X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=0963b310575470461cb778dcc12cc43978f3cb03;hb=833fafa77f2f63bea98ce1d6e1e4ee3e46e7bd53;hp=3979ebecf3af9e9e09bdfa72d3aeb7c894bef6cf;hpb=391968dd70ca76090306df9b5852bbef10ab4ede;p=jalview.git
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
old mode 100755
new mode 100644
index 3979ebe..0963b31
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,570 +1,1885 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.datamodel.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.awt.*;
-import java.util.*;
-import javax.swing.BorderFactory;
-import java.awt.event.*;
-import javax.swing.table.*;
-import java.io.*;
-import jalview.io.JalviewFileChooser;
-
-public class FeatureSettings extends JPanel
-{
-
- final FeatureRenderer fr;
- final AlignmentPanel ap;
- final AlignViewport av;
- Hashtable allFeatures;
- Object [][] originalData;
- final JInternalFrame frame;
- JScrollPane scrollPane = new JScrollPane();
- JTable table;
- JPanel groupPanel;
-
- public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
- {
- this.ap = ap;
- this.av = av;
- fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
- av.alignment.getSequences();
- frame = new JInternalFrame();
- frame.setContentPane(this);
- Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300);
-
- setTableData();
-
- final JSlider transparency = new JSlider(0, 70, 0);
- transparency.addChangeListener(new ChangeListener()
- {
- public void stateChanged(ChangeEvent evt)
- {
- fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
- ap.repaint();
- }
- });
-
- JPanel transPanel = new JPanel(new FlowLayout());
- transPanel.add(new JLabel("Transparency"));
- transPanel.add(transparency);
-
- //////////////////////////////////////////////
- //We're going to need those OK cancel buttons
- JPanel buttonPanel = new JPanel(new FlowLayout());
- JButton button = new JButton("OK");
- button.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- try
- {
- frame.setClosed(true);
- }
- catch (Exception exe)
- {}
- }
- });
- buttonPanel.add(button);
- button = new JButton("Cancel");
- button.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- try
- {
- updateFeatureRenderer(originalData);
- frame.setClosed(true);
- }
- catch (Exception exe)
- {}
- }
- });
- buttonPanel.add(button);
-
- button = new JButton("Load Colours");
- button.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- load();
- }
- });
- buttonPanel.add(button);
- button = new JButton("Save Colours");
- button.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- save();
- }
- });
- buttonPanel.add(button);
-
- this.setLayout(new BorderLayout());
- JPanel bigPanel = new JPanel(new BorderLayout());
- bigPanel.add(transPanel, BorderLayout.SOUTH);
- bigPanel.add(scrollPane, BorderLayout.CENTER);
- if(groupPanel!=null)
- {
- groupPanel.setLayout(
- new GridLayout(groupPanel.getComponentCount()/3, 4));
- groupPanel.validate();
- bigPanel.add(groupPanel, BorderLayout.NORTH);
- }
- add(bigPanel, BorderLayout.CENTER);
- add(buttonPanel, BorderLayout.SOUTH);
-
-
- }
-
- void setTableData()
- {
- if (fr.featureGroups == null)
- fr.featureGroups = new Hashtable();
- else
- fr.featureGroups.clear();
-
- allFeatures = new Hashtable();
- SequenceFeature[] features;
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- features = av.alignment.getSequenceAt(i).getDatasetSequence().
- getSequenceFeatures();
-
- if (features == null)
- continue;
-
- int index = 0;
- while (index < features.length)
- {
- if(features[index].getFeatureGroup()!=null
- && !fr.featureGroups.containsKey(features[index].getFeatureGroup()))
- {
- fr.featureGroups.put(features[index].getFeatureGroup(), new Boolean(true));
- if(groupPanel==null)
- groupPanel = new JPanel();
-
- final JCheckBox check = new JCheckBox(features[index].getFeatureGroup(), true);
- check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent evt)
- {
- if (fr.featureGroups.containsKey(check.getText()))
- {
- fr.featureGroups.put(check.getText(),
- new Boolean(check.isSelected()));
- ap.seqPanel.seqCanvas.repaint();
- if (ap.overviewPanel != null)
- ap.overviewPanel.updateOverviewImage();
- }
- resetTable();
- }
- });
- groupPanel.add(check);
- }
- if (!allFeatures.contains(features[index].getType()))
- {
- if(features[index].featureGroup!=null)
- allFeatures.put(features[index].getType(), features[index].featureGroup);
- else
- allFeatures.put(features[index].getType(), "NOGROUP");
- }
- index++;
- }
- }
- if(allFeatures.size()<1)
- {
- try
- { frame.setClosed(true); }
- catch (Exception ex){}
-
- JOptionPane.showInternalMessageDialog(
- Desktop.desktop, "No features have been added to this alignment!",
- "No Sequence Features", JOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
- resetTable();
- }
-
- void resetTable()
- {
- int fSize = allFeatures.size();
-
- String type;
- boolean originalExists = false;
- if (originalData != null)
- originalExists = true;
- else
- originalData = new Object[fSize][3];
-
- Object[][] tmp = new Object[fSize][3];
- int tmpIndex = 0;
-
- Enumeration en = allFeatures.keys();
- int i=0;
- while(en.hasMoreElements())
- {
- type = en.nextElement().toString();
- Color col = fr.getColour(type);
-
-
- //This will ignore any features which are in groups not shown
- if(fr.featureGroups==null
- || ((Boolean)fr.featureGroups.get(allFeatures.get(type))).booleanValue())
- {
- tmp[tmpIndex][0] = type;
- tmp[tmpIndex][1] = col;
- if (av.featuresDisplayed != null)
- tmp[tmpIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));
- else
- tmp[tmpIndex][2] = new Boolean(true);
-
- tmpIndex++;
- }
-
-
- if (!originalExists)
- {
- originalData[i][0] = type;
- originalData[i][1] = col;
- if (av.featuresDisplayed != null)
- originalData[i][2] = new Boolean(av.featuresDisplayed.contains(type));
- else
- originalData[i][2] = new Boolean(true);
- }
- i++;
- }
-
- Object [][]data = new Object[tmpIndex][3];
- System.arraycopy(tmp, 0, data,0, tmpIndex);
-
- table = new JTable(new FeatureTableModel(data));
- scrollPane.setViewportView(table);
- 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());
-
- table.getColumnModel().getColumn(0).setPreferredWidth(200);
-
- table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-
- table.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- selectedRow = table.rowAtPoint(evt.getPoint());
- }
- });
-
- table.addMouseMotionListener(new MouseMotionAdapter()
- {
- 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);
-
- selectedRow = newRow;
- }
- }
- });
-
- updateFeatureRenderer(data);
-
- }
-
- void load()
- {
- JalviewFileChooser chooser = new JalviewFileChooser(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");
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- File file = chooser.getSelectedFile();
-
- try
- {
- InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
-
- jalview.binding.JalviewUserColours jucs = new jalview.binding.
- JalviewUserColours();
- jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
-
-
- for (int i = 0; i < jucs.getColourCount(); i++)
- {
- fr.setColour( jucs.getColour(i).getName(),
- new Color(Integer.parseInt( jucs.getColour(i).getRGB(), 16)));
- }
-
- setTableData();
- ap.repaint();
- }
- catch (Exception ex)
- {
- System.out.println("Error loading User ColourFile\n" + ex);
- }
- }
- }
-
- void save()
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[] { "fc" },
- new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Save Feature Colour Scheme");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
- ucs.setSchemeName("Sequence Features");
- try
- {
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(choice), "UTF-8"));
-
- Enumeration e = fr.featureColours.keys();
- while(e.hasMoreElements())
- {
-
-
- jalview.binding.Colour col = new jalview.binding.Colour();
- col.setName(e.nextElement().toString());
- col.setRGB(jalview.util.Format.getHexString(
- fr.getColour(col.getName())));
- ucs.addColour(col);
- }
-
- ucs.marshal(out);
- out.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- }
-
- public void updateFeatureRenderer(Object [][] data)
- {
- fr.setFeaturePriority( data );
- ap.repaint();
-
- if(ap.overviewPanel!=null)
- ap.overviewPanel.updateOverviewImage();
- }
-
- int selectedRow =-1;
-
-
- /////////////////////////////////////////////////////////////////////////
- // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
- /////////////////////////////////////////////////////////////////////////
- class FeatureTableModel
- extends AbstractTableModel
- {
- FeatureTableModel(Object[][] data)
- {
- this.data = data;
- }
-
- private String[] columnNames = {"Feature Type", "Colour","Display"};
- private Object[][] data;
-
- public Object[][] getData()
- {
- return data;
- }
-
- public int getColumnCount() {
- return columnNames.length;
- }
-
- public Object[] getRow(int row)
- {
- return data[row];
- }
-
- public int getRowCount() {
- return data.length;
- }
-
- public String getColumnName(int col) {
- return columnNames[col];
- }
-
- public Object getValueAt(int row, int col) {
- return data[row][col];
- }
-
- public Class getColumnClass(int c) {
- return getValueAt(0, c).getClass();
- }
-
- public boolean isCellEditable(int row, int col) {
- return col==0 ? false:true;
- }
-
- public void setValueAt(Object value, int row, int col) {
- data[row][col] = value;
- fireTableCellUpdated(row, col);
- updateFeatureRenderer(data);
- }
-
- }
- class ColorRenderer extends JLabel
- implements TableCellRenderer {
- javax.swing.border.Border unselectedBorder = null;
- javax.swing.border.Border selectedBorder = null;
-
- public ColorRenderer() {
- setOpaque(true); //MUST do this for background to show up.
- }
-
- public Component getTableCellRendererComponent(
- JTable table, Object color,
- boolean isSelected, boolean hasFocus,
- int row, int column) {
- Color newColor = (Color)color;
- setBackground(newColor);
- if (isSelected) {
- if (selectedBorder == null) {
- selectedBorder = BorderFactory.createMatteBorder(2,5,2,5,
- table.getSelectionBackground());
- }
- setBorder(selectedBorder);
- } else {
- if (unselectedBorder == null) {
- unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5,
- table.getBackground());
- }
- setBorder(unselectedBorder);
- }
-
- setToolTipText("RGB value: " + newColor.getRed() + ", "
- + newColor.getGreen() + ", "
- + newColor.getBlue());
- return this;
- }
- }
-}
-
- class ColorEditor extends AbstractCellEditor
- implements TableCellEditor,
- ActionListener {
- Color currentColor;
- JButton button;
- JColorChooser colorChooser;
- JDialog dialog;
- protected static final String EDIT = "edit";
-
- 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);
- //Set up the dialog that the button brings up.
- colorChooser = new JColorChooser();
- dialog = JColorChooser.createDialog(button,
- "Select new Colour",
- true, //modal
- colorChooser,
- this, //OK button handler
- null); //no CANCEL button handler
- }
-
- /**
- * Handles events from the editor button and from
- * the dialog's OK button.
- */
- public void actionPerformed(ActionEvent e) {
-
- if (EDIT.equals(e.getActionCommand())) {
- //The user has clicked the cell, so
- //bring up the dialog.
- button.setBackground(currentColor);
- colorChooser.setColor(currentColor);
- dialog.setVisible(true);
-
- //Make the renderer reappear.
- fireEditingStopped();
-
- } else { //User pressed dialog's "OK" button.
- currentColor = colorChooser.getColor();
- }
- }
-
- //Implement the one CellEditor method that AbstractCellEditor doesn't.
- public Object getCellEditorValue() {
- return currentColor;
- }
-
- //Implement the one method defined by TableCellEditor.
- public Component getTableCellEditorComponent(JTable table,
- Object value,
- boolean isSelected,
- int row,
- int column) {
- currentColor = (Color)value;
- return button;
- }
-}
+/*
+ * 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 jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Help.HelpId;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+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;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+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.HashSet;
+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.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;
+
+ jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
+
+ JPanel settingsPane = new JPanel();
+
+ JPanel dasSettingsPane = new JPanel();
+
+ final FeatureRenderer fr;
+
+ public final AlignFrame af;
+
+ Object[][] originalData;
+
+ private float originalTransparency;
+
+ final JInternalFrame frame;
+
+ JScrollPane scrollPane = new JScrollPane();
+
+ JTable table;
+
+ JPanel groupPanel;
+
+ JSlider transparency = new JSlider();
+
+ JPanel transPanel = new JPanel(new GridLayout(1, 2));
+
+ private static final int MIN_WIDTH = 400;
+
+ private static final int MIN_HEIGHT = 400;
+
+ /**
+ * Constructor
+ *
+ * @param af
+ */
+ public FeatureSettings(AlignFrame af)
+ {
+ this.af = af;
+ fr = af.getFeatureRenderer();
+ // allow transparency to be recovered
+ transparency.setMaximum(100
+ - (int) ((originalTransparency = fr.getTransparency()) * 100));
+
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ 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(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 (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.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)
+ {
+ /*
+ * 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().isShowSequenceFeatures() || !fr.hasRenderOrder())
+ {
+ fr.findAllFeatures(true); // display everything!
+ }
+
+ discoverAllFeatureData();
+ final PropertyChangeListener change;
+ 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 seuqence
+ // feature types only
+ fs.handlingUpdate = false;
+ }
+ }
+
+ });
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (Platform.isAMac())
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 475, 480);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 400, 450);
+ }
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ fr.removePropertyChangeListener(change);
+ dassourceBrowser.fs = null;
+ };
+ });
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+
+ protected void popupSort(final int selectedRow, final String type,
+ final Object typeCol, final Map minmax, int x,
+ int y)
+ {
+ 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.af.avc
+ .sortAlignmentByFeatureScore(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)
+ {
+ me.af.avc
+ .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
+ { type }));
+ }
+
+ });
+ men.add(dens);
+ if (minmax != null)
+ {
+ 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!
+ * chb.setSelected(minmax.get(type) != null); chb.addActionListener(new
+ * ActionListener() {
+ *
+ * public void actionPerformed(ActionEvent e) {
+ * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
+ * null); } else { minmax.put(type, typeMinMax); } }
+ *
+ * });
+ *
+ * men.add(chb);
+ */
+ 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(!featureColour.isSimpleColour());
+ men.add(mxcol);
+ mxcol.addActionListener(new ActionListener()
+ {
+ JColorChooser colorChooser;
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (e.getSource() == mxcol)
+ {
+ if (featureColour.isSimpleColour())
+ {
+ FeatureColourChooser fc = new FeatureColourChooser(me.fr,
+ type);
+ fc.addActionListener(this);
+ }
+ else
+ {
+ // bring up simple color chooser
+ colorChooser = new JColorChooser();
+ JDialog dialog = JColorChooser.createDialog(me,
+ "Select new Colour", true, // modal
+ colorChooser, this, // OK button handler
+ null); // no CANCEL button handler
+ colorChooser.setColor(featureColour.getMaxColour());
+ dialog.setVisible(true);
+ }
+ }
+ else
+ {
+ if (e.getSource() instanceof FeatureColourChooser)
+ {
+ FeatureColourChooser fc = (FeatureColourChooser) e
+ .getSource();
+ table.setValueAt(fc.getLastColour(), selectedRow, 1);
+ table.validate();
+ }
+ else
+ {
+ // probably the color chooser!
+ table.setValueAt(new FeatureColour(colorChooser.getColor()),
+ selectedRow, 1);
+ table.validate();
+ me.updateFeatureRenderer(
+ ((FeatureTableModel) table.getModel()).getData(),
+ false);
+ }
+ }
+ }
+
+ });
+ }
+ }
+ 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);
+ }
+
+ /**
+ * true when Feature Settings are updating from feature renderer
+ */
+ private boolean handlingUpdate = false;
+
+ /**
+ * holds {featureCount, totalExtent} for each feature type
+ */
+ Map typeWidth = null;
+
+ @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());
+ af.alignPanel.getSeqPanel().seqCanvas.repaint();
+ if (af.alignPanel.overviewPanel != null)
+ {
+ af.alignPanel.overviewPanel.updateOverviewImage();
+ }
+
+ resetTable(new String[] { grp });
+ }
+ });
+ groupPanel.add(check);
+ return visible;
+ }
+
+ boolean resettingTable = false;
+
+ 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()][3];
+ 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][0] = type;
+ data[dataIndex][1] = fr.getFeatureStyle(type);
+ data[dataIndex][2] = new Boolean(
+ 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][0] = type;
+
+ data[dataIndex][1] = fr.getFeatureStyle(type);
+ if (data[dataIndex][1] == null)
+ {
+ // "Colour has been updated in another view!!"
+ fr.clearRenderOrder();
+ return;
+ }
+
+ data[dataIndex][2] = new Boolean(true);
+ dataIndex++;
+ displayableTypes.remove(type);
+ }
+
+ if (originalData == null)
+ {
+ originalData = new Object[data.length][3];
+ for (int i = 0; i < data.length; i++)
+ {
+ System.arraycopy(data[i], 0, originalData[i], 0, 3);
+ }
+ }
+ 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[0];
+ boolean found = false;
+ for (Object[] current : currentData)
+ {
+ if (type.equals(current[0]))
+ {
+ found = true;
+ /*
+ * currently dependent on object equality here;
+ * really need an equals method on FeatureColour
+ */
+ if (!row[1].equals(current[1]))
+ {
+ /*
+ * feature colour has changed externally - update originalData
+ */
+ for (Object[] original : originalData)
+ {
+ if (type.equals(original[0]))
+ {
+ original[1] = row[1];
+ break;
+ }
+ }
+ }
+ break;
+ }
+ }
+ if (!found)
+ {
+ /*
+ * new feature detected - add to original data (on top)
+ */
+ Object[][] newData = new Object[originalData.length + 1][3];
+ for (int i = 0; i < originalData.length; i++)
+ {
+ System.arraycopy(originalData[i], 0, newData[i + 1], 0, 3);
+ }
+ 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);
+ }
+ }
+
+ 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"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File file = chooser.getSelectedFile();
+
+ try
+ {
+ InputStreamReader in = new InputStreamReader(
+ new FileInputStream(file), "UTF-8");
+
+ JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+
+ for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+ {
+ String name;
+ jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
+ if (newcol.hasMax())
+ {
+ Color mincol = null, maxcol = null;
+ try
+ {
+ mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
+ maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
+
+ } catch (Exception e)
+ {
+ Cache.log.warn("Couldn't parse out graduated feature color.",
+ e);
+ }
+ FeatureColourI gcol = new FeatureColour(mincol, maxcol,
+ newcol.getMin(), newcol.getMax());
+ if (newcol.hasAutoScale())
+ {
+ gcol.setAutoScaled(newcol.getAutoScale());
+ }
+ if (newcol.hasColourByLabel())
+ {
+ gcol.setColourByLabel(newcol.getColourByLabel());
+ }
+ if (newcol.hasThreshold())
+ {
+ gcol.setThreshold(newcol.getThreshold());
+ }
+ if (newcol.getThreshType().length() > 0)
+ {
+ String ttyp = newcol.getThreshType();
+ if (ttyp.equalsIgnoreCase("ABOVE"))
+ {
+ gcol.setAboveThreshold(true);
+ }
+ if (ttyp.equalsIgnoreCase("BELOW"))
+ {
+ gcol.setBelowThreshold(true);
+ }
+ }
+ fr.setColour(name = newcol.getName(), gcol);
+ }
+ else
+ {
+ 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());
+ }
+ if (table != null)
+ {
+ resetTable(null);
+ Object[][] data = ((FeatureTableModel) table.getModel())
+ .getData();
+ ensureOrder(data);
+ updateFeatureRenderer(data, false);
+ table.repaint();
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error loading User Colour File\n" + ex);
+ }
+ }
+ }
+
+ 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 value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
+ ucs.setSchemeName("Sequence Features");
+ try
+ {
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(choice), "UTF-8"));
+
+ Set fr_colours = fr.getAllFeatureColours();
+ Iterator 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();
+ sortOrder[i] = fr.getOrder(sortTypes[i]);
+ i++;
+ }
+ QuickSort.sort(sortOrder, sortTypes);
+ sortOrder = null;
+ for (i = 0; i < sortTypes.length; i++)
+ {
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+ col.setName(sortTypes[i]);
+ FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
+ if (fcol.isSimpleColour())
+ {
+ 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);
+ }
+ ucs.marshal(out);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ public void invertSelection()
+ {
+ for (int i = 0; i < table.getRowCount(); i++)
+ {
+ Boolean value = (Boolean) table.getValueAt(i, 2);
+
+ table.setValueAt(new Boolean(!value.booleanValue()), i, 2);
+ }
+ }
+
+ 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;
+ int num = 0;
+ for (int i = 0; i < data.length; i++)
+ {
+ awidth = typeWidth.get(data[i][0]);
+ 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.
+ num++;
+ }
+ 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][0].toString());
+ if (width[i] < 0)
+ {
+ width[i] = fr.setOrder(data[i][0].toString(), i / data.length);
+ }
+ }
+ else
+ {
+ width[i] /= max; // normalize
+ 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
+ }
+
+ updateFeatureRenderer(data, false);
+ table.repaint();
+ }
+
+ public void close()
+ {
+ try
+ {
+ frame.setClosed(true);
+ } 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
+ */
+ private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
+ {
+ if (fr.setFeaturePriority(data, visibleNew))
+ {
+ af.alignPanel.paintAlignment(true);
+ }
+ }
+
+ int selectedRow = -1;
+
+ JTabbedPane tabbedPane = new JTabbedPane();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ BorderLayout borderLayout2 = new BorderLayout();
+
+ BorderLayout borderLayout3 = new BorderLayout();
+
+ JPanel bigPanel = new JPanel();
+
+ BorderLayout borderLayout4 = new BorderLayout();
+
+ JButton invert = new JButton();
+
+ JPanel buttonPanel = new JPanel();
+
+ JButton cancel = new JButton();
+
+ JButton ok = new JButton();
+
+ JButton loadColours = new JButton();
+
+ JButton saveColours = new JButton();
+
+ JPanel dasButtonPanel = new JPanel();
+
+ JButton fetchDAS = new JButton();
+
+ JButton saveDAS = new JButton();
+
+ JButton cancelDAS = new JButton();
+
+ JButton optimizeOrder = new JButton();
+
+ JButton sortByScore = new JButton();
+
+ JButton sortByDens = new JButton();
+
+ JButton help = new JButton();
+
+ JPanel transbuttons = new JPanel(new GridLayout(5, 1));
+
+ private void jbInit() throws Exception
+ {
+ this.setLayout(borderLayout1);
+ settingsPane.setLayout(borderLayout2);
+ dasSettingsPane.setLayout(borderLayout3);
+ bigPanel.setLayout(borderLayout4);
+
+ groupPanel = new JPanel();
+ bigPanel.add(groupPanel, BorderLayout.NORTH);
+
+ invert.setFont(JvSwingUtils.getLabelFont());
+ invert.setText(MessageManager.getString("label.invert_selection"));
+ invert.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ invertSelection();
+ }
+ });
+ optimizeOrder.setFont(JvSwingUtils.getLabelFont());
+ 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.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ af.avc.sortAlignmentByFeatureScore(null);
+ }
+ });
+ sortByDens.setFont(JvSwingUtils.getLabelFont());
+ 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)
+ {
+ 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.setFont(JvSwingUtils.getLabelFont());
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ close();
+ }
+ });
+ loadColours.setFont(JvSwingUtils.getLabelFont());
+ loadColours.setText(MessageManager.getString("label.load_colours"));
+ loadColours.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ load();
+ }
+ });
+ saveColours.setFont(JvSwingUtils.getLabelFont());
+ saveColours.setText(MessageManager.getString("label.save_colours"));
+ saveColours.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ save();
+ }
+ });
+ transparency.addChangeListener(new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
+ 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);
+ }
+ });
+ dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
+ dasSettingsPane.setBorder(null);
+ cancelDAS.setEnabled(false);
+ cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
+ cancelDAS.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cancelDAS_actionPerformed(e);
+ }
+ });
+ this.add(tabbedPane, java.awt.BorderLayout.CENTER);
+ tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
+ settingsPane);
+ tabbedPane.addTab(MessageManager.getString("label.das_settings"),
+ dasSettingsPane);
+ 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);
+ buttonPanel.add(cancel);
+ buttonPanel.add(loadColours);
+ buttonPanel.add(saveColours);
+ bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
+ dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
+ dasButtonPanel.add(fetchDAS);
+ dasButtonPanel.add(cancelDAS);
+ dasButtonPanel.add(saveDAS);
+ settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);
+ settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
+ }
+
+ public void fetchDAS_actionPerformed(ActionEvent e)
+ {
+ fetchDAS.setEnabled(false);
+ cancelDAS.setEnabled(true);
+ dassourceBrowser.setGuiEnabled(false);
+ Vector selectedSources = dassourceBrowser
+ .getSelectedSources();
+ doDasFeatureFetch(selectedSources, true, true);
+ }
+
+ /**
+ * get the features from selectedSources for all or the current selection
+ *
+ * @param selectedSources
+ * @param checkDbRefs
+ * @param promptFetchDbRefs
+ */
+ private void doDasFeatureFetch(List selectedSources,
+ boolean checkDbRefs, boolean promptFetchDbRefs)
+ {
+ SequenceI[] dataset, seqs;
+ int iSize;
+ AlignmentViewport vp = af.getViewport();
+ if (vp.getSelectionGroup() != null
+ && vp.getSelectionGroup().getSize() > 0)
+ {
+ iSize = vp.getSelectionGroup().getSize();
+ dataset = new SequenceI[iSize];
+ seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
+ }
+ else
+ {
+ iSize = vp.getAlignment().getHeight();
+ seqs = vp.getAlignment().getSequencesArray();
+ }
+
+ dataset = new SequenceI[iSize];
+ for (int i = 0; i < iSize; i++)
+ {
+ dataset[i] = seqs[i].getDatasetSequence();
+ }
+
+ cancelDAS.setEnabled(true);
+ dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
+ this, selectedSources, checkDbRefs, promptFetchDbRefs);
+ af.getViewport().setShowSequenceFeatures(true);
+ af.showSeqFeatures.setSelected(true);
+ }
+
+ /**
+ * blocking call to initialise the das source browser
+ */
+ public void initDasSources()
+ {
+ dassourceBrowser.initDasSources();
+ }
+
+ /**
+ * examine the current list of das sources and return any matching the given
+ * nicknames in sources
+ *
+ * @param sources
+ * Vector of Strings to resolve to DAS source nicknames.
+ * @return sources that are present in source list.
+ */
+ public List resolveSourceNicknames(Vector sources)
+ {
+ return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
+ }
+
+ /**
+ * get currently selected das sources. ensure you have called initDasSources
+ * before calling this.
+ *
+ * @return vector of selected das source nicknames
+ */
+ public Vector getSelectedSources()
+ {
+ return dassourceBrowser.getSelectedSources();
+ }
+
+ /**
+ * properly initialise DAS fetcher and then initiate a new thread to fetch
+ * features from the named sources (rather than any turned on by default)
+ *
+ * @param sources
+ * @param block
+ * if true then runs in same thread, otherwise passes to the Swing
+ * executor
+ */
+ public void fetchDasFeatures(Vector sources, boolean block)
+ {
+ initDasSources();
+ List resolved = dassourceBrowser.sourceRegistry
+ .resolveSourceNicknames(sources);
+ if (resolved.size() == 0)
+ {
+ resolved = dassourceBrowser.getSelectedSources();
+ }
+ if (resolved.size() > 0)
+ {
+ final List dassources = resolved;
+ fetchDAS.setEnabled(false);
+ // cancelDAS.setEnabled(true); doDasFetch does this.
+ Runnable fetcher = new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ doDasFeatureFetch(dassources, true, false);
+
+ }
+ };
+ if (block)
+ {
+ fetcher.run();
+ }
+ else
+ {
+ SwingUtilities.invokeLater(fetcher);
+ }
+ }
+ }
+
+ public void saveDAS_actionPerformed(ActionEvent e)
+ {
+ dassourceBrowser
+ .saveProperties(jalview.bin.Cache.applicationProperties);
+ }
+
+ public void complete()
+ {
+ fetchDAS.setEnabled(true);
+ cancelDAS.setEnabled(false);
+ dassourceBrowser.setGuiEnabled(true);
+
+ }
+
+ public void cancelDAS_actionPerformed(ActionEvent e)
+ {
+ if (dasFeatureFetcher != null)
+ {
+ dasFeatureFetcher.cancel();
+ }
+ complete();
+ }
+
+ public void noDasSourceActive()
+ {
+ complete();
+ JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.getString("label.no_das_sources_selected_warn"),
+ MessageManager.getString("label.no_das_sources_selected_title"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
+ }
+
+ // ///////////////////////////////////////////////////////////////////////
+ // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
+ // ///////////////////////////////////////////////////////////////////////
+ class FeatureTableModel extends AbstractTableModel
+ {
+ FeatureTableModel(Object[][] data)
+ {
+ this.data = data;
+ }
+
+ private String[] columnNames = {
+ MessageManager.getString("label.feature_type"),
+ MessageManager.getString("action.colour"),
+ MessageManager.getString("label.display") };
+
+ private Object[][] 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];
+ }
+
+ @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;
+ fireTableCellUpdated(row, col);
+ updateFeatureRenderer(data);
+ }
+
+ }
+
+ class ColorRenderer extends JLabel implements TableCellRenderer
+ {
+ javax.swing.border.Border unselectedBorder = null;
+
+ javax.swing.border.Border selectedBorder = null;
+
+ final String baseTT = "Click to edit, right/apple click for menu.";
+
+ 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;
+ // JLabel comp = new JLabel();
+ // comp.
+ setOpaque(true);
+ // comp.
+ // setBounds(getBounds());
+ Color newColor;
+ setToolTipText(baseTT);
+ 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);
+ newColor = cellColour.getColour();
+ setBackground(newColor);
+ }
+ 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);
+ }
+
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
+ int w, int h)
+ {
+ boolean thr = false;
+ String tt = "";
+ String tx = "";
+ if (gcol.isAboveThreshold())
+ {
+ thr = true;
+ tx += ">";
+ tt += "Thresholded (Above " + gcol.getThreshold() + ") ";
+ }
+ if (gcol.isBelowThreshold())
+ {
+ thr = true;
+ tx += "<";
+ tt += "Thresholded (Below " + gcol.getThreshold() + ") ";
+ }
+ if (gcol.isColourByLabel())
+ {
+ tt = "Coloured by label text. " + tt;
+ if (thr)
+ {
+ tx += " ";
+ }
+ tx += "Label";
+ comp.setIcon(null);
+ }
+ else
+ {
+ Color newColor = gcol.getMaxColour();
+ comp.setBackground(newColor);
+ // System.err.println("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);
+ if (tt.length() > 0)
+ {
+ if (comp.getToolTipText() == null)
+ {
+ comp.setToolTipText(tt);
+ }
+ else
+ {
+ comp.setToolTipText(tt + " " + comp.getToolTipText());
+ }
+ }
+ }
+}
+
+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);
+ }
+ }
+}
+
+class ColorEditor extends AbstractCellEditor
+ implements TableCellEditor, ActionListener
+{
+ FeatureSettings me;
+
+ FeatureColourI currentColor;
+
+ FeatureColourChooser chooser;
+
+ String type;
+
+ JButton button;
+
+ JColorChooser colorChooser;
+
+ JDialog dialog;
+
+ protected static final String EDIT = "edit";
+
+ int selectedRow = 0;
+
+ public ColorEditor(FeatureSettings me)
+ {
+ this.me = me;
+ // 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);
+ // Set up the dialog that the button brings up.
+ colorChooser = new JColorChooser();
+ dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal
+ colorChooser, this, // OK button handler
+ null); // no CANCEL button handler
+ }
+
+ /**
+ * Handles events from the editor button and from the dialog's OK button.
+ */
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+
+ if (EDIT.equals(e.getActionCommand()))
+ {
+ // The user has clicked the cell, so
+ // bring up the dialog.
+ if (currentColor.isSimpleColour())
+ {
+ // bring up simple color chooser
+ button.setBackground(currentColor.getColour());
+ colorChooser.setColor(currentColor.getColour());
+ dialog.setVisible(true);
+ }
+ else
+ {
+ // bring up graduated chooser.
+ chooser = new FeatureColourChooser(me.fr, type);
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
+ chooser.addActionListener(this);
+ }
+ // Make the renderer reappear.
+ fireEditingStopped();
+
+ }
+ else
+ { // User pressed dialog's "OK" button.
+ if (currentColor.isSimpleColour())
+ {
+ currentColor = new FeatureColour(colorChooser.getColor());
+ }
+ else
+ {
+ currentColor = chooser.getLastColour();
+ }
+ me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
+ fireEditingStopped();
+ me.table.validate();
+ }
+ }
+
+ // 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 table, Object value,
+ boolean isSelected, int row, int column)
+ {
+ currentColor = (FeatureColourI) value;
+ this.selectedRow = row;
+ type = me.table.getValueAt(row, 0).toString();
+ button.setOpaque(true);
+ button.setBackground(me.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;
+ }
+}