*/
package jalview.gui;
-import java.util.*;
-import java.util.regex.Pattern;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.RenderingHints;
+import java.awt.Toolkit;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
-import java.awt.image.*;
-import javax.swing.*;
+import java.awt.image.BufferedImage;
+import java.util.Vector;
+import java.util.regex.Pattern;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.util.MessageManager;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
Graphics2D g = (Graphics2D) bi.getGraphics();
g.rotate(Math.toRadians(90));
g.drawImage(temp, 0, -bi.getWidth(this), this);
- image = (Image) bi;
+ image = bi;
addMouseListener(this);
addMouseMotionListener(this);
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
+ refresh();
+
+ }
+
+ /**
+ * Redraw sensibly.
+ */
+ protected void refresh()
+ {
ap.validateAnnotationDimensions(false);
ap.addNotify();
ap.repaint();
- // validate();
- // ap.paintAlignment(true);
}
/**
*/
public void mouseClicked(MouseEvent evt)
{
- AlignmentAnnotation[] aa = ap.av.getAlignment()
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
if (SwingUtilities.isLeftMouseButton(evt))
{
}
else if (aa[selectedRow].sequenceRef != null)
{
- Vector sr = new Vector();
- sr.addElement(aa[selectedRow].sequenceRef);
if (evt.getClickCount() == 1)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+ ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
+ .asList(new SequenceI[]
+ { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- SequenceGroup sg = new SequenceGroup();
- sg.addSequence(aa[selectedRow].sequenceRef, false);
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg!=null)
+ {
+ // we make a copy rather than edit the current selection if no modifiers pressed
+ // see Enhancement JAL-1557
+ if (!(evt.isControlDown() || evt.isShiftDown()))
+ {
+ sg = new SequenceGroup(sg);
+ sg.clear();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ } else {
+ if (evt.isControlDown())
+ {
+ sg.addOrRemove(aa[selectedRow].sequenceRef, true);
+ } else {
+ // notionally, we should also add intermediate sequences from last added sequence ?
+ sg.addSequence(aa[selectedRow].sequenceRef, true);
+ }
+ }
+ } else {
+ sg = new SequenceGroup();
+ sg.setStartRes(0);
+ sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
ap.av.setSelectionGroup(sg);
ap.av.sendSelection();
ap.paintAlignment(false);
item = new JMenuItem(HIDE);
item.addActionListener(this);
pop.add(item);
+ // JAL-1264 hide all sequence-specific annotations of this type
+ final String label = aa[selectedRow].label;
+ if (selectedRow < aa.length)
+ {
+ if (aa[selectedRow].sequenceRef != null)
+ {
+ JMenuItem hideType = new JMenuItem();
+ String text = MessageManager.getString("label.hide_all") + " " + label;
+ hideType.setText(text);
+ hideType.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ for (AlignmentAnnotation ann : ap.av.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (ann.sequenceRef != null && ann.label != null
+ && ann.label.equals(label))
+ {
+ ann.visible = false;
+ }
+ }
+ refresh();
+ }
+ });
+ pop.add(hideType);
+ }
+ }
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
pop.add(item);
}
}
- else if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ else if (label.indexOf("Consensus") > -1)
{
pop.addSeparator();
// av and sequencegroup need to implement same interface for
*/
package jalview.gui;
import jalview.analysis.AlignmentSorter;
import jalview.bin.Cache;
import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.JalviewFileChooser;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
+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.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+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
{
DasSourceBrowser dassourceBrowser;
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.minmax, evt.getX(),
(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.minmax, evt.getX(),
+ evt.getY());
+ }
+ }
});
table.addMouseMotionListener(new MouseMotionAdapter()
file), "UTF-8");
jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
- jucs = (jalview.schemabinding.version2.JalviewUserColours) jucs
+ jucs = jucs
.unmarshal(in);
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
public void stateChanged(ChangeEvent evt)
{
- fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
af.alignPanel.paintAlignment(true);
}
});
git://source.jalview.org / jalview.git / commitdiff