/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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.FeatureColourI;
+import jalview.api.FeatureSettingsControllerI;
import jalview.bin.Cache;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Help.HelpId;
+import jalview.io.JalviewFileChooser;
+import jalview.schemabinding.version2.JalviewUserColours;
+import jalview.schemes.FeatureColour;
+import jalview.util.Format;
import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.QuickSort;
+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.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.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;
Object[][] originalData;
+ private float originalTransparency;
+
final JInternalFrame frame;
JScrollPane scrollPane = new JScrollPane();
{
this.af = af;
fr = af.getFeatureRenderer();
-
- transparency.setMaximum(100 - (int) (fr.transparency * 100));
+ // allow transparency to be recovered
+ 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());
table.setDefaultEditor(Color.class, new ColorEditor(this));
- table.setDefaultEditor(GraduatedColor.class, new ColorEditor(this));
- table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer());
+ table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
+ table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
table.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
- if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger())
+ {
+ popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
+ table.getValueAt(selectedRow, 1), fr.getMinMax(),
+ evt.getX(), evt.getY());
+ }
+ else if (evt.getClickCount() == 2)
+ {
+ boolean invertSelection = evt.isAltDown();
+ boolean toggleSelection = Platform.isControlDown(evt);
+ boolean extendSelection = evt.isShiftDown();
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(
+ invertSelection, extendSelection, toggleSelection,
+ (String) table.getValueAt(selectedRow, 0));
+ }
+ }
+
+ // isPopupTrigger fires on mouseReleased on Windows
+ @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.getValueAt(selectedRow, 1), fr.getMinMax(),
+ 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);
-
+ /*
+ * reposition 'selectedRow' to 'newRow' (the dragged to location)
+ * this could be more than one row away for a very fast drag action
+ * so just swap it with adjacent rows until we get it there
+ */
+ Object[][] data = ((FeatureTableModel) table.getModel())
+ .getData();
+ int direction = newRow < selectedRow ? -1 : 1;
+ for (int i = selectedRow; i != newRow; i += direction)
+ {
+ Object[] temp = data[i];
+ data[i] = data[i + direction];
+ data[i + direction] = temp;
+ }
+ updateFeatureRenderer(data);
+ table.repaint();
selectedRow = newRow;
}
}
});
-
+ // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ // MessageManager.getString("label.feature_settings_click_drag")));
scrollPane.setViewportView(table);
dassourceBrowser = new DasSourceBrowser(this);
dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
- if (af.getViewport().featuresDisplayed == null
- || fr.renderOrder == null)
+ if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
{
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 = new JInternalFrame();
frame.setContentPane(this);
- if (new jalview.util.Platform().isAMac())
+ if (Platform.isAMac())
{
- Desktop.addInternalFrame(frame, "Sequence Feature Settings", 475, 480);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 475, 480);
}
else
{
- Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 400, 450);
}
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("Settings for " + type);
- JMenuItem scr = new JMenuItem("Sort by Score");
+ final FeatureColourI featureColour = (FeatureColourI) typeCol;
+
+ JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
+ "label.settings_for_param", new String[] { type }));
+ JMenuItem scr = new JMenuItem(
+ MessageManager.getString("label.sort_by_score"));
men.add(scr);
final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- me.sortByScore(new String[]
- { type });
+ me.af.avc.sortAlignmentByFeatureScore(Arrays
+ .asList(new String[] { type }));
}
});
- JMenuItem dens = new JMenuItem("Sort by Density");
+ JMenuItem dens = new JMenuItem(
+ MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- me.sortByDens(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
// positional features
final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
"Graduated Colour");
- mxcol.setSelected(!(typeCol instanceof Color));
+ mxcol.setSelected(!featureColour.isSimpleColour());
men.add(mxcol);
mxcol.addActionListener(new ActionListener()
{
JColorChooser colorChooser;
+ @Override
public void actionPerformed(ActionEvent e)
{
if (e.getSource() == mxcol)
{
- if (typeCol instanceof Color)
+ if (featureColour.isSimpleColour())
{
FeatureColourChooser fc = new FeatureColourChooser(me.fr,
type);
"Select new Colour", true, // modal
colorChooser, this, // OK button handler
null); // no CANCEL button handler
- colorChooser.setColor(((GraduatedColor) typeCol)
- .getMaxColor());
+ colorChooser.setColor(featureColour.getMaxColour());
dialog.setVisible(true);
}
}
else
{
// probably the color chooser!
- table.setValueAt(colorChooser.getColor(), selectedRow, 1);
+ table.setValueAt(
+ new FeatureColour(colorChooser.getColor()),
+ selectedRow, 1);
table.validate();
me.updateFeatureRenderer(
((FeatureTableModel) table.getModel()).getData(),
});
}
}
+ JMenuItem selCols = new JMenuItem(
+ MessageManager.getString("label.select_columns_containing"));
+ selCols.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
+ false, type);
+ }
+ });
+ JMenuItem clearCols = new JMenuItem(
+ MessageManager.getString("label.select_columns_not_containing"));
+ clearCols.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
+ false, type);
+ }
+ });
+ JMenuItem hideCols = new JMenuItem(
+ MessageManager.getString("label.hide_columns_containing"));
+ hideCols.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ fr.ap.alignFrame.hideFeatureColumns(type, true);
+ }
+ });
+ JMenuItem hideOtherCols = new JMenuItem(
+ MessageManager.getString("label.hide_columns_not_containing"));
+ hideOtherCols.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ fr.ap.alignFrame.hideFeatureColumns(type, false);
+ }
+ });
+ men.add(selCols);
+ men.add(clearCols);
+ men.add(hideCols);
+ men.add(hideOtherCols);
men.show(table, x, y);
}
/**
* contains a float[3] for each feature type string. created by setTableData
*/
- Hashtable typeWidth = null;
+ Map<String, float[]> typeWidth = null;
- synchronized public void setTableData()
+ @Override
+ synchronized public void discoverAllFeatureData()
{
- if (fr.featureGroups == null)
- {
- fr.featureGroups = new Hashtable();
- }
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
+ Vector<String> allFeatures = new Vector<String>();
+ Vector<String> allGroups = new Vector<String>();
SequenceFeature[] tmpfeatures;
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)
{
if (!allGroups.contains(group))
{
allGroups.addElement(group);
- if (group != null)
- {
- checkGroupState(group);
- }
+ checkGroupState(group);
}
}
}
/**
+ * Synchronise gui group list and check visibility of group
*
* @param group
- * @return true if group has been seen before and is already added to set.
+ * @return true if group is visible
*/
private boolean checkGroupState(String group)
{
- boolean visible;
- if (fr.featureGroups.containsKey(group))
- {
- visible = ((Boolean) fr.featureGroups.get(group)).booleanValue();
- }
- else
- {
- visible = true; // new group is always made visible
- }
+ boolean visible = fr.checkGroupVisibility(group, true);
if (groupPanel == null)
{
if (alreadyAdded)
{
- return true;
+ return visible;
}
-
- fr.featureGroups.put(group, new Boolean(visible));
final String grp = group;
final JCheckBox check = new JCheckBox(group, visible);
check.setFont(new Font("Serif", Font.BOLD, 12));
check.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
- fr.featureGroups.put(check.getText(),
- new Boolean(check.isSelected()));
- af.alignPanel.seqPanel.seqCanvas.repaint();
+ fr.setGroupVisibility(check.getText(), check.isSelected());
+ 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);
- return false;
+ return visible;
}
boolean resettingTable = false;
return;
}
resettingTable = true;
- typeWidth = new Hashtable();
+ typeWidth = new Hashtable<String, float[]>();
// TODO: change avWidth calculation to 'per-sequence' average and use long
// rather than float
float[] avWidth = null;
SequenceFeature[] tmpfeatures;
String group = null, type;
- Vector visibleChecks = new Vector();
+ Vector<String> visibleChecks = new Vector<String>();
// Find out which features should be visible depending on which groups
// are selected / deselected
{
tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures();
+ .getSequenceFeatures();
if (tmpfeatures == null)
{
continue;
continue;
}
- if (group == null || fr.featureGroups.get(group) == null
- || ((Boolean) fr.featureGroups.get(group)).booleanValue())
+ if (group == null || checkGroupState(group))
{
- if (group != null)
- checkGroupState(group);
type = tmpfeatures[index].getType();
if (!visibleChecks.contains(type))
{
}
else
{
- avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
+ avWidth = typeWidth.get(tmpfeatures[index].getType());
}
avWidth[0]++;
if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd())
Object[][] data = new Object[fSize][3];
int dataIndex = 0;
- if (fr.renderOrder != null)
+ if (fr.hasRenderOrder())
{
if (!handlingUpdate)
+ {
fr.findAllFeatures(groupChanged != null); // prod to update
- // colourschemes. but don't
- // affect display
- // First add the checks in the previous render order,
- // in case the window has been closed and reopened
- for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
+ // colourschemes. but don't
+ // affect display
+ // First add the checks in the previous render order,
+ // in case the window has been closed and reopened
+ }
+ List<String> frl = fr.getRenderOrder();
+ for (int ro = frl.size() - 1; ro > -1; ro--)
{
- type = fr.renderOrder[ro];
+ type = frl.get(ro);
if (!visibleChecks.contains(type))
{
data[dataIndex][0] = type;
data[dataIndex][1] = fr.getFeatureStyle(type);
- data[dataIndex][2] = new Boolean(
- af.getViewport().featuresDisplayed.containsKey(type));
+ data[dataIndex][2] = new Boolean(af.getViewport()
+ .getFeaturesDisplayed().isVisible(type));
dataIndex++;
visibleChecks.removeElement(type);
}
if (data[dataIndex][1] == null)
{
// "Colour has been updated in another view!!"
- fr.renderOrder = null;
+ fr.clearRenderOrder();
return;
}
if (groupPanel != null)
{
- groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1,
- 4));
+ groupPanel.setLayout(new GridLayout(
+ fr.getFeatureGroupsSize() / 4 + 1, 4));
groupPanel.validate();
bigPanel.add(groupPanel, BorderLayout.NORTH);
{
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.setToolTipText("Load");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_feature_colours"));
+ chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
InputStreamReader in = new InputStreamReader(new FileInputStream(
file), "UTF-8");
- jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
- jucs = (jalview.schemabinding.version2.JalviewUserColours) jucs
- .unmarshal(in);
+ JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
Cache.log.warn("Couldn't parse out graduated feature color.",
e);
}
- GraduatedColor gcol = new GraduatedColor(mincol, maxcol,
+ FeatureColourI gcol = new FeatureColour(mincol, maxcol,
newcol.getMin(), newcol.getMax());
if (newcol.hasAutoScale())
{
}
if (newcol.hasThreshold())
{
- gcol.setThresh(newcol.getThreshold());
- gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default
+ gcol.setThreshold(newcol.getThreshold());
}
if (newcol.getThreshType().length() > 0)
{
String ttyp = newcol.getThreshType();
- if (ttyp.equalsIgnoreCase("NONE"))
- {
- gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD);
- }
if (ttyp.equalsIgnoreCase("ABOVE"))
{
- gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ gcol.setAboveThreshold(true);
}
if (ttyp.equalsIgnoreCase("BELOW"))
{
- gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ gcol.setBelowThreshold(true);
}
}
fr.setColour(name = newcol.getName(), gcol);
}
else
{
- fr.setColour(name = jucs.getColour(i).getName(), new Color(
- Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+ Color color = new Color(Integer.parseInt(jucs.getColour(i)
+ .getRGB(), 16));
+ fr.setColour(name = jucs.getColour(i).getName(),
+ new FeatureColour(color));
}
fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
}
void save()
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "fc" }, new String[]
- { "Sequence Feature Colours" }, "Sequence Feature Colours");
+ 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.setToolTipText("Save");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_feature_colours"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
PrintWriter out = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(choice), "UTF-8"));
- Iterator e = fr.featureColours.keySet().iterator();
- float[] sortOrder = new float[fr.featureColours.size()];
- String[] sortTypes = new String[fr.featureColours.size()];
+ Set<String> fr_colours = fr.getAllFeatureColours();
+ Iterator<String> e = fr_colours.iterator();
+ float[] sortOrder = new float[fr_colours.size()];
+ String[] sortTypes = new String[fr_colours.size()];
int i = 0;
while (e.hasNext())
{
- sortTypes[i] = e.next().toString();
+ sortTypes[i] = e.next();
sortOrder[i] = fr.getOrder(sortTypes[i]);
i++;
}
- jalview.util.QuickSort.sort(sortOrder, sortTypes);
+ QuickSort.sort(sortOrder, sortTypes);
sortOrder = null;
- Object fcol;
- GraduatedColor gcol;
for (i = 0; i < sortTypes.length; i++)
{
jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
col.setName(sortTypes[i]);
- col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
- .getName())));
- fcol = fr.getFeatureStyle(sortTypes[i]);
- if (fcol instanceof GraduatedColor)
+ FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
+ if (fcol.isSimpleColour())
{
- gcol = (GraduatedColor) fcol;
- col.setMin(gcol.getMin());
- col.setMax(gcol.getMax());
- col.setMinRGB(jalview.util.Format.getHexString(gcol
- .getMinColor()));
- col.setAutoScale(gcol.isAutoScale());
- col.setThreshold(gcol.getThresh());
- col.setColourByLabel(gcol.isColourByLabel());
- switch (gcol.getThreshType())
- {
- case AnnotationColourGradient.NO_THRESHOLD:
- col.setThreshType("NONE");
- break;
- case AnnotationColourGradient.ABOVE_THRESHOLD:
- col.setThreshType("ABOVE");
- break;
- case AnnotationColourGradient.BELOW_THRESHOLD:
- col.setThreshType("BELOW");
- break;
- }
+ col.setRGB(Format.getHexString(fcol.getColour()));
+ }
+ else
+ {
+ col.setRGB(Format.getHexString(fcol.getMaxColour()));
+ col.setMin(fcol.getMin());
+ col.setMax(fcol.getMax());
+ col.setMinRGB(jalview.util.Format.getHexString(fcol
+ .getMinColour()));
+ col.setAutoScale(fcol.isAutoScaled());
+ col.setThreshold(fcol.getThreshold());
+ col.setColourByLabel(fcol.isColourByLabel());
+ col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" : (fcol
+ .isBelowThreshold() ? "BELOW" : "NONE"));
}
ucs.addColour(col);
}
public void orderByAvWidth()
{
if (table == null || table.getModel() == null)
+ {
return;
+ }
Object[][] data = ((FeatureTableModel) table.getModel()).getData();
float[] width = new float[data.length];
float[] awidth;
int num = 0;
for (int i = 0; i < data.length; i++)
{
- awidth = (float[]) typeWidth.get(data[i][0]);
+ awidth = typeWidth.get(data[i][0]);
if (awidth[0] > 0)
{
width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
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();
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;
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
{
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();
}
});
sortByScore.setFont(JvSwingUtils.getLabelFont());
- sortByScore.setText(MessageManager.getString("label.seq_sort_by_score"));
+ sortByScore
+ .setText(MessageManager.getString("label.seq_sort_by_score"));
sortByScore.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- sortByScore(null);
+ af.avc.sortAlignmentByFeatureScore(null);
}
});
sortByDens.setFont(JvSwingUtils.getLabelFont());
- sortByDens.setText("Seq Sort by density");
+ sortByDens.setText(MessageManager
+ .getString("label.sequence_sort_by_density"));
sortByDens.addActionListener(new ActionListener()
{
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ af.avc.sortAlignmentByFeatureDensity(null);
+ }
+ });
+ 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();
+ }
+ }
+ });
+ help.setFont(JvSwingUtils.getLabelFont());
+ help.setText(MessageManager.getString("action.help"));
+ help.addActionListener(new ActionListener()
+ {
+ @Override
public void actionPerformed(ActionEvent e)
{
- sortByDens(null);
+ try
+ {
+ Help.showHelpWindow(HelpId.SequenceFeatureSettings);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
}
});
cancel.setFont(JvSwingUtils.getLabelFont());
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
+ fr.setTransparency(originalTransparency);
updateFeatureRenderer(originalData);
close();
}
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((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()
{
+ @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("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);
settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
}
- protected void sortByDens(String[] typ)
- {
- sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
- }
-
- protected void sortBy(String[] typ, String methodText, final String method)
- {
- if (typ == null)
- {
- typ = getDisplayedFeatureTypes();
- }
- String gps[] = null;
- gps = getDisplayedFeatureGroups();
- if (typ != null)
- {
- ArrayList types = new ArrayList();
- for (int i = 0; i < typ.length; i++)
- {
- if (typ[i] != null)
- {
- types.add(typ[i]);
- }
- typ = new String[types.size()];
- types.toArray(typ);
- }
- }
- if (gps != null)
- {
- ArrayList grps = new ArrayList();
-
- for (int i = 0; i < gps.length; i++)
- {
- if (gps[i] != null)
- {
- grps.add(gps[i]);
- }
- }
- gps = new String[grps.size()];
- grps.toArray(gps);
- }
- AlignmentPanel alignPanel = af.alignPanel;
- AlignmentI al = alignPanel.av.getAlignment();
-
- int start, stop;
- SequenceGroup sg = alignPanel.av.getSelectionGroup();
- if (sg != null)
- {
- start = sg.getStartRes();
- stop = sg.getEndRes();
- }
- else
- {
- start = 0;
- stop = al.getWidth();
- }
- SequenceI[] oldOrder = al.getSequencesArray();
- AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
- af.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av
- .getAlignment()));
- alignPanel.paintAlignment(true);
-
- }
-
- protected void sortByScore(String[] typ)
- {
- sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
- }
-
- private String[] getDisplayedFeatureTypes()
- {
- String[] typ = null;
- if (fr != null)
- {
- synchronized (fr.renderOrder)
- {
- typ = new String[fr.renderOrder.length];
- System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length);
- for (int i = 0; i < typ.length; i++)
- {
- if (af.viewport.featuresDisplayed.get(typ[i]) == null)
- {
- typ[i] = null;
- }
- }
- }
- }
- return typ;
- }
-
- private String[] getDisplayedFeatureGroups()
- {
- String[] gps = null;
- if (fr != null)
- {
-
- if (fr.featureGroups != null)
- {
- Iterator en = fr.featureGroups.keySet().iterator();
- gps = new String[fr.featureColours.size()];
- int g = 0;
- boolean valid = false;
- while (en.hasNext())
- {
- String gp = (String) en.next();
- Boolean on = (Boolean) fr.featureGroups.get(gp);
- if (on != null && on.booleanValue())
- {
- valid = true;
- gps[g++] = gp;
- }
- }
- while (g < gps.length)
- {
- gps[g++] = null;
- }
- if (!valid)
- {
- return null;
- }
- }
- }
- return gps;
- }
-
public void fetchDAS_actionPerformed(ActionEvent e)
{
fetchDAS.setEnabled(false);
cancelDAS.setEnabled(true);
dassourceBrowser.setGuiEnabled(false);
- Vector selectedSources = dassourceBrowser.getSelectedSources();
+ Vector<jalviewSourceI> selectedSources = dassourceBrowser
+ .getSelectedSources();
doDasFeatureFetch(selectedSources, true, true);
}
{
SequenceI[] dataset, seqs;
int iSize;
- AlignViewport vp = af.getViewport();
+ AlignmentViewport vp = af.getViewport();
if (vp.getSelectionGroup() != null
&& vp.getSelectionGroup().getSize() > 0)
{
* Vector of Strings to resolve to DAS source nicknames.
* @return sources that are present in source list.
*/
- public List<jalviewSourceI> resolveSourceNicknames(Vector sources)
+ public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
{
return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
}
*
* @return vector of selected das source nicknames
*/
- public Vector getSelectedSources()
+ public Vector<jalviewSourceI> getSelectedSources()
{
return dassourceBrowser.getSelectedSources();
}
* if true then runs in same thread, otherwise passes to the Swing
* executor
*/
- public void fetchDasFeatures(Vector sources, boolean block)
+ public void fetchDasFeatures(Vector<String> sources, boolean block)
{
initDasSources();
List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
Runnable fetcher = new Runnable()
{
+ @Override
public void run()
{
doDasFeatureFetch(dassources, true, false);
public void noDasSourceActive()
{
complete();
- JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.getString("label.no_das_sources_selected_warn"),
- MessageManager.getString("label.no_das_sources_selected_title"), JOptionPane.DEFAULT_OPTION,
- JOptionPane.INFORMATION_MESSAGE);
+ JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.no_das_sources_selected_warn"),
+ MessageManager
+ .getString("label.no_das_sources_selected_title"),
+ JOptionPane.DEFAULT_OPTION,
+ JOptionPane.INFORMATION_MESSAGE);
}
// ///////////////////////////////////////////////////////////////////////
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;
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);
}
- public Component getTableCellRendererComponent(JTable table,
+ @Override
+ public Component getTableCellRendererComponent(JTable tbl,
Object color, boolean isSelected, boolean hasFocus, int row,
int column)
{
+ FeatureColourI cellColour = (FeatureColourI) color;
// JLabel comp = new JLabel();
// comp.
setOpaque(true);
// setBounds(getBounds());
Color newColor;
setToolTipText(baseTT);
- setBackground(table.getBackground());
- if (color instanceof GraduatedColor)
+ setBackground(tbl.getBackground());
+ if (!cellColour.isSimpleColour())
{
- Rectangle cr = table.getCellRect(row, column, false);
- FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color,
+ Rectangle cr = tbl.getCellRect(row, column, false);
+ FeatureSettings.renderGraduatedColor(this, cellColour,
(int) cr.getWidth(), (int) cr.getHeight());
}
{
this.setText("");
this.setIcon(null);
- newColor = (Color) color;
- // comp.
+ newColor = cellColour.getColour();
setBackground(newColor);
- // comp.setToolTipText("RGB value: " + newColor.getRed() + ", "
- // + newColor.getGreen() + ", " + newColor.getBlue());
}
if (isSelected)
{
if (selectedBorder == null)
{
selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
- table.getSelectionBackground());
+ tbl.getSelectionBackground());
}
- // comp.
setBorder(selectedBorder);
}
else
if (unselectedBorder == null)
{
unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
- table.getBackground());
+ tbl.getBackground());
}
- // comp.
setBorder(unselectedBorder);
}
* @param comp
* @param gcol
*/
- public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol)
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol)
{
int w = comp.getWidth(), h = comp.getHeight();
if (w < 20)
renderGraduatedColor(comp, gcol, w, h);
}
- public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol,
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
int w, int h)
{
boolean thr = false;
String tt = "";
String tx = "";
- if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD)
+ if (gcol.isAboveThreshold())
{
thr = true;
tx += ">";
- tt += "Thresholded (Above " + gcol.getThresh() + ") ";
+ tt += "Thresholded (Above " + gcol.getThreshold() + ") ";
}
- if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
+ if (gcol.isBelowThreshold())
{
thr = true;
tx += "<";
- tt += "Thresholded (Below " + gcol.getThresh() + ") ";
+ tt += "Thresholded (Below " + gcol.getThreshold() + ") ";
}
if (gcol.isColourByLabel())
{
}
else
{
- Color newColor = gcol.getMaxColor();
+ Color newColor = gcol.getMaxColour();
comp.setBackground(newColor);
// System.err.println("Width is " + w / 2);
Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
class FeatureIcon implements Icon
{
- GraduatedColor gcol;
+ FeatureColourI gcol;
Color backg;
Color mpcolour = Color.white;
- FeatureIcon(GraduatedColor gfc, Color bg, int w, int h, boolean mspace)
+ FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace)
{
gcol = gfc;
backg = bg;
}
}
+ @Override
public int getIconWidth()
{
return width;
}
+ @Override
public int getIconHeight()
{
return height;
}
+ @Override
public void paintIcon(Component c, Graphics g, int x, int y)
{
g.setColor(backg);
g.fillRect(0, 0, width, height);
// need an icon here.
- g.setColor(gcol.getMaxColor());
+ g.setColor(gcol.getMaxColour());
g.setFont(new Font("Verdana", Font.PLAIN, 9));
}
else
{
- Color minCol = gcol.getMinColor();
+ Color minCol = gcol.getMinColour();
g.setColor(minCol);
g.fillRect(0, 0, s1, height);
if (midspace)
g.setColor(Color.white);
g.fillRect(s1, 0, e1 - s1, height);
}
- g.setColor(gcol.getMaxColor());
+ g.setColor(gcol.getMaxColour());
g.fillRect(0, e1, width - e1, height);
}
}
{
FeatureSettings me;
- GraduatedColor currentGColor;
+ FeatureColourI currentColor;
FeatureColourChooser chooser;
String type;
- Color currentColor;
-
JButton button;
JColorChooser colorChooser;
/**
* Handles events from the editor button and from the dialog's OK button.
*/
+ @Override
public void actionPerformed(ActionEvent e)
{
{
// The user has clicked the cell, so
// bring up the dialog.
- if (currentColor != null)
+ if (currentColor.isSimpleColour())
{
// bring up simple color chooser
- button.setBackground(currentColor);
- colorChooser.setColor(currentColor);
+ button.setBackground(currentColor.getColour());
+ colorChooser.setColor(currentColor.getColour());
dialog.setVisible(true);
}
else
}
else
{ // User pressed dialog's "OK" button.
- if (currentColor != null)
+ if (currentColor.isSimpleColour())
{
- currentColor = colorChooser.getColor();
+ currentColor = new FeatureColour(colorChooser.getColor());
}
else
{
- // class cast exceptions may be raised if the chooser created on a
- // non-graduated color
- currentGColor = (GraduatedColor) chooser.getLastColour();
+ currentColor = chooser.getLastColour();
}
me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
fireEditingStopped();
}
// Implement the one CellEditor method that AbstractCellEditor doesn't.
+ @Override
public Object getCellEditorValue()
{
- if (currentColor == null)
- {
- return currentGColor;
- }
return currentColor;
}
// Implement the one method defined by TableCellEditor.
+ @Override
public Component getTableCellEditorComponent(JTable table, Object value,
boolean isSelected, int row, int column)
{
- currentGColor = null;
- currentColor = null;
+ currentColor = (FeatureColourI) value;
this.selectedRow = row;
type = me.table.getValueAt(row, 0).toString();
button.setOpaque(true);
button.setBackground(me.getBackground());
- if (value instanceof GraduatedColor)
+ if (!currentColor.isSimpleColour())
{
- currentGColor = (GraduatedColor) value;
JLabel btn = new JLabel();
btn.setSize(button.getSize());
- FeatureSettings.renderGraduatedColor(btn, currentGColor);
+ FeatureSettings.renderGraduatedColor(btn, currentColor);
button.setBackground(btn.getBackground());
button.setIcon(btn.getIcon());
button.setText(btn.getText());
{
button.setText("");
button.setIcon(null);
- currentColor = (Color) value;
- button.setBackground(currentColor);
+ button.setBackground(currentColor.getColour());
}
return button;
}
git://source.jalview.org / jalview.git / blobdiff