X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=d30f5a066721148ae3827d51fd06deaa94eb3aa6;hb=3f62f10ab0f8985945e460c70c89b530446d6afa;hp=ec5176fd14acab8cdc77c851728bdadfefe67ced;hpb=566b164f60df39a2fcb35a9d174273a043691931;p=jalview.git
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
old mode 100755
new mode 100644
index ec5176f..132bb2b
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,648 +1,1865 @@
-/*
- * 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;
- Object [][] originalData;
- final JInternalFrame frame;
- JScrollPane scrollPane = new JScrollPane();
- JTable table;
- JPanel groupPanel;
-
- boolean alignmentHasFeatures = false;
-
- 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);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
-
- setTableData();
-
- final JSlider transparency = new JSlider(0, 70, 100 - (int)(fr.transparency*100) );
- 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);
- JButton button = new JButton("Invert Selection");
- transPanel.add(button);
- button.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- invertSelection();
- }
- });
-
- //////////////////////////////////////////////
- //We're going to need those OK cancel buttons
- JPanel buttonPanel = new JPanel(new FlowLayout());
- 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(fr.featureGroups.size() / 4 + 1, 4));
-
- groupPanel.validate();
- bigPanel.add(groupPanel, BorderLayout.NORTH);
- }
- add(bigPanel, BorderLayout.CENTER);
- add(buttonPanel, BorderLayout.SOUTH);
-
-
- }
-
- void setTableData()
- {
- alignmentHasFeatures = false;
-
- if (fr.featureGroups == null)
- fr.featureGroups = new Hashtable();
-
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
- SequenceFeature[] tmpfeatures;
- String group;
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)
- continue;
-
- alignmentHasFeatures = true;
-
- tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
-
- int index = 0;
- while (index < tmpfeatures.length)
- {
- if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0)
- {
- index++;
- continue;
- }
-
- if(tmpfeatures[index].getFeatureGroup()!=null)
- {
- group = tmpfeatures[index].featureGroup;
- if(!allGroups.contains(group))
- {
- allGroups.addElement(group);
-
- boolean visible = true;
- if (fr.featureGroups.containsKey(group))
- {
- visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
- }
-
- fr.featureGroups.put(group, new Boolean(visible));
-
- if (groupPanel == null)
- {
- groupPanel = new JPanel();
- }
-
- final JCheckBox check = new JCheckBox(group, visible);
- check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent evt)
- {
- fr.featureGroups.put(check.getText(),
- new Boolean(check.isSelected()));
- ap.seqPanel.seqCanvas.repaint();
- if (ap.overviewPanel != null)
- ap.overviewPanel.updateOverviewImage();
-
- resetTable(true);
- }
- });
- groupPanel.add(check);
-
- }
-
- }
-
- if (!allFeatures.contains(tmpfeatures[index].getType()))
- {
- allFeatures.addElement(tmpfeatures[index].getType());
- }
- index ++;
- }
- }
-
-
- if(!alignmentHasFeatures)
- {
- 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(false);
- }
-
- void resetTable(boolean groupsChanged)
- {
- SequenceFeature [] tmpfeatures;
- String group=null, type;
- Vector visibleChecks = new Vector();
-
- //Find out which features should be visible depending on which groups
- //are selected / deselected
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)
- continue;
-
- tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
- int index = 0;
- while (index < tmpfeatures.length)
- {
- group = tmpfeatures[index].featureGroup;
-
- if(tmpfeatures[index].begin==0 && tmpfeatures[index].end==0)
- {
- index ++;
- continue;
- }
-
- if (group==null || fr.featureGroups.get(group)==null ||
- ((Boolean) fr.featureGroups.get(group)).booleanValue())
- {
- type = tmpfeatures[index].getType();
- if(!visibleChecks.contains(type) )
- {
- visibleChecks.addElement(type);
- }
- }
- index++;
- }
- }
-
- int fSize = visibleChecks.size();
- Object [][] data = new Object[fSize][3];
- int dataIndex = 0;
-
- if(fr.renderOrder!=null)
- {
- //First add the checks in the previous render order,
- //in case the window has been closed and reopened
- for(int ro=fr.renderOrder.length-1; ro>-1; ro--)
- {
- type = fr.renderOrder[ro];
-
- if(!visibleChecks.contains(type))
- continue;
-
- data[dataIndex][0] = type;
- data[dataIndex][1] = fr.getColour(type);
- data[dataIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));
- dataIndex++;
- visibleChecks.removeElement(type);
- }
- }
-
- fSize = visibleChecks.size();
- for(int i=0; i.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.gui.Help.HelpId;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemabinding.version2.Filter;
+import jalview.schemabinding.version2.JalviewUserColours;
+import jalview.schemabinding.version2.MatcherSet;
+import jalview.schemes.FeatureColour;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+
+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.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.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.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.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+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;
+import javax.swing.table.TableColumn;
+
+public class FeatureSettings extends JPanel
+ implements FeatureSettingsControllerI
+{
+ 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;
+
+ final FeatureRenderer fr;
+
+ public final AlignFrame af;
+
+ /*
+ * 'original' fields hold settings to restore on Cancel
+ */
+ Object[][] originalData;
+
+ private float originalTransparency;
+
+ private Map originalFilters;
+
+ final JInternalFrame frame;
+
+ JScrollPane scrollPane = new JScrollPane();
+
+ JTable table;
+
+ JPanel groupPanel;
+
+ JSlider transparency = new JSlider();
+
+ /*
+ * when true, constructor is still executing - so ignore UI events
+ */
+ protected volatile boolean inConstruction = true;
+
+ int selectedRow = -1;
+
+ JButton fetchDAS = new JButton();
+
+ JButton saveDAS = new JButton();
+
+ JButton cancelDAS = new JButton();
+
+ boolean resettingTable = false;
+
+ /*
+ * true when Feature Settings are updating from feature renderer
+ */
+ private boolean handlingUpdate = false;
+
+ /*
+ * holds {featureCount, totalExtent} for each feature type
+ */
+ Map typeWidth = null;
+
+ /**
+ * Constructor
+ *
+ * @param af
+ */
+ public FeatureSettings(AlignFrame alignFrame)
+ {
+ this.af = alignFrame;
+ fr = af.getFeatureRenderer();
+
+ // save transparency for restore on Cancel
+ originalTransparency = fr.getTransparency();
+ int originalTransparencyAsPercent = (int) (originalTransparency * 100);
+ transparency.setMaximum(100 - originalTransparencyAsPercent);
+
+ originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
+
+ 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());
+ switch (column)
+ {
+ case TYPE_COLUMN:
+ tip = JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.feature_settings_click_drag"));
+ break;
+ case FILTER_COLUMN:
+ int row = table.rowAtPoint(e.getPoint());
+ FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
+ column);
+ tip = o.isEmpty()
+ ? MessageManager
+ .getString("label.configure_feature_tooltip")
+ : o.toString();
+ break;
+ default:
+ break;
+ }
+ return tip;
+ }
+ };
+ 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.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this));
+ table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer());
+
+ TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
+ new ColorRenderer(), new ColorEditor(this));
+ table.addColumn(colourColumn);
+
+ TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75,
+ new FilterRenderer(), new FilterEditor(this));
+ table.addColumn(filterColumn);
+
+ table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+ table.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ selectedRow = table.rowAtPoint(evt.getPoint());
+ String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
+ if (evt.isPopupTrigger())
+ {
+ Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
+ popupSort(selectedRow, type, colour, 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, type);
+ }
+ }
+
+ // 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);
+ popupSort(selectedRow, type, colour, 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);
+
+ 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 sequence feature types only
+ fs.handlingUpdate = false;
+ }
+ }
+
+ });
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (Platform.isAMac())
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, 480);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, 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);
+ };
+ });
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ inConstruction = false;
+ }
+
+ protected void popupSort(final int rowSelected, 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);
+
+ 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);
+ }
+
+ @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 });
+ af.alignPanel.paintAlignment(true, true);
+ }
+ });
+ 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] = 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][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] = new Boolean(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"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File file = chooser.getSelectedFile();
+ load(file);
+ }
+ }
+
+ /**
+ * 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");
+
+ JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+
+ /*
+ * load feature colours
+ */
+ for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+ {
+ jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
+ FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
+ fr.setColour(newcol.getName(), colour);
+ fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
+ }
+
+ /*
+ * load feature filters; loaded filters will replace any that are
+ * currently defined, other defined filters are left unchanged
+ */
+ for (int i = 0; i < jucs.getFilterCount(); i++)
+ {
+ jalview.schemabinding.version2.Filter filterModel = jucs
+ .getFilter(i);
+ String featureType = filterModel.getFeatureType();
+ FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(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)
+ {
+ System.out.println("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 value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ save(chooser.getSelectedFile());
+ }
+ }
+
+ /**
+ * 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);
+ jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
+ featureType, fcol);
+ ucs.addColour(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();
+ MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
+ filter.isAnded());
+ Filter filterModel = new Filter();
+ filterModel.setFeatureType(featureType);
+ filterModel.setMatcherSet(ms);
+ ucs.addFilter(filterModel);
+ }
+ }
+
+ 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();
+ }
+
+ 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)
+ {
+ FeatureSettingsBean[] rowData = getTableAsBeans(data);
+
+ if (fr.setFeaturePriority(rowData, visibleNew))
+ {
+ af.alignPanel.paintAlignment(true, true);
+ }
+ }
+
+ /**
+ * 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());
+
+ 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();
+ }
+ });
+
+ JButton sortByScore = new JButton(
+ MessageManager.getString("label.seq_sort_by_score"));
+ sortByScore.setFont(JvSwingUtils.getLabelFont());
+ sortByScore.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ af.avc.sortAlignmentByFeatureScore(null);
+ }
+ });
+ JButton sortByDens = new JButton(
+ MessageManager.getString("label.sequence_sort_by_density"));
+ sortByDens.setFont(JvSwingUtils.getLabelFont());
+ sortByDens.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ af.avc.sortAlignmentByFeatureDensity(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();
+ }
+ }
+ });
+ 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();
+ }
+ }
+ });
+
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ cancel.setFont(JvSwingUtils.getLabelFont());
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ fr.setTransparency(originalTransparency);
+ fr.setFeatureFilters(originalFilters);
+ updateFeatureRenderer(originalData);
+ close();
+ }
+ });
+
+ JButton ok = new JButton(MessageManager.getString("action.ok"));
+ ok.setFont(JvSwingUtils.getLabelFont());
+ ok.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ close();
+ }
+ });
+
+ 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);
+ af.alignPanel.paintAlignment(true, true);
+ }
+ }
+ });
+
+ transparency.setMaximum(70);
+ transparency.setToolTipText(
+ MessageManager.getString("label.transparency_tip"));
+
+ JPanel transPanel = new JPanel(new GridLayout(1, 2));
+ bigPanel.add(transPanel, 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);
+ transPanel.add(transparency);
+ transPanel.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);
+ }
+
+ // ///////////////////////////////////////////////////////////////////////
+ // 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 the object in column c of the first row of the table
+ */
+ @Override
+ public Class getColumnClass(int c)
+ {
+ Object v = getValueAt(0, c);
+ return v == null ? null : v.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;
+ setOpaque(true);
+ 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);
+ 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);
+ String asText = theFilter.toString();
+ setBackground(tbl.getBackground());
+ this.setText(asText);
+ this.setIcon(null);
+
+ 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;
+ StringBuilder tt = new StringBuilder();
+ StringBuilder tx = new StringBuilder();
+
+ if (gcol.isColourByAttribute())
+ {
+ tx.append(String.join(":", gcol.getAttributeName()));
+ }
+ else if (!gcol.isColourByLabel())
+ {
+ tx.append(MessageManager.getString("label.score"));
+ }
+ tx.append(" ");
+ if (gcol.isAboveThreshold())
+ {
+ thr = true;
+ tx.append(">");
+ tt.append("Thresholded (Above ").append(gcol.getThreshold())
+ .append(") ");
+ }
+ if (gcol.isBelowThreshold())
+ {
+ thr = true;
+ tx.append("<");
+ tt.append("Thresholded (Below ").append(gcol.getThreshold())
+ .append(") ");
+ }
+ if (gcol.isColourByLabel())
+ {
+ tt.append("Coloured by label text. ").append(tt);
+ if (thr)
+ {
+ tx.append(" ");
+ }
+ if (!gcol.isColourByAttribute())
+ {
+ tx.append("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.toString());
+ if (tt.length() > 0)
+ {
+ if (comp.getToolTipText() == null)
+ {
+ comp.setToolTipText(tt.toString());
+ }
+ else
+ {
+ comp.setToolTipText(
+ tt.append(" ").append(comp.getToolTipText()).toString());
+ }
+ }
+ }
+
+ class ColorEditor extends AbstractCellEditor
+ implements TableCellEditor, ActionListener
+ {
+ FeatureSettings me;
+
+ FeatureColourI currentColor;
+
+ FeatureTypeSettings chooser;
+
+ String type;
+
+ JButton button;
+
+ JColorChooser colorChooser;
+
+ JDialog dialog;
+
+ protected static final String EDIT = "edit";
+
+ int rowSelected = 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,
+ MessageManager.getString("label.select_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)
+ {
+ // todo test e.getSource() instead here
+ 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 FeatureTypeSettings(me.fr, type);
+ /**
+ * @j2sNative
+ */
+ {
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
+ }
+ chooser.addActionListener(this);
+ // Make the renderer reappear.
+ fireEditingStopped();
+ }
+ }
+ else
+ {
+ if (currentColor.isSimpleColour())
+ {
+ /*
+ * read off colour picked in colour chooser after OK pressed
+ */
+ currentColor = new FeatureColour(colorChooser.getColor());
+ me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+ }
+ 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 = me.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();
+ 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 theTable, Object value,
+ boolean isSelected, int row, int column)
+ {
+ currentColor = (FeatureColourI) value;
+ this.rowSelected = row;
+ type = me.table.getValueAt(row, TYPE_COLUMN).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;
+ }
+ }
+
+ /**
+ * 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.
+ */
+ class FilterEditor extends AbstractCellEditor
+ implements TableCellEditor, ActionListener
+ {
+ FeatureSettings me;
+
+ FeatureMatcherSetI currentFilter;
+
+ Point lastLocation;
+
+ String type;
+
+ JButton button;
+
+ protected static final String EDIT = "edit";
+
+ int rowSelected = 0;
+
+ public FilterEditor(FeatureSettings me)
+ {
+ this.me = me;
+ 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(me.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 = me.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();
+ me.table.validate();
+ }
+ }
+
+ @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 = me.table.getValueAt(row, TYPE_COLUMN).toString();
+ button.setOpaque(true);
+ button.setBackground(me.getBackground());
+ button.setText(currentFilter.toString());
+ button.setToolTipText(currentFilter.toString());
+ button.setIcon(null);
+ return button;
+ }
+ }
+}
+
+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);
+ }
+ }
+}