me.af.avc.sortAlignmentByFeatureDensity(new String[]
- { type });
+ me.af.avc.sortAlignmentByFeatureDensity(Arrays
+ .asList(new String[] { type }));
}
});
men.add(dens);
if (minmax != null)
{
- final Object typeMinMax = minmax.get(type);
+ final float[][] typeMinMax = minmax.get(type);
/*
* final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); //
* this is broken at the moment and isn't that useful anyway!
*
* men.add(chb);
*/
- if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+ if (typeMinMax != null && typeMinMax[0] != null)
{
// if (table.getValueAt(row, column));
// graduated colourschemes for those where minmax exists for the
{
JColorChooser colorChooser;
+ @Override
public void actionPerformed(ActionEvent e)
{
if (e.getSource() == mxcol)
*/
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)
{
check.setFont(new Font("Serif", Font.BOLD, 12));
check.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
fr.setGroupVisibility(check.getText(), check.isSelected());
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);
updateFeatureRenderer(data, true);
}
+ /**
+ * Update the priority order of features; only repaint if this changed the
+ * order of visible features
+ *
+ * @param data
+ * @param visibleNew
+ */
private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
{
- fr.setFeaturePriority(data, visibleNew);
- af.alignPanel.paintAlignment(true);
+ if (fr.setFeaturePriority(data, visibleNew))
+ {
+ af.alignPanel.paintAlignment(true);
+ }
}
int selectedRow = -1;
invert.setText(MessageManager.getString("label.invert_selection"));
invert.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
invertSelection();
optimizeOrder.setText(MessageManager.getString("label.optimise_order"));
optimizeOrder.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
orderByAvWidth();
.setText(MessageManager.getString("label.seq_sort_by_score"));
sortByScore.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
af.avc.sortAlignmentByFeatureScore(null);
.getString("label.sequence_sort_by_density"));
sortByDens.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
af.avc.sortAlignmentByFeatureDensity(null);
help.setText(MessageManager.getString("action.help"));
help.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
try
help.setText(MessageManager.getString("action.help"));
help.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
try
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
fr.setTransparency(originalTransparency);
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
close();
loadColours.setText(MessageManager.getString("label.load_colours"));
loadColours.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
load();
saveColours.setText(MessageManager.getString("label.save_colours"));
saveColours.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
save();
});
transparency.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
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);
cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
cancelDAS.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancelDAS_actionPerformed(e);
}
});
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)
{
Runnable fetcher = new Runnable()
{
+ @Override
public void run()
{
doDasFeatureFetch(dassources, true, false);
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;
this.data = data;
}
+ @Override
public int getColumnCount()
{
return columnNames.length;
return data[row];
}
+ @Override
public int getRowCount()
{
return data.length;
}
+ @Override
public String getColumnName(int col)
{
return columnNames[col];
}
+ @Override
public Object getValueAt(int row, int col)
{
return data[row][col];
}
+ @Override
public Class getColumnClass(int c)
{
return getValueAt(0, c).getClass();
}
+ @Override
public boolean isCellEditable(int row, int col)
{
return col == 0 ? false : true;
}
+ @Override
public void setValueAt(Object value, int row, int col)
{
data[row][col] = value;
setVerticalTextPosition(SwingConstants.CENTER);
}
+ @Override
public Component getTableCellRendererComponent(JTable table,
Object color, boolean isSelected, boolean hasFocus, int row,
int column)
}
}
+ @Override
public int getIconWidth()
{
return width;
}
+ @Override
public int getIconHeight()
{
return height;
}
+ @Override
public void paintIcon(Component c, Graphics g, int x, int y)
{
/**
* Handles events from the editor button and from the dialog's OK button.
*/
+ @Override
public void actionPerformed(ActionEvent e)
{
}
// Implement the one CellEditor method that AbstractCellEditor doesn't.
+ @Override
public Object getCellEditorValue()
{
if (currentColor == null)
}
// Implement the one method defined by TableCellEditor.
+ @Override
public Component getTableCellEditorComponent(JTable table, Object value,
boolean isSelected, int row, int column)
{
git://source.jalview.org / jalview.git / blobdiff