/*
* 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.
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.GridLayout;
import java.awt.Point;
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.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Set;
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.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JScrollPane;
import javax.swing.JSlider;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
import javax.swing.ToolTipManager;
import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.JTableHeader;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.Marshaller;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.controller.FeatureSettingsControllerGuiI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcher;
import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.Help.HelpId;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
import jalview.viewmodel.styles.ViewStyle;
import jalview.xml.binding.jalview.JalviewUserColours;
import jalview.xml.binding.jalview.JalviewUserColours.Colour;
import jalview.xml.binding.jalview.JalviewUserColours.Filter;
import jalview.xml.binding.jalview.ObjectFactory;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI, FeatureSettingsControllerGuiI
{
private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
.getString("label.sequence_feature_colours");
/*
* column indices of fields in Feature Settings table
*/
static final int TYPE_COLUMN = 0;
static final int COLOUR_COLUMN = 1;
static final int FILTER_COLUMN = 2;
static final int SHOW_COLUMN = 3;
private static final int COLUMN_COUNT = 4;
private static final int MIN_WIDTH = 400;
private static final int MIN_HEIGHT = 400;
private final static String BASE_TOOLTIP = MessageManager
.getString("label.click_to_edit");
final FeatureRenderer fr;
public final AlignFrame af;
/*
* 'original' fields hold settings to restore on Cancel
*/
Object[][] originalData;
private float originalTransparency;
private ViewStyleI originalViewStyle;
private Map originalFilters;
final JInternalFrame frame;
JScrollPane scrollPane = new JScrollPane();
JTable table;
JPanel groupPanel;
JSlider transparency = new JSlider();
private JCheckBox showComplementOnTop;
private JCheckBox showComplement;
/*
* when true, constructor is still executing - so ignore UI events
*/
protected volatile boolean inConstruction = true;
int selectedRow = -1;
boolean resettingTable = false;
/*
* true when Feature Settings are updating from feature renderer
*/
private boolean handlingUpdate = false;
/*
* a change listener to ensure the dialog is updated if
* FeatureRenderer discovers new features
*/
private PropertyChangeListener change;
/*
* holds {featureCount, totalExtent} for each feature type
*/
Map typeWidth = null;
private void storeOriginalSettings()
{
// save transparency for restore on Cancel
originalTransparency = fr.getTransparency();
updateTransparencySliderFromFR();
originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
originalViewStyle = new ViewStyle(af.viewport.getViewStyle());
}
private void updateTransparencySliderFromFR()
{
boolean incon = inConstruction;
inConstruction = true;
int transparencyAsPercent = (int) (fr.getTransparency() * 100);
transparency.setValue(100 - transparencyAsPercent);
inConstruction = incon;
}
/**
* Constructor
*
* @param af
*/
public FeatureSettings(AlignFrame alignFrame)
{
this.af = alignFrame;
fr = af.getFeatureRenderer();
storeOriginalSettings();
try
{
jbInit();
} catch (Exception ex)
{
ex.printStackTrace();
}
table = new JTable()
{
@Override
public String getToolTipText(MouseEvent e)
{
String tip = null;
int column = table.columnAtPoint(e.getPoint());
int row = table.rowAtPoint(e.getPoint());
switch (column)
{
case TYPE_COLUMN:
tip = JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.feature_settings_click_drag"));
break;
case COLOUR_COLUMN:
FeatureColourI colour = (FeatureColourI) table.getValueAt(row,
column);
tip = getColorTooltip(colour, true);
break;
case FILTER_COLUMN:
FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
column);
tip = o.isEmpty()
? MessageManager
.getString("label.configure_feature_tooltip")
: o.toString();
break;
default:
break;
}
return tip;
}
/**
* Position the tooltip near the bottom edge of, and half way across, the
* current cell
*/
@Override
public Point getToolTipLocation(MouseEvent e)
{
Point point = e.getPoint();
int column = table.columnAtPoint(point);
int row = table.rowAtPoint(point);
Rectangle r = getCellRect(row, column, false);
Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3);
return loc;
}
};
JTableHeader tableHeader = table.getTableHeader();
tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12));
tableHeader.setReorderingAllowed(false);
table.setFont(new Font("Verdana", Font.PLAIN, 12));
ToolTipManager.sharedInstance().registerComponent(table);
table.setDefaultEditor(FeatureColour.class, new ColorEditor());
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor());
table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer());
TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
new ColorRenderer(), new ColorEditor());
table.addColumn(colourColumn);
TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75,
new FilterRenderer(), new FilterEditor());
table.addColumn(filterColumn);
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
table.addMouseListener(new MouseAdapter()
{
@Override
public void mousePressed(MouseEvent evt)
{
Point pt = evt.getPoint();
selectedRow = table.rowAtPoint(pt);
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
if (evt.isPopupTrigger())
{
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
showPopupMenu(selectedRow, type, colour, evt.getPoint());
}
else if (evt.getClickCount() == 2
&& table.columnAtPoint(pt) == TYPE_COLUMN)
{
boolean invertSelection = evt.isAltDown();
boolean toggleSelection = Platform.isControlDown(evt);
boolean extendSelection = evt.isShiftDown();
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
invertSelection, extendSelection, toggleSelection, type);
fr.ap.av.sendSelection();
}
}
// isPopupTrigger fires on mouseReleased on Windows
@Override
public void mouseReleased(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
if (evt.isPopupTrigger())
{
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
showPopupMenu(selectedRow, type, colour, evt.getPoint());
}
}
});
table.addMouseMotionListener(new MouseMotionAdapter()
{
@Override
public void mouseDragged(MouseEvent evt)
{
int newRow = table.rowAtPoint(evt.getPoint());
if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
{
/*
* 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);
if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
{
fr.findAllFeatures(true); // display everything!
}
discoverAllFeatureData();
final FeatureSettings fs = this;
fr.addPropertyChangeListener(change = new PropertyChangeListener()
{
@Override
public void propertyChange(PropertyChangeEvent evt)
{
if (!fs.resettingTable && !fs.handlingUpdate)
{
fs.handlingUpdate = true;
fs.resetTable(null);
// new groups may be added with new sequence feature types only
fs.handlingUpdate = false;
}
}
});
SplitContainerI splitframe = af.getSplitViewContainer();
if (splitframe != null)
{
frame = null; // keeps eclipse happy
splitframe.addFeatureSettingsUI(this);
}
else
{
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setFrameIcon(null);
Rectangle bounds = af.getFeatureSettingsGeometry();
String title;
if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels(
af.alignPanel.av.getSequenceSetId()).length > 1)
{
title = MessageManager.formatMessage(
"label.sequence_feature_settings_for_view",
af.alignPanel.getViewName());
}
else
{
title = MessageManager.getString("label.sequence_feature_settings");
}
if (bounds == null)
{
if (Platform.isAMacAndNotJS())
{
Desktop.addInternalFrame(frame, title, 600, 480);
}
else
{
Desktop.addInternalFrame(frame, title, 600, 450);
}
}
else
{
Desktop.addInternalFrame(frame, title, false, bounds.width,
bounds.height);
frame.setBounds(bounds);
frame.setVisible(true);
}
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
@Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
featureSettings_isClosed();
};
});
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
inConstruction = false;
}
/**
* Sets the state of buttons to show complement features from viewport
* settings
*/
private void updateComplementButtons()
{
showComplement.setSelected(af.getViewport().isShowComplementFeatures());
showComplementOnTop
.setSelected(af.getViewport().isShowComplementFeaturesOnTop());
}
@Override
public AlignViewControllerGuiI getAlignframe()
{
return af;
}
@Override
public void featureSettings_isClosed()
{
fr.removePropertyChangeListener(change);
change = null;
}
/**
* Constructs and shows a popup menu of possible actions on the selected row
* and feature type
*
* @param rowSelected
* @param type
* @param typeCol
* @param pt
*/
protected void showPopupMenu(final int rowSelected, final String type,
final Object typeCol, final Point pt)
{
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);
scr.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
sortByScore(Arrays.asList(new String[] { type }));
}
});
JMenuItem dens = new JMenuItem(
MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
sortByDensity(Arrays.asList(new String[] { type }));
}
});
men.add(dens);
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);
fr.ap.av.sendSelection();
}
});
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);
fr.ap.av.sendSelection();
}
});
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);
fr.ap.av.sendSelection();
}
});
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);
fr.ap.av.sendSelection();
}
});
men.add(selCols);
men.add(clearCols);
men.add(hideCols);
men.add(hideOtherCols);
men.show(table, pt.x, pt.y);
}
/**
* Sort the sequences in the alignment by the number of features for the given
* feature types (or all features if null)
*
* @param featureTypes
*/
protected void sortByDensity(List featureTypes)
{
af.avc.sortAlignmentByFeatureDensity(featureTypes);
}
/**
* Sort the sequences in the alignment by average score for the given feature
* types (or all features if null)
*
* @param featureTypes
*/
protected void sortByScore(List featureTypes)
{
af.avc.sortAlignmentByFeatureScore(featureTypes);
}
/**
* Returns true if at least one feature type is visible. Else shows a warning
* dialog and returns false.
*
* @param title
* @return
*/
private boolean canSortBy(String title)
{
if (fr.getDisplayedFeatureTypes().isEmpty())
{
JvOptionPane.showMessageDialog(this,
MessageManager.getString("label.no_features_to_sort_by"),
title, JvOptionPane.OK_OPTION);
return false;
}
return true;
}
@Override
synchronized public void discoverAllFeatureData()
{
Set allGroups = new HashSet<>();
AlignmentI alignment = af.getViewport().getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceI seq = alignment.getSequenceAt(i);
for (String group : seq.getFeatures().getFeatureGroups(true))
{
if (group != null && !allGroups.contains(group))
{
allGroups.add(group);
checkGroupState(group);
}
}
}
resetTable(null);
validate();
}
/**
* Synchronise gui group list and check visibility of group
*
* @param group
* @return true if group is visible
*/
private boolean checkGroupState(String group)
{
boolean visible = fr.checkGroupVisibility(group, true);
for (int g = 0; g < groupPanel.getComponentCount(); g++)
{
if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group))
{
((JCheckBox) groupPanel.getComponent(g)).setSelected(visible);
return visible;
}
}
final String grp = group;
final JCheckBox check = new JCheckBox(group, visible);
check.setFont(new Font("Serif", Font.BOLD, 12));
check.setToolTipText(group);
check.addItemListener(new ItemListener()
{
@Override
public void itemStateChanged(ItemEvent evt)
{
fr.setGroupVisibility(check.getText(), check.isSelected());
resetTable(new String[] { grp });
refreshDisplay();
}
});
groupPanel.add(check);
return visible;
}
synchronized void resetTable(String[] groupChanged)
{
if (resettingTable)
{
return;
}
resettingTable = true;
typeWidth = new Hashtable<>();
// TODO: change avWidth calculation to 'per-sequence' average and use long
// rather than float
Set displayableTypes = new HashSet<>();
Set foundGroups = new HashSet<>();
/*
* determine which feature types may be visible depending on
* which groups are selected, and recompute average width data
*/
for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i);
/*
* get the sequence's groups for positional features
* and keep track of which groups are visible
*/
Set groups = seq.getFeatures().getFeatureGroups(true);
Set visibleGroups = new HashSet<>();
for (String group : groups)
{
if (group == null || checkGroupState(group))
{
visibleGroups.add(group);
}
}
foundGroups.addAll(groups);
/*
* get distinct feature types for visible groups
* record distinct visible types, and their count and total length
*/
Set types = seq.getFeatures().getFeatureTypesForGroups(true,
visibleGroups.toArray(new String[visibleGroups.size()]));
for (String type : types)
{
displayableTypes.add(type);
float[] avWidth = typeWidth.get(type);
if (avWidth == null)
{
avWidth = new float[2];
typeWidth.put(type, avWidth);
}
// todo this could include features with a non-visible group
// - do we greatly care?
// todo should we include non-displayable features here, and only
// update when features are added?
avWidth[0] += seq.getFeatures().getFeatureCount(true, type);
avWidth[1] += seq.getFeatures().getTotalFeatureLength(type);
}
}
Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT];
int dataIndex = 0;
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
}
List frl = fr.getRenderOrder();
for (int ro = frl.size() - 1; ro > -1; ro--)
{
String type = frl.get(ro);
if (!displayableTypes.contains(type))
{
continue;
}
data[dataIndex][TYPE_COLUMN] = type;
data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type);
data[dataIndex][FILTER_COLUMN] = featureFilter == null
? new FeatureMatcherSet()
: featureFilter;
data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(
af.getViewport().getFeaturesDisplayed().isVisible(type));
dataIndex++;
displayableTypes.remove(type);
}
}
/*
* process any extra features belonging only to
* a group which was just selected
*/
while (!displayableTypes.isEmpty())
{
String type = displayableTypes.iterator().next();
data[dataIndex][TYPE_COLUMN] = type;
data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
if (data[dataIndex][COLOUR_COLUMN] == null)
{
// "Colour has been updated in another view!!"
fr.clearRenderOrder();
return;
}
FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type);
data[dataIndex][FILTER_COLUMN] = featureFilter == null
? new FeatureMatcherSet()
: featureFilter;
data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(true);
dataIndex++;
displayableTypes.remove(type);
}
if (originalData == null)
{
originalData = new Object[data.length][COLUMN_COUNT];
for (int i = 0; i < data.length; i++)
{
System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT);
}
}
else
{
updateOriginalData(data);
}
table.setModel(new FeatureTableModel(data));
table.getColumnModel().getColumn(0).setPreferredWidth(200);
groupPanel.setLayout(
new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4));
pruneGroups(foundGroups);
groupPanel.validate();
updateFeatureRenderer(data, groupChanged != null);
resettingTable = false;
}
/**
* Updates 'originalData' (used for restore on Cancel) if we detect that
* changes have been made outwith this dialog
*
* - a new feature type added (and made visible)
* - a feature colour changed (in the Amend Features dialog)
*
*
* @param foundData
*/
protected void updateOriginalData(Object[][] foundData)
{
// todo LinkedHashMap instead of Object[][] would be nice
Object[][] currentData = ((FeatureTableModel) table.getModel())
.getData();
for (Object[] row : foundData)
{
String type = (String) row[TYPE_COLUMN];
boolean found = false;
for (Object[] current : currentData)
{
if (type.equals(current[TYPE_COLUMN]))
{
found = true;
/*
* currently dependent on object equality here;
* really need an equals method on FeatureColour
*/
if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN]))
{
/*
* feature colour has changed externally - update originalData
*/
for (Object[] original : originalData)
{
if (type.equals(original[TYPE_COLUMN]))
{
original[COLOUR_COLUMN] = row[COLOUR_COLUMN];
break;
}
}
}
break;
}
}
if (!found)
{
/*
* new feature detected - add to original data (on top)
*/
Object[][] newData = new Object[originalData.length
+ 1][COLUMN_COUNT];
for (int i = 0; i < originalData.length; i++)
{
System.arraycopy(originalData[i], 0, newData[i + 1], 0,
COLUMN_COUNT);
}
newData[0] = row;
originalData = newData;
}
}
}
/**
* Remove from the groups panel any checkboxes for groups that are not in the
* foundGroups set. This enables removing a group from the display when the
* last feature in that group is deleted.
*
* @param foundGroups
*/
protected void pruneGroups(Set foundGroups)
{
for (int g = 0; g < groupPanel.getComponentCount(); g++)
{
JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g);
if (!foundGroups.contains(checkbox.getText()))
{
groupPanel.remove(checkbox);
}
}
}
/**
* reorder data based on the featureRenderers global priority list.
*
* @param data
*/
private void ensureOrder(Object[][] data)
{
boolean sort = false;
float[] order = new float[data.length];
for (int i = 0; i < order.length; i++)
{
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);
}
}
/**
* Offers a file chooser dialog, and then loads the feature colours and
* filters from file in XML format and unmarshals to Jalview feature settings
*/
void load()
{
JalviewFileChooser chooser = new JalviewFileChooser("fc",
SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
chooser.setResponseHandler(0, () -> {
File file = chooser.getSelectedFile();
load(file);
});
chooser.showOpenDialog(this);
}
/**
* Loads feature colours and filters from XML stored in the given file
*
* @param file
*/
void load(File file)
{
try
{
InputStreamReader in = new InputStreamReader(
new FileInputStream(file), "UTF-8");
JAXBContext jc = JAXBContext
.newInstance("jalview.xml.binding.jalview");
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(in);
JAXBElement jbe = um.unmarshal(streamReader,
JalviewUserColours.class);
JalviewUserColours jucs = jbe.getValue();
// JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
/*
* load feature colours
*/
for (int i = jucs.getColour().size() - 1; i >= 0; i--)
{
Colour newcol = jucs.getColour().get(i);
FeatureColourI colour = jalview.project.Jalview2XML
.parseColour(newcol);
fr.setColour(newcol.getName(), colour);
fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
}
/*
* load feature filters; loaded filters will replace any that are
* currently defined, other defined filters are left unchanged
*/
for (int i = 0; i < jucs.getFilter().size(); i++)
{
Filter filterModel = jucs.getFilter().get(i);
String featureType = filterModel.getFeatureType();
FeatureMatcherSetI filter = jalview.project.Jalview2XML
.parseFilter(featureType, filterModel.getMatcherSet());
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
}
}
/*
* update feature settings table
*/
if (table != null)
{
resetTable(null);
Object[][] data = ((FeatureTableModel) table.getModel()).getData();
ensureOrder(data);
updateFeatureRenderer(data, false);
table.repaint();
}
} catch (Exception ex)
{
jalview.bin.Console.outPrintln("Error loading User Colour File\n" + ex);
}
}
/**
* Offers a file chooser dialog, and then saves the current feature colours
* and any filters to the selected file in XML format
*/
void save()
{
JalviewFileChooser chooser = new JalviewFileChooser("fc",
SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int option = chooser.showSaveDialog(this);
if (option == JalviewFileChooser.APPROVE_OPTION)
{
File file = chooser.getSelectedFile();
save(file);
}
}
/**
* Saves feature colours and filters to the given file
*
* @param file
*/
void save(File file)
{
JalviewUserColours ucs = new JalviewUserColours();
ucs.setSchemeName("Sequence Features");
try
{
PrintWriter out = new PrintWriter(
new OutputStreamWriter(new FileOutputStream(file), "UTF-8"));
/*
* sort feature types by colour order, from 0 (highest)
* to 1 (lowest)
*/
Set fr_colours = fr.getAllFeatureColours();
String[] sortedTypes = fr_colours
.toArray(new String[fr_colours.size()]);
Arrays.sort(sortedTypes, new Comparator()
{
@Override
public int compare(String type1, String type2)
{
return Float.compare(fr.getOrder(type1), fr.getOrder(type2));
}
});
/*
* save feature colours
*/
for (String featureType : sortedTypes)
{
FeatureColourI fcol = fr.getFeatureStyle(featureType);
Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
fcol);
ucs.getColour().add(col);
}
/*
* save any feature filters
*/
for (String featureType : sortedTypes)
{
FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
if (filter != null && !filter.isEmpty())
{
Iterator iterator = filter.getMatchers()
.iterator();
FeatureMatcherI firstMatcher = iterator.next();
jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
.marshalFilter(firstMatcher, iterator, filter.isAnded());
Filter filterModel = new Filter();
filterModel.setFeatureType(featureType);
filterModel.setMatcherSet(ms);
ucs.getFilter().add(filterModel);
}
}
JAXBContext jaxbContext = JAXBContext
.newInstance(JalviewUserColours.class);
Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
jaxbMarshaller.marshal(
new ObjectFactory().createJalviewUserColours(ucs), out);
// jaxbMarshaller.marshal(object, pout);
// marshaller.marshal(object);
out.flush();
// ucs.marshal(out);
out.close();
} catch (Exception ex)
{
ex.printStackTrace();
}
}
public void invertSelection()
{
Object[][] data = ((FeatureTableModel) table.getModel()).getData();
for (int i = 0; i < data.length; i++)
{
data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN];
}
updateFeatureRenderer(data, true);
table.repaint();
}
public void orderByAvWidth()
{
if (table == null || table.getModel() == null)
{
return;
}
Object[][] data = ((FeatureTableModel) table.getModel()).getData();
float[] width = new float[data.length];
float[] awidth;
float max = 0;
for (int i = 0; i < data.length; i++)
{
awidth = typeWidth.get(data[i][TYPE_COLUMN]);
if (awidth[0] > 0)
{
width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
// weight - but have to make per
// sequence, too (awidth[2])
// if (width[i]==1) // hack to distinguish single width sequences.
}
else
{
width[i] = 0;
}
if (max < width[i])
{
max = width[i];
}
}
boolean sort = false;
for (int i = 0; i < width.length; i++)
{
// awidth = (float[]) typeWidth.get(data[i][0]);
if (width[i] == 0)
{
width[i] = fr.getOrder(data[i][TYPE_COLUMN].toString());
if (width[i] < 0)
{
width[i] = fr.setOrder(data[i][TYPE_COLUMN].toString(),
i / data.length);
}
}
else
{
width[i] /= max; // normalize
fr.setOrder(data[i][TYPE_COLUMN].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
}
updateFeatureRenderer(data, false);
table.repaint();
}
/**
* close ourselves but leave any existing UI handlers (e.g a CDS/Protein
* tabbed feature settings dialog) intact
*/
public void closeOldSettings()
{
closeDialog(false);
}
/**
* close the feature settings dialog (and any containing frame)
*/
public void close()
{
closeDialog(true);
}
private void closeDialog(boolean closeContainingFrame)
{
try
{
if (frame != null)
{
af.setFeatureSettingsGeometry(frame.getBounds());
frame.setClosed(true);
}
else
{
SplitContainerI sc = af.getSplitViewContainer();
sc.closeFeatureSettings(this, closeContainingFrame);
af.featureSettings = null;
}
} catch (Exception exe)
{
}
}
public void updateFeatureRenderer(Object[][] data)
{
updateFeatureRenderer(data, true);
}
/**
* Update the priority order of features; only repaint if this changed the
* order of visible features
*
* @param data
* @param visibleNew
*/
void updateFeatureRenderer(Object[][] data, boolean visibleNew)
{
FeatureSettingsBean[] rowData = getTableAsBeans(data);
if (fr.setFeaturePriority(rowData, visibleNew))
{
refreshDisplay();
}
}
/**
* Converts table data into an array of data beans
*/
private FeatureSettingsBean[] getTableAsBeans(Object[][] data)
{
FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length];
for (int i = 0; i < data.length; i++)
{
String type = (String) data[i][TYPE_COLUMN];
FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN];
FeatureMatcherSetI theFilter = (FeatureMatcherSetI) data[i][FILTER_COLUMN];
Boolean isShown = (Boolean) data[i][SHOW_COLUMN];
rowData[i] = new FeatureSettingsBean(type, colour, theFilter,
isShown);
}
return rowData;
}
private void jbInit() throws Exception
{
this.setLayout(new BorderLayout());
final boolean hasComplement = af.getViewport()
.getCodingComplement() != null;
JPanel settingsPane = new JPanel();
settingsPane.setLayout(new BorderLayout());
JPanel bigPanel = new JPanel();
bigPanel.setLayout(new BorderLayout());
groupPanel = new JPanel();
bigPanel.add(groupPanel, BorderLayout.NORTH);
JButton invert = new JButton(
MessageManager.getString("label.invert_selection"));
invert.setFont(JvSwingUtils.getLabelFont());
invert.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
invertSelection();
}
});
JButton optimizeOrder = new JButton(
MessageManager.getString("label.optimise_order"));
optimizeOrder.setFont(JvSwingUtils.getLabelFont());
optimizeOrder.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
orderByAvWidth();
}
});
final String byScoreLabel = MessageManager
.getString("label.seq_sort_by_score");
JButton sortByScore = new JButton(byScoreLabel);
sortByScore.setFont(JvSwingUtils.getLabelFont());
sortByScore.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
if (canSortBy(byScoreLabel))
{
sortByScore(null);
}
}
});
final String byDensityLabel = MessageManager
.getString("label.sequence_sort_by_density");
JButton sortByDens = new JButton(byDensityLabel);
sortByDens.setFont(JvSwingUtils.getLabelFont());
sortByDens.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
if (canSortBy(byDensityLabel))
{
sortByDensity(null);
}
}
});
JButton help = new JButton(MessageManager.getString("action.help"));
help.setFont(JvSwingUtils.getLabelFont());
help.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
try
{
Help.showHelpWindow(HelpId.SequenceFeatureSettings);
} catch (HelpSetException e1)
{
e1.printStackTrace();
}
}
});
// Cancel for a SplitFrame should just revert changes to the currently
// displayed
// settings. May want to do this for either or both - so need a splitview
// feature settings cancel/OK.
JButton cancel = new JButton(MessageManager
.getString(hasComplement ? "action.revert" : "action.cancel"));
cancel.setToolTipText(MessageManager.getString(hasComplement
? "action.undo_changes_to_feature_settings"
: "action.undo_changes_to_feature_settings_and_close_the_dialog"));
cancel.setFont(JvSwingUtils.getLabelFont());
// TODO: disable cancel (and apply!) until current settings are different
cancel.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
revert();
refreshDisplay();
if (!hasComplement)
{
close();
}
}
});
// Cancel for the whole dialog should cancel both CDS and Protein.
// OK for an individual feature settings just applies changes, but dialog
// remains open
JButton ok = new JButton(MessageManager
.getString(hasComplement ? "action.apply" : "action.ok"));
ok.setFont(JvSwingUtils.getLabelFont());
ok.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
if (!hasComplement)
{
close();
}
else
{
storeOriginalSettings();
}
}
});
JButton loadColours = new JButton(
MessageManager.getString("label.load_colours"));
loadColours.setFont(JvSwingUtils.getLabelFont());
loadColours.setToolTipText(
MessageManager.getString("label.load_colours_tooltip"));
loadColours.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
load();
}
});
JButton saveColours = new JButton(
MessageManager.getString("label.save_colours"));
saveColours.setFont(JvSwingUtils.getLabelFont());
saveColours.setToolTipText(
MessageManager.getString("label.save_colours_tooltip"));
saveColours.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
save();
}
});
transparency.addChangeListener(new ChangeListener()
{
@Override
public void stateChanged(ChangeEvent evt)
{
if (!inConstruction)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
refreshDisplay();
}
}
});
transparency.setMaximum(70);
transparency.setToolTipText(
MessageManager.getString("label.transparency_tip"));
boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
String text = MessageManager
.formatMessage("label.show_linked_features",
nucleotide
? MessageManager.getString("label.protein")
.toLowerCase(Locale.ROOT)
: "CDS");
showComplement = new JCheckBox(text);
showComplement.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
af.getViewport()
.setShowComplementFeatures(showComplement.isSelected());
refreshDisplay();
}
});
showComplementOnTop = new JCheckBox(
MessageManager.getString("label.on_top"));
showComplementOnTop.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
af.getViewport().setShowComplementFeaturesOnTop(
showComplementOnTop.isSelected());
refreshDisplay();
}
});
updateComplementButtons();
JPanel lowerPanel = new JPanel(new GridLayout(1, 2));
bigPanel.add(lowerPanel, BorderLayout.SOUTH);
JPanel transbuttons = new JPanel(new GridLayout(5, 1));
transbuttons.add(optimizeOrder);
transbuttons.add(invert);
transbuttons.add(sortByScore);
transbuttons.add(sortByDens);
transbuttons.add(help);
JPanel transPanelLeft = new JPanel(
new GridLayout(hasComplement ? 4 : 2, 1));
transPanelLeft.add(new JLabel(" Colour transparency" + ":"));
transPanelLeft.add(transparency);
if (hasComplement)
{
JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT));
cp.add(showComplement);
cp.add(showComplementOnTop);
transPanelLeft.add(cp);
}
lowerPanel.add(transPanelLeft);
lowerPanel.add(transbuttons);
JPanel buttonPanel = new JPanel();
buttonPanel.add(ok);
buttonPanel.add(cancel);
buttonPanel.add(loadColours);
buttonPanel.add(saveColours);
bigPanel.add(scrollPane, BorderLayout.CENTER);
settingsPane.add(bigPanel, BorderLayout.CENTER);
settingsPane.add(buttonPanel, BorderLayout.SOUTH);
this.add(settingsPane);
}
/**
* Repaints alignment, structure and overview (if shown). If there is a
* complementary view which is showing this view's features, then also
* repaints that.
*/
void refreshDisplay()
{
af.alignPanel.paintAlignment(true, true);
AlignViewportI complement = af.getViewport().getCodingComplement();
if (complement != null && complement.isShowComplementFeatures())
{
AlignFrame af2 = Desktop.getAlignFrameFor(complement);
af2.alignPanel.paintAlignment(true, true);
}
}
/**
* Answers a suitable tooltip to show on the colour cell of the table
*
* @param fcol
* @param withHint
* if true include 'click to edit' and similar text
* @return
*/
public static String getColorTooltip(FeatureColourI fcol,
boolean withHint)
{
if (fcol == null)
{
return null;
}
if (fcol.isSimpleColour())
{
return withHint ? BASE_TOOLTIP : null;
}
String description = fcol.getDescription();
description = description.replaceAll("<", "<");
description = description.replaceAll(">", ">");
StringBuilder tt = new StringBuilder(description);
if (withHint)
{
tt.append("
").append(BASE_TOOLTIP).append("");
}
return JvSwingUtils.wrapTooltip(true, tt.toString());
}
public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
int w, int h)
{
boolean thr = false;
StringBuilder tx = new StringBuilder();
if (gcol.isColourByAttribute())
{
tx.append(FeatureMatcher
.toAttributeDisplayName(gcol.getAttributeName()));
}
else if (!gcol.isColourByLabel())
{
tx.append(MessageManager.getString("label.score"));
}
tx.append(" ");
if (gcol.isAboveThreshold())
{
thr = true;
tx.append(">");
}
if (gcol.isBelowThreshold())
{
thr = true;
tx.append("<");
}
if (gcol.isColourByLabel())
{
if (thr)
{
tx.append(" ");
}
if (!gcol.isColourByAttribute())
{
tx.append("Label");
}
comp.setIcon(null);
}
else
{
Color newColor = gcol.getMaxColour();
comp.setBackground(newColor);
// jalview.bin.Console.errPrintln("Width is " + w / 2);
Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
comp.setIcon(ficon);
// tt+="RGB value: Max (" + newColor.getRed() + ", "
// + newColor.getGreen() + ", " + newColor.getBlue()
// + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
// + ", " + minCol.getBlue() + ")");
}
comp.setHorizontalAlignment(SwingConstants.CENTER);
comp.setText(tx.toString());
}
// ///////////////////////////////////////////////////////////////////////
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
// ///////////////////////////////////////////////////////////////////////
class FeatureTableModel extends AbstractTableModel
{
private String[] columnNames = {
MessageManager.getString("label.feature_type"),
MessageManager.getString("action.colour"),
MessageManager.getString("label.configuration"),
MessageManager.getString("label.show") };
private Object[][] data;
FeatureTableModel(Object[][] data)
{
this.data = data;
}
public Object[][] getData()
{
return data;
}
public void setData(Object[][] data)
{
this.data = data;
}
@Override
public int getColumnCount()
{
return columnNames.length;
}
public Object[] getRow(int row)
{
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];
}
/**
* Answers the class of column c of the table
*/
@Override
public Class> getColumnClass(int c)
{
switch (c)
{
case TYPE_COLUMN:
return String.class;
case COLOUR_COLUMN:
return FeatureColour.class;
case FILTER_COLUMN:
return FeatureMatcherSet.class;
default:
return Boolean.class;
}
}
@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;
fireTableCellUpdated(row, col);
updateFeatureRenderer(data);
}
}
class ColorRenderer extends JLabel implements TableCellRenderer
{
Border unselectedBorder = null;
Border selectedBorder = null;
public ColorRenderer()
{
setOpaque(true); // MUST do this for background to show up.
setHorizontalTextPosition(SwingConstants.CENTER);
setVerticalTextPosition(SwingConstants.CENTER);
}
@Override
public Component getTableCellRendererComponent(JTable tbl, Object color,
boolean isSelected, boolean hasFocus, int row, int column)
{
FeatureColourI cellColour = (FeatureColourI) color;
setOpaque(true);
setBackground(tbl.getBackground());
if (!cellColour.isSimpleColour())
{
Rectangle cr = tbl.getCellRect(row, column, false);
FeatureSettings.renderGraduatedColor(this, cellColour,
(int) cr.getWidth(), (int) cr.getHeight());
}
else
{
this.setText("");
this.setIcon(null);
setBackground(cellColour.getColour());
}
if (isSelected)
{
if (selectedBorder == null)
{
selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
tbl.getSelectionBackground());
}
setBorder(selectedBorder);
}
else
{
if (unselectedBorder == null)
{
unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
tbl.getBackground());
}
setBorder(unselectedBorder);
}
return this;
}
}
class FilterRenderer extends JLabel implements TableCellRenderer
{
javax.swing.border.Border unselectedBorder = null;
javax.swing.border.Border selectedBorder = null;
public FilterRenderer()
{
setOpaque(true); // MUST do this for background to show up.
setHorizontalTextPosition(SwingConstants.CENTER);
setVerticalTextPosition(SwingConstants.CENTER);
}
@Override
public Component getTableCellRendererComponent(JTable tbl,
Object filter, boolean isSelected, boolean hasFocus, int row,
int column)
{
FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter;
setOpaque(true);
setBackground(tbl.getBackground());
this.setIcon(null);
if (theFilter != null)
{
String asText = theFilter.toString();
this.setText(asText);
}
if (isSelected)
{
if (selectedBorder == null)
{
selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
tbl.getSelectionBackground());
}
setBorder(selectedBorder);
}
else
{
if (unselectedBorder == null)
{
unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
tbl.getBackground());
}
setBorder(unselectedBorder);
}
return this;
}
}
/**
* update comp using rendering settings from gcol
*
* @param comp
* @param gcol
*/
public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol)
{
int w = comp.getWidth(), h = comp.getHeight();
if (w < 20)
{
w = (int) comp.getPreferredSize().getWidth();
h = (int) comp.getPreferredSize().getHeight();
if (w < 20)
{
w = 80;
h = 12;
}
}
renderGraduatedColor(comp, gcol, w, h);
}
@SuppressWarnings("serial")
class ColorEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
FeatureColourI currentColor;
FeatureTypeSettings chooser;
String type;
JButton button;
protected static final String EDIT = "edit";
int rowSelected = 0;
public ColorEditor()
{
// Set up the editor (from the table's point of view),
// which is a button.
// This button brings up the color chooser dialog,
// which is the editor from the user's point of view.
button = new JButton();
button.setActionCommand(EDIT);
button.addActionListener(this);
button.setBorderPainted(false);
}
/**
* Handles events from the editor button, and from the colour/filters
* dialog's OK button
*/
@Override
public void actionPerformed(ActionEvent e)
{
if (button == e.getSource())
{
if (currentColor.isSimpleColour())
{
/*
* simple colour chooser
*/
String ttl = MessageManager
.formatMessage("label.select_colour_for", type);
ColourChooserListener listener = new ColourChooserListener()
{
@Override
public void colourSelected(Color c)
{
currentColor = new FeatureColour(c);
table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
fireEditingStopped();
}
@Override
public void cancel()
{
fireEditingStopped();
}
};
JalviewColourChooser.showColourChooser(button, ttl,
currentColor.getColour(), listener);
}
else
{
/*
* variable colour and filters dialog
*/
chooser = new FeatureTypeSettings(fr, type);
if (!Platform.isJS())
/**
* Java only
*
* @j2sIgnore
*/
{
chooser.setRequestFocusEnabled(true);
chooser.requestFocus();
}
chooser.addActionListener(this);
fireEditingStopped();
}
}
else
{
/*
* after OK in variable colour dialog, any changes to colour
* (or filters!) are already set in FeatureRenderer, so just
* update table data without triggering updateFeatureRenderer
*/
currentColor = fr.getFeatureColours().get(type);
FeatureMatcherSetI currentFilter = fr.getFeatureFilter(type);
if (currentFilter == null)
{
currentFilter = new FeatureMatcherSet();
}
Object[] data = ((FeatureTableModel) table.getModel())
.getData()[rowSelected];
data[COLOUR_COLUMN] = currentColor;
data[FILTER_COLUMN] = currentFilter;
fireEditingStopped();
// SwingJS needs an explicit repaint() here,
// rather than relying upon no validation having
// occurred since the stopEditing call was made.
// Its laying out has not been stopped by the modal frame
table.validate();
table.repaint();
}
}
/**
* Override allows access to this method from anonymous inner classes
*/
@Override
protected void fireEditingStopped()
{
super.fireEditingStopped();
}
// Implement the one CellEditor method that AbstractCellEditor doesn't.
@Override
public Object getCellEditorValue()
{
return currentColor;
}
// Implement the one method defined by TableCellEditor.
@Override
public Component getTableCellEditorComponent(JTable theTable,
Object value, boolean isSelected, int row, int column)
{
currentColor = (FeatureColourI) value;
this.rowSelected = row;
type = table.getValueAt(row, TYPE_COLUMN).toString();
button.setOpaque(true);
button.setBackground(FeatureSettings.this.getBackground());
if (!currentColor.isSimpleColour())
{
JLabel btn = new JLabel();
btn.setSize(button.getSize());
FeatureSettings.renderGraduatedColor(btn, currentColor);
button.setBackground(btn.getBackground());
button.setIcon(btn.getIcon());
button.setText(btn.getText());
}
else
{
button.setText("");
button.setIcon(null);
button.setBackground(currentColor.getColour());
}
return button;
}
}
/**
* The cell editor for the Filter column. It displays the text of any filters
* for the feature type in that row (in full as a tooltip, possible
* abbreviated as display text). On click in the cell, opens the Feature
* Display Settings dialog at the Filters tab.
*/
@SuppressWarnings("serial")
class FilterEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
FeatureMatcherSetI currentFilter;
Point lastLocation;
String type;
JButton button;
protected static final String EDIT = "edit";
int rowSelected = 0;
public FilterEditor()
{
button = new JButton();
button.setActionCommand(EDIT);
button.addActionListener(this);
button.setBorderPainted(false);
}
/**
* Handles events from the editor button
*/
@Override
public void actionPerformed(ActionEvent e)
{
if (button == e.getSource())
{
FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type);
chooser.addActionListener(this);
chooser.setRequestFocusEnabled(true);
chooser.requestFocus();
if (lastLocation != null)
{
// todo open at its last position on screen
chooser.setBounds(lastLocation.x, lastLocation.y,
chooser.getWidth(), chooser.getHeight());
chooser.validate();
}
fireEditingStopped();
}
else if (e.getSource() instanceof Component)
{
/*
* after OK in variable colour dialog, any changes to filter
* (or colours!) are already set in FeatureRenderer, so just
* update table data without triggering updateFeatureRenderer
*/
FeatureColourI currentColor = fr.getFeatureColours().get(type);
currentFilter = fr.getFeatureFilter(type);
if (currentFilter == null)
{
currentFilter = new FeatureMatcherSet();
}
Object[] data = ((FeatureTableModel) table.getModel())
.getData()[rowSelected];
data[COLOUR_COLUMN] = currentColor;
data[FILTER_COLUMN] = currentFilter;
fireEditingStopped();
// SwingJS needs an explicit repaint() here,
// rather than relying upon no validation having
// occurred since the stopEditing call was made.
// Its laying out has not been stopped by the modal frame
table.validate();
table.repaint();
}
}
@Override
public Object getCellEditorValue()
{
return currentFilter;
}
@Override
public Component getTableCellEditorComponent(JTable theTable,
Object value, boolean isSelected, int row, int column)
{
currentFilter = (FeatureMatcherSetI) value;
this.rowSelected = row;
type = table.getValueAt(row, TYPE_COLUMN).toString();
button.setOpaque(true);
button.setBackground(FeatureSettings.this.getBackground());
button.setText(currentFilter.toString());
button.setIcon(null);
return button;
}
}
public boolean isOpen()
{
if (af.getSplitViewContainer() != null)
{
return af.getSplitViewContainer().isFeatureSettingsOpen();
}
return frame != null && !frame.isClosed();
}
@Override
public void revert()
{
fr.setTransparency(originalTransparency);
fr.setFeatureFilters(originalFilters);
updateFeatureRenderer(originalData);
af.getViewport().setViewStyle(originalViewStyle);
updateTransparencySliderFromFR();
updateComplementButtons();
refreshDisplay();
}
}
class FeatureIcon implements Icon
{
FeatureColourI gcol;
Color backg;
boolean midspace = false;
int width = 50, height = 20;
int s1, e1; // start and end of midpoint band for thresholded symbol
Color mpcolour = Color.white;
FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace)
{
gcol = gfc;
backg = bg;
width = w;
height = h;
midspace = mspace;
if (midspace)
{
s1 = width / 3;
e1 = s1 * 2;
}
else
{
s1 = width / 2;
e1 = s1;
}
}
@Override
public int getIconWidth()
{
return width;
}
@Override
public int getIconHeight()
{
return height;
}
@Override
public void paintIcon(Component c, Graphics g, int x, int y)
{
if (gcol.isColourByLabel())
{
g.setColor(backg);
g.fillRect(0, 0, width, height);
// need an icon here.
g.setColor(gcol.getMaxColour());
g.setFont(new Font("Verdana", Font.PLAIN, 9));
// g.setFont(g.getFont().deriveFont(
// AffineTransform.getScaleInstance(
// width/g.getFontMetrics().stringWidth("Label"),
// height/g.getFontMetrics().getHeight())));
g.drawString(MessageManager.getString("label.label"), 0, 0);
}
else
{
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.getMaxColour());
// g.fillRect(0, e1, width - e1, height); // BH 2018
g.fillRect(e1, 0, width - e1, height);
}
}
}