X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=aeac9599c1ea7d6a3a9935809fc8377fbb4fa39a;hb=e1aa3fdd1ca82abf5acc0cd3c2b86a5ca1083941;hp=4c0450cca8128a1854277ae99df62c90a9d5a1d1;hpb=50fc0be07fc2672defdcca49c51bf28eb49ffba4;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java old mode 100755 new mode 100644 index 4c0450c..aeac959 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,690 +1,1423 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 + * 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. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; +import jalview.api.AlignViewControllerGuiI; +import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; +import jalview.api.FeatureSettingsControllerI; +import jalview.api.SplitContainerI; +import jalview.api.ViewStyleI; +import jalview.controller.FeatureSettingsControllerGuiI; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; +import jalview.datamodel.features.FeatureMatcher; +import jalview.datamodel.features.FeatureMatcherI; +import jalview.datamodel.features.FeatureMatcherSet; +import jalview.datamodel.features.FeatureMatcherSetI; +import jalview.gui.Help.HelpId; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.schemes.FeatureColour; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; +import jalview.viewmodel.styles.ViewStyle; +import jalview.xml.binding.jalview.JalviewUserColours; +import jalview.xml.binding.jalview.JalviewUserColours.Colour; +import jalview.xml.binding.jalview.JalviewUserColours.Filter; +import jalview.xml.binding.jalview.ObjectFactory; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.Dimension; +import java.awt.FlowLayout; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Point; +import java.awt.Rectangle; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.event.MouseMotionAdapter; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.util.Arrays; +import java.util.Comparator; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; +import java.util.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.border.Border; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; +import javax.swing.table.AbstractTableModel; +import javax.swing.table.JTableHeader; +import javax.swing.table.TableCellEditor; +import javax.swing.table.TableCellRenderer; +import javax.swing.table.TableColumn; +import javax.xml.bind.JAXBContext; +import javax.xml.bind.JAXBElement; +import javax.xml.bind.Marshaller; +import javax.xml.stream.XMLInputFactory; +import javax.xml.stream.XMLStreamReader; + +public class FeatureSettings extends JPanel + implements FeatureSettingsControllerI, FeatureSettingsControllerGuiI +{ + private static final String SEQUENCE_FEATURE_COLOURS = MessageManager + .getString("label.sequence_feature_colours"); + + /* + * column indices of fields in Feature Settings table + */ + static final int TYPE_COLUMN = 0; -import javax.swing.*; -import javax.swing.event.*; -import javax.swing.table.*; + static final int COLOUR_COLUMN = 1; -import jalview.datamodel.*; -import jalview.io.*; + static final int FILTER_COLUMN = 2; -public class FeatureSettings - extends JPanel -{ - DasSourceBrowser dassourceBrowser; - jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher; - JPanel settingsPane = new JPanel(); - JPanel dasSettingsPane = new JPanel(); + static final int SHOW_COLUMN = 3; + + private static final int COLUMN_COUNT = 4; + + private static final int MIN_WIDTH = 400; + + private static final int MIN_HEIGHT = 400; + + private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit"); final FeatureRenderer fr; + public final AlignFrame af; + + /* + * 'original' fields hold settings to restore on Cancel + */ Object[][] originalData; + + private float originalTransparency; + + private ViewStyleI originalViewStyle; + + private Map originalFilters; + final JInternalFrame frame; + JScrollPane scrollPane = new JScrollPane(); + JTable table; + JPanel groupPanel; - JSlider transparency = new JSlider(); - JPanel transPanel = new JPanel(new FlowLayout()); + JSlider transparency= new JSlider(); + + private JCheckBox showComplementOnTop; + + private JCheckBox showComplement; - public FeatureSettings(AlignFrame af) + /* + * when true, constructor is still executing - so ignore UI events + */ + protected volatile boolean inConstruction = true; + + int selectedRow = -1; + + boolean resettingTable = false; + + /* + * true when Feature Settings are updating from feature renderer + */ + private boolean handlingUpdate = false; + + /* + * a change listener to ensure the dialog is updated if + * FeatureRenderer discovers new features + */ + private PropertyChangeListener change; + + /* + * holds {featureCount, totalExtent} for each feature type + */ + Map typeWidth = null; + + private void storeOriginalSettings() { - this.af = af; + // save transparency for restore on Cancel + originalTransparency = fr.getTransparency(); + + updateTransparencySliderFromFR(); + + originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy + originalViewStyle = new ViewStyle(af.viewport.getViewStyle()); + } + + private void updateTransparencySliderFromFR() + { + boolean incon = inConstruction; + inConstruction = true; + + int transparencyAsPercent = (int) (fr.getTransparency() * 100); + transparency.setValue(100 - transparencyAsPercent); + inConstruction = incon; + } + /** + * Constructor + * + * @param af + */ + public FeatureSettings(AlignFrame alignFrame) + { + this.af = alignFrame; fr = af.getFeatureRenderer(); - transparency.setMaximum(100 - (int) (fr.transparency * 100)); + storeOriginalSettings(); try { jbInit(); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } - table = new JTable(); - table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); + table = new JTable() + { + @Override + public String getToolTipText(MouseEvent e) + { + String tip = null; + int column = table.columnAtPoint(e.getPoint()); + int row = table.rowAtPoint(e.getPoint()); + + switch (column) + { + case TYPE_COLUMN: + tip = JvSwingUtils.wrapTooltip(true, MessageManager + .getString("label.feature_settings_click_drag")); + break; + case COLOUR_COLUMN: + FeatureColourI colour = (FeatureColourI) table.getValueAt(row, + column); + tip = getColorTooltip(colour, true); + break; + case FILTER_COLUMN: + FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row, + column); + tip = o.isEmpty() + ? MessageManager + .getString("label.configure_feature_tooltip") + : o.toString(); + break; + default: + break; + } + + return tip; + } + + /** + * Position the tooltip near the bottom edge of, and half way across, the + * current cell + */ + @Override + public Point getToolTipLocation(MouseEvent e) + { + Point point = e.getPoint(); + int column = table.columnAtPoint(point); + int row = table.rowAtPoint(point); + Rectangle r = getCellRect(row, column, false); + Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3); + return loc; + } + }; + JTableHeader tableHeader = table.getTableHeader(); + tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12)); + tableHeader.setReorderingAllowed(false); table.setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setDefaultRenderer(Color.class, - new ColorRenderer()); - table.setDefaultEditor(Color.class, - new ColorEditor()); + 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) { + Point pt = evt.getPoint(); + selectedRow = table.rowAtPoint(pt); + String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); + if (evt.isPopupTrigger()) + { + Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); + popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(), + evt.getY()); + } + else if (evt.getClickCount() == 2 + && table.columnAtPoint(pt) == TYPE_COLUMN) + { + boolean invertSelection = evt.isAltDown(); + boolean toggleSelection = Platform.isControlDown(evt); + boolean extendSelection = evt.isShiftDown(); + fr.ap.alignFrame.avc.markColumnsContainingFeatures( + invertSelection, extendSelection, toggleSelection, type); + fr.ap.av.sendSelection(); + } + } + + // isPopupTrigger fires on mouseReleased on Windows + @Override + public void mouseReleased(MouseEvent evt) + { selectedRow = table.rowAtPoint(evt.getPoint()); + if (evt.isPopupTrigger()) + { + String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); + Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); + 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) + if (newRow != selectedRow && selectedRow != -1 && newRow != -1) { - Object[] temp = new Object[3]; - temp[0] = table.getValueAt(selectedRow, 0); - temp[1] = table.getValueAt(selectedRow, 1); - temp[2] = table.getValueAt(selectedRow, 2); - - table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0); - table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1); - table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2); - - table.setValueAt(temp[0], newRow, 0); - table.setValueAt(temp[1], newRow, 1); - table.setValueAt(temp[2], newRow, 2); - + /* + * reposition 'selectedRow' to 'newRow' (the dragged to location) + * this could be more than one row away for a very fast drag action + * so just swap it with adjacent rows until we get it there + */ + Object[][] data = ((FeatureTableModel) table.getModel()) + .getData(); + int direction = newRow < selectedRow ? -1 : 1; + for (int i = selectedRow; i != newRow; i += direction) + { + Object[] temp = data[i]; + data[i] = data[i + direction]; + data[i + direction] = temp; + } + updateFeatureRenderer(data); + table.repaint(); selectedRow = newRow; } } }); - + // table.setToolTipText(JvSwingUtils.wrapTooltip(true, + // MessageManager.getString("label.feature_settings_click_drag"))); scrollPane.setViewportView(table); - dassourceBrowser = new DasSourceBrowser(); - dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - - if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null) + if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) { fr.findAllFeatures(true); // display everything! } - setTableData(); - final PropertyChangeListener change; - final FeatureSettings fs=this; - fr.addPropertyChangeListener(change=new PropertyChangeListener() { + discoverAllFeatureData(); + final FeatureSettings fs = this; + fr.addPropertyChangeListener(change = new PropertyChangeListener() + { + @Override public void propertyChange(PropertyChangeEvent evt) { - if (!fs.resettingTable && !fs.handlingUpdate) { - fs.handlingUpdate=true; - fs.resetTable(null); // new groups may be added with new seuqence feature types only - fs.handlingUpdate=false; + 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); - Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450); - frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + SplitContainerI splitframe = af.getSplitViewContainer(); + if (splitframe != null) { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + frame = null; // keeps eclipse happy + splitframe.addFeatureSettingsUI(this); + } + else + { + frame = new JInternalFrame(); + frame.setContentPane(this); + Rectangle bounds = af.getFeatureSettingsGeometry(); + String title; + if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels( + af.alignPanel.av.getSequenceSetId()).length > 1) { - fr.removePropertyChangeListener(change); + title = MessageManager.formatMessage( + "label.sequence_feature_settings_for_view", + af.alignPanel.getViewName()); } - ; - }); - frame.setLayer(JLayeredPane.PALETTE_LAYER); + else + { + title = MessageManager.getString("label.sequence_feature_settings"); + } + if (bounds == null) + { + if (Platform.isAMac()) + { + Desktop.addInternalFrame(frame, title, 600, 480); + } + else + { + Desktop.addInternalFrame(frame, title, 600, 450); + } + } + else + { + Desktop.addInternalFrame(frame, title, + false, bounds.width, bounds.height); + frame.setBounds(bounds); + frame.setVisible(true); + } + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); + + frame.addInternalFrameListener( + new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + featureSettings_isClosed(); + }; + }); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + } + inConstruction = false; } + /** - * true when Feature Settings are updating from feature renderer - */ - private boolean handlingUpdate=false; - - /** - * contains a float[3] for each feature type string. created by setTableData + * Sets the state of buttons to show complement features from viewport + * settings */ - Hashtable typeWidth=null; - synchronized public void setTableData() + private void updateComplementButtons() { - if (fr.featureGroups == null) + showComplement.setSelected(af.getViewport().isShowComplementFeatures()); + showComplementOnTop + .setSelected(af.getViewport().isShowComplementFeaturesOnTop()); + } + + @Override + public AlignViewControllerGuiI getAlignframe() + { + return af; + } + + @Override + public void featureSettings_isClosed() + { + fr.removePropertyChangeListener(change); + change = null; + } + + protected void popupSort(final int rowSelected, final String type, + final Object typeCol, final Map minmax, int x, + int y) + { + JPopupMenu men = new JPopupMenu(MessageManager + .formatMessage("label.settings_for_param", new String[] + { type })); + JMenuItem scr = new JMenuItem( + MessageManager.getString("label.sort_by_score")); + men.add(scr); + scr.addActionListener(new ActionListener() { - fr.featureGroups = new Hashtable(); - } - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); - SequenceFeature[] tmpfeatures; - String group; - for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) + @Override + public void actionPerformed(ActionEvent e) + { + sortByScore(Arrays.asList(new String[] { type })); + } + }); + JMenuItem dens = new JMenuItem( + MessageManager.getString("label.sort_by_density")); + dens.addActionListener(new ActionListener() { - if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence(). - getSequenceFeatures() == null) + @Override + public void actionPerformed(ActionEvent e) { - continue; + sortByDensity(Arrays.asList(new String[] { type })); } + }); + men.add(dens); - tmpfeatures = af.getViewport().alignment.getSequenceAt(i). - getDatasetSequence().getSequenceFeatures(); - - int index = 0; - while (index < tmpfeatures.length) + JMenuItem selCols = new JMenuItem( + MessageManager.getString("label.select_columns_containing")); + selCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) { - if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) - { - index++; - continue; - } + fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, + false, type); + fr.ap.av.sendSelection(); + } + }); + JMenuItem clearCols = new JMenuItem(MessageManager + .getString("label.select_columns_not_containing")); + clearCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, + false, type); + fr.ap.av.sendSelection(); + } + }); + JMenuItem hideCols = new JMenuItem( + MessageManager.getString("label.hide_columns_containing")); + hideCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + fr.ap.alignFrame.hideFeatureColumns(type, true); + fr.ap.av.sendSelection(); + } + }); + JMenuItem hideOtherCols = new JMenuItem( + MessageManager.getString("label.hide_columns_not_containing")); + hideOtherCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + fr.ap.alignFrame.hideFeatureColumns(type, false); + fr.ap.av.sendSelection(); + } + }); + men.add(selCols); + men.add(clearCols); + men.add(hideCols); + men.add(hideOtherCols); + men.show(table, x, y); + } - if (tmpfeatures[index].getFeatureGroup() != null) - { - group = tmpfeatures[index].featureGroup; - if (!allGroups.contains(group)) - { - allGroups.addElement(group); - if (group!=null) - { - checkGroupState(group); - } - } - } + /** + * Sort the sequences in the alignment by the number of features for the given + * feature types (or all features if null) + * + * @param featureTypes + */ + protected void sortByDensity(List featureTypes) + { + af.avc.sortAlignmentByFeatureDensity(featureTypes); + } + + /** + * Sort the sequences in the alignment by average score for the given feature + * types (or all features if null) + * + * @param featureTypes + */ + protected void sortByScore(List featureTypes) + { + af.avc.sortAlignmentByFeatureScore(featureTypes); + } + + /** + * Returns true if at least one feature type is visible. Else shows a warning + * dialog and returns false. + * + * @param title + * @return + */ + private boolean canSortBy(String title) + { + if (fr.getDisplayedFeatureTypes().isEmpty()) + { + JvOptionPane.showMessageDialog(this, + MessageManager.getString("label.no_features_to_sort_by"), + title, JvOptionPane.OK_OPTION); + return false; + } + return true; + } + + @Override + synchronized public void discoverAllFeatureData() + { + Set allGroups = new HashSet<>(); + AlignmentI alignment = af.getViewport().getAlignment(); - if (!allFeatures.contains(tmpfeatures[index].getType())) + 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)) { - allFeatures.addElement(tmpfeatures[index].getType()); + allGroups.add(group); + checkGroupState(group); } - index++; } } - + resetTable(null); validate(); } + /** + * Synchronise gui group list and check visibility of group * * @param group - * @return true if group has been seen before and is already added to set. + * @return true if group is visible */ - private boolean checkGroupState(String group) { - boolean visible; - if (fr.featureGroups.containsKey(group)) - { - visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue(); - } else { - visible=true; // new group is always made visible - } + private boolean checkGroupState(String group) + { + boolean visible = fr.checkGroupVisibility(group, true); - if (groupPanel == null) + for (int g = 0; g < groupPanel.getComponentCount(); g++) + { + if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group)) { - groupPanel = new JPanel(); - } - - boolean alreadyAdded = false; - for (int g = 0; g < groupPanel.getComponentCount(); g++) - { - if ( ( (JCheckBox) groupPanel.getComponent(g)) - .getText().equals(group)) - { - alreadyAdded = true; - ((JCheckBox)groupPanel.getComponent(g)).setSelected(visible); - break; - } + ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible); + return visible; } + } - if (alreadyAdded) + 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) { - - return true; + fr.setGroupVisibility(check.getText(), check.isSelected()); + resetTable(new String[] { grp }); + refreshDisplay(); } - - fr.featureGroups.put(group, new Boolean(visible)); - final String grp = group; - final JCheckBox check = new JCheckBox(group, visible); - check.setFont(new Font("Serif", Font.BOLD, 12)); - check.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent evt) - { - fr.featureGroups.put(check.getText(), - new Boolean(check.isSelected())); - af.alignPanel.seqPanel.seqCanvas.repaint(); - if (af.alignPanel.overviewPanel != null) - { - af.alignPanel.overviewPanel.updateOverviewImage(); - } - - resetTable(new String[] { grp } ); - } - }); - groupPanel.add(check); - return false; + }); + groupPanel.add(check); + return visible; } - boolean resettingTable=false; - void resetTable(String[] groupChanged) - { - resettingTable=true; - typeWidth=new Hashtable(); - // TODO: change avWidth calculation to 'per-sequence' average and use long rather than float - float[] avWidth=null; - SequenceFeature[] tmpfeatures; - String group = null, type; - Vector visibleChecks = new Vector(); - //Find out which features should be visible depending on which groups - //are selected / deselected - //and recompute average width ordering - for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) + 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++) { - tmpfeatures = af.getViewport().alignment.getSequenceAt(i). - getDatasetSequence().getSequenceFeatures(); - if (tmpfeatures == null) - { - continue; - } + SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i); - int index = 0; - while (index < tmpfeatures.length) + /* + * 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) { - group = tmpfeatures[index].featureGroup; - - if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) + if (group == null || checkGroupState(group)) { - index++; - continue; - } - - if (group == null || fr.featureGroups.get(group) == null || - ( (Boolean) fr.featureGroups.get(group)).booleanValue()) - { - if (group!=null) - checkGroupState(group); - type = tmpfeatures[index].getType(); - if (!visibleChecks.contains(type)) - { - visibleChecks.addElement(type); - } - } - if (!typeWidth.containsKey(tmpfeatures[index].getType())) { - typeWidth.put(tmpfeatures[index].getType(), avWidth=new float[3]); - } else { - avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType()); + visibleGroups.add(group); } - avWidth[0]++; - if (tmpfeatures[index].getBegin()>tmpfeatures[index].getEnd()) + } + 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[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd(); - } else { - avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin(); + avWidth = new float[2]; + typeWidth.put(type, avWidth); } - index++; + // 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); } } - int fSize = visibleChecks.size(); - Object[][] data = new Object[fSize][3]; + Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT]; int dataIndex = 0; - if (fr.renderOrder != null) + if (fr.hasRenderOrder()) { if (!handlingUpdate) - fr.findAllFeatures(groupChanged!=null); // prod to update colourschemes. but don't affect display - //First add the checks in the previous render order, - //in case the window has been closed and reopened - for (int ro = fr.renderOrder.length - 1; ro > -1; ro--) { - type = fr.renderOrder[ro]; + 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 (!visibleChecks.contains(type)) + if (!displayableTypes.contains(type)) { continue; } - data[dataIndex][0] = type; - data[dataIndex][1] = fr.getColour(type); - data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type)); + data[dataIndex][TYPE_COLUMN] = type; + data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); + FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); + data[dataIndex][FILTER_COLUMN] = featureFilter == null + ? new FeatureMatcherSet() + : featureFilter; + data[dataIndex][SHOW_COLUMN] = Boolean.valueOf( + af.getViewport().getFeaturesDisplayed().isVisible(type)); dataIndex++; - visibleChecks.removeElement(type); + displayableTypes.remove(type); } } - fSize = visibleChecks.size(); - for (int i = 0; i < fSize; i++) + /* + * process any extra features belonging only to + * a group which was just selected + */ + while (!displayableTypes.isEmpty()) { - //These must be extra features belonging to the group - //which was just selected - type = visibleChecks.elementAt(i).toString(); - data[dataIndex][0] = type; + String type = displayableTypes.iterator().next(); + data[dataIndex][TYPE_COLUMN] = type; - data[dataIndex][1] = fr.getColour(type); - if (data[dataIndex][1] == null) + data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); + if (data[dataIndex][COLOUR_COLUMN] == null) { - //"Colour has been updated in another view!!" - fr.renderOrder = null; + // "Colour has been updated in another view!!" + fr.clearRenderOrder(); return; } - - data[dataIndex][2] = new Boolean(true); + FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); + data[dataIndex][FILTER_COLUMN] = featureFilter == null + ? new FeatureMatcherSet() + : featureFilter; + data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(true); dataIndex++; + displayableTypes.remove(type); } if (originalData == null) { - originalData = new Object[data.length][3]; - System.arraycopy(data, 0, originalData, 0, data.length); + 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); - if (groupPanel != null) - { - groupPanel.setLayout( - new GridLayout(fr.featureGroups.size() / 4 + 1, 4)); + groupPanel.setLayout( + new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4)); + pruneGroups(foundGroups); + groupPanel.validate(); + + updateFeatureRenderer(data, groupChanged != null); + resettingTable = false; + } - groupPanel.validate(); - bigPanel.add(groupPanel, BorderLayout.NORTH); + /** + * 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; + } } + } - updateFeatureRenderer(data, groupChanged!=null); - resettingTable=false; + /** + * 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; + boolean sort = false; float[] order = new float[data.length]; - for (int i=0;i1) - sort = sort || order[i-1]>order[i]; + 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(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"); + 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); + } + } - try + /** + * Loads feature colours and filters from XML stored in the given file + * + * @param file + */ + void load(File file) + { + try + { + InputStreamReader in = new InputStreamReader( + new FileInputStream(file), "UTF-8"); + + JAXBContext jc = JAXBContext + .newInstance("jalview.xml.binding.jalview"); + javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); + XMLStreamReader streamReader = XMLInputFactory.newInstance() + .createXMLStreamReader(in); + JAXBElement jbe = um.unmarshal(streamReader, + JalviewUserColours.class); + JalviewUserColours jucs = jbe.getValue(); + + // JalviewUserColours jucs = JalviewUserColours.unmarshal(in); + + /* + * load feature colours + */ + for (int i = jucs.getColour().size() - 1; i >= 0; i--) { - InputStreamReader in = new InputStreamReader(new FileInputStream( - file), "UTF-8"); - - jalview.binding.JalviewUserColours jucs = new jalview.binding. - JalviewUserColours(); - jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in); + Colour newcol = jucs.getColour().get(i); + FeatureColourI colour = jalview.project.Jalview2XML + .parseColour(newcol); + fr.setColour(newcol.getName(), colour); + fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size()); + } - for (int i = jucs.getColourCount()-1; i >=0; i--) + /* + * load feature filters; loaded filters will replace any that are + * currently defined, other defined filters are left unchanged + */ + for (int i = 0; i < jucs.getFilter().size(); i++) + { + Filter filterModel = jucs.getFilter().get(i); + String featureType = filterModel.getFeatureType(); + FeatureMatcherSetI filter = jalview.project.Jalview2XML + .parseFilter(featureType, filterModel.getMatcherSet()); + if (!filter.isEmpty()) { - String name; - fr.setColour(name=jucs.getColour(i).getName(), - new Color(Integer.parseInt(jucs.getColour(i).getRGB(), - 16))); - 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(); + fr.setFeatureFilter(featureType, filter); } } - catch (Exception ex) + + /* + * update feature settings table + */ + if (table != null) { - System.out.println("Error loading User Colour File\n" + ex); + 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(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"); + 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.binding.JalviewUserColours ucs = new jalview.binding. - JalviewUserColours(); - ucs.setSchemeName("Sequence Features"); - try - { - PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(choice), "UTF-8")); + save(chooser.getSelectedFile()); + } + } - Enumeration e = fr.featureColours.keys(); - float[] sortOrder = new float[fr.featureColours.size()]; - String[] sortTypes = new String[fr.featureColours.size()]; - int i=0; - while (e.hasMoreElements()) + /** + * 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) { - sortTypes[i] = e.nextElement().toString(); - sortOrder[i] = fr.getOrder(sortTypes[i]); - i++; - } - jalview.util.QuickSort.sort(sortOrder, sortTypes); - sortOrder=null; - for (i=0; i iterator = filter.getMatchers().iterator(); + FeatureMatcherI firstMatcher = iterator.next(); + jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML + .marshalFilter(firstMatcher, iterator, + filter.isAnded()); + Filter filterModel = new Filter(); + filterModel.setFeatureType(featureType); + filterModel.setMatcherSet(ms); + ucs.getFilter().add(filterModel); + } } + JAXBContext jaxbContext = JAXBContext + .newInstance(JalviewUserColours.class); + Marshaller jaxbMarshaller = jaxbContext.createMarshaller(); + jaxbMarshaller.marshal( + new ObjectFactory().createJalviewUserColours(ucs), out); + + // jaxbMarshaller.marshal(object, pout); + // marshaller.marshal(object); + out.flush(); + + // ucs.marshal(out); + out.close(); + } catch (Exception ex) + { + ex.printStackTrace(); } } public void invertSelection() { - for (int i = 0; i < table.getRowCount(); i++) + Object[][] data = ((FeatureTableModel) table.getModel()).getData(); + for (int i = 0; i < data.length; i++) { - Boolean value = (Boolean) table.getValueAt(i, 2); - - table.setValueAt( - new Boolean(!value.booleanValue()), - i, 2); + data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN]; } + updateFeatureRenderer(data, true); + table.repaint(); } - public void orderByAvWidth() { - if (table==null || table.getModel()==null) + + 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;i0) { - 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 (max0) - sort = sort || width[i-1]>width[i]; + 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); + // update global priority order + } + + updateFeatureRenderer(data, false); table.repaint(); } + + /** + * close ourselves but leave any existing UI handlers (e.g a CDS/Protein tabbed + * feature settings dialog) intact + */ + public void closeOldSettings() + { + closeDialog(false); + } + + /** + * close the feature settings dialog (and any containing frame) + */ public void close() { + closeDialog(true); + } + + private void closeDialog(boolean closeContainingFrame) + { try { - frame.setClosed(true); + if (frame != null) + { + af.setFeatureSettingsGeometry(frame.getBounds()); + frame.setClosed(true); + } + else + { + SplitContainerI sc = af.getSplitViewContainer(); + sc.closeFeatureSettings(this, closeContainingFrame); + af.featureSettings = null; + } + } catch (Exception exe) + { + } + + } + + public void updateFeatureRenderer(Object[][] data) + { + updateFeatureRenderer(data, true); + } + + /** + * Update the priority order of features; only repaint if this changed the order + * of visible features + * + * @param data + * @param visibleNew + */ + private void updateFeatureRenderer(Object[][] data, boolean visibleNew) + { + FeatureSettingsBean[] rowData = getTableAsBeans(data); + + if (fr.setFeaturePriority(rowData, visibleNew)) + { + refreshDisplay(); + } + } + + /** + * Converts table data into an array of data beans + */ + private FeatureSettingsBean[] getTableAsBeans(Object[][] data) + { + FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length]; + for (int i = 0; i < data.length; i++) + { + String type = (String) data[i][TYPE_COLUMN]; + FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN]; + FeatureMatcherSetI theFilter = (FeatureMatcherSetI) data[i][FILTER_COLUMN]; + Boolean isShown = (Boolean) data[i][SHOW_COLUMN]; + rowData[i] = new FeatureSettingsBean(type, colour, theFilter, + isShown); } - catch (Exception exe) - {} - + return rowData; } - public void updateFeatureRenderer(Object[][] data) - { - updateFeatureRenderer(data, true); - } - private void updateFeatureRenderer(Object[][] data, boolean visibleNew) + private void jbInit() throws Exception { - fr.setFeaturePriority(data, visibleNew); - af.alignPanel.paintAlignment(true); + this.setLayout(new BorderLayout()); - if (af.alignPanel.overviewPanel != null) - { - af.alignPanel.overviewPanel.updateOverviewImage(); - } - } + final boolean hasComplement = af.getViewport() + .getCodingComplement() != null; - 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(); - JPanel transbuttons = new JPanel(new BorderLayout()); - private void jbInit() - throws Exception - { - this.setLayout(borderLayout1); - settingsPane.setLayout(borderLayout2); - dasSettingsPane.setLayout(borderLayout3); - bigPanel.setLayout(borderLayout4); - invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - invert.setText("Invert Selection"); + 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(); } }); - optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - optimizeOrder.setText("Optimise Order"); - optimizeOrder.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { + + JButton optimizeOrder = new JButton( + MessageManager.getString("label.optimise_order")); + optimizeOrder.setFont(JvSwingUtils.getLabelFont()); + optimizeOrder.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { orderByAvWidth(); } }); - cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - cancel.setText("Cancel"); + + final String byScoreLabel = MessageManager.getString("label.seq_sort_by_score"); + JButton sortByScore = new JButton(byScoreLabel); + sortByScore.setFont(JvSwingUtils.getLabelFont()); + sortByScore.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (canSortBy(byScoreLabel)) + { + sortByScore(null); + } + } + }); + final String byDensityLabel = MessageManager.getString("label.sequence_sort_by_density"); + JButton sortByDens = new JButton(byDensityLabel); + sortByDens.setFont(JvSwingUtils.getLabelFont()); + sortByDens.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (canSortBy(byDensityLabel)) + { + sortByDensity(null); + } + } + }); + + JButton help = new JButton(MessageManager.getString("action.help")); + help.setFont(JvSwingUtils.getLabelFont()); + help.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + Help.showHelpWindow(HelpId.SequenceFeatureSettings); + } catch (HelpSetException e1) + { + e1.printStackTrace(); + } + } + }); + // Cancel for a SplitFrame should just revert changes to the currently displayed + // settings. May want to do this for either or both - so need a splitview + // feature settings cancel/OK. + JButton cancel = new JButton(MessageManager + .getString(hasComplement ? "action.revert" : "action.cancel")); + cancel.setToolTipText(MessageManager.getString(hasComplement + ? "action.undo_changes_to_feature_settings" + : "action.undo_changes_to_feature_settings_and_close_the_dialog")); + cancel.setFont(JvSwingUtils.getLabelFont()); + // TODO: disable cancel (and apply!) until current settings are different cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - updateFeatureRenderer(originalData); - close(); + revert(); + refreshDisplay(); + if (!hasComplement) + { + close(); + } } }); - ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - ok.setText("OK"); + // Cancel for the whole dialog should cancel both CDS and Protein. + // OK for an individual feature settings just applies changes, but dialog + // remains open + JButton ok = new JButton(MessageManager + .getString(hasComplement ? "action.apply" : "action.ok")); + ok.setFont(JvSwingUtils.getLabelFont()); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - close(); + if (!hasComplement) + { + close(); + } + else + { + storeOriginalSettings(); + } } }); - loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - loadColours.setText("Load Colours"); + + 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(); } }); - saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - saveColours.setText("Save Colours"); + + 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(); @@ -692,136 +1425,207 @@ public class FeatureSettings }); transparency.addChangeListener(new ChangeListener() { + @Override public void stateChanged(ChangeEvent evt) { - fr.setTransparency( (float) (100 - transparency.getValue()) / 100f); - af.alignPanel.paintAlignment(true); + if (!inConstruction) + { + fr.setTransparency((100 - transparency.getValue()) / 100f); + refreshDisplay(); + } } }); transparency.setMaximum(70); - fetchDAS.setText("Fetch DAS Features"); - fetchDAS.addActionListener(new ActionListener() + transparency.setToolTipText( + MessageManager.getString("label.transparency_tip")); + + boolean nucleotide = af.getViewport().getAlignment().isNucleotide(); + String text = MessageManager.formatMessage("label.show_linked_features", + nucleotide + ? MessageManager.getString("label.protein") + .toLowerCase() + : "CDS"); + showComplement = new JCheckBox(text); + showComplement.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - fetchDAS_actionPerformed(e); + af.getViewport() + .setShowComplementFeatures(showComplement.isSelected()); + refreshDisplay(); } }); - saveDAS.setText("Save as default"); - saveDAS.addActionListener(new ActionListener() + + showComplementOnTop = new JCheckBox( + MessageManager.getString("label.on_top")); + showComplementOnTop.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - saveDAS_actionPerformed(e); + af.getViewport().setShowComplementFeaturesOnTop( + showComplementOnTop.isSelected()); + refreshDisplay(); } }); - dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); - dasSettingsPane.setBorder(null); - cancelDAS.setEnabled(false); - cancelDAS.setText("Cancel Fetch"); - cancelDAS.addActionListener(new ActionListener() + + updateComplementButtons(); + + JPanel lowerPanel = new JPanel(new GridLayout(1, 2)); + bigPanel.add(lowerPanel, BorderLayout.SOUTH); + + JPanel transbuttons = new JPanel(new GridLayout(5, 1)); + transbuttons.add(optimizeOrder); + transbuttons.add(invert); + transbuttons.add(sortByScore); + transbuttons.add(sortByDens); + transbuttons.add(help); + + JPanel transPanelLeft = new JPanel( + new GridLayout(hasComplement ? 4 : 2, 1)); + transPanelLeft.add(new JLabel(" Colour transparency" + ":")); + transPanelLeft.add(transparency); + if (hasComplement) { - public void actionPerformed(ActionEvent e) - { - cancelDAS_actionPerformed(e); - } - }); - this.add(tabbedPane, java.awt.BorderLayout.CENTER); - tabbedPane.addTab("Feature Settings", settingsPane); - tabbedPane.addTab("DAS Settings", dasSettingsPane); - bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); - transPanel.add(transparency); - transbuttons.add(invert, java.awt.BorderLayout.NORTH); - transbuttons.add(optimizeOrder,java.awt.BorderLayout.SOUTH); - transPanel.add(transbuttons); + JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT)); + cp.add(showComplement); + cp.add(showComplementOnTop); + transPanelLeft.add(cp); + } + lowerPanel.add(transPanelLeft); + lowerPanel.add(transbuttons); + + JPanel buttonPanel = new JPanel(); buttonPanel.add(ok); buttonPanel.add(cancel); buttonPanel.add(loadColours); buttonPanel.add(saveColours); - bigPanel.add(scrollPane, 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); + bigPanel.add(scrollPane, BorderLayout.CENTER); + settingsPane.add(bigPanel, BorderLayout.CENTER); + settingsPane.add(buttonPanel, BorderLayout.SOUTH); + this.add(settingsPane); } - public void fetchDAS_actionPerformed(ActionEvent e) + /** + * Repaints alignment, structure and overview (if shown). If there is a + * complementary view which is showing this view's features, then also + * repaints that. + */ + void refreshDisplay() { - fetchDAS.setEnabled(false); - cancelDAS.setEnabled(true); - Vector selectedSources = dassourceBrowser.getSelectedSources(); - - SequenceI[] dataset, seqs; - int iSize; + af.alignPanel.paintAlignment(true, true); + AlignViewportI complement = af.getViewport().getCodingComplement(); + if (complement != null && complement.isShowComplementFeatures()) + { + AlignFrame af2 = Desktop.getAlignFrameFor(complement); + af2.alignPanel.paintAlignment(true, true); + } + } - if (af.getViewport().getSelectionGroup() != null - && af.getViewport().getSelectionGroup().getSize() > 0) + /** + * Answers a suitable tooltip to show on the colour cell of the table + * + * @param fcol + * @param withHint + * if true include 'click to edit' and similar text + * @return + */ + public static String getColorTooltip(FeatureColourI fcol, + boolean withHint) + { + if (fcol == null) { - iSize = af.getViewport().getSelectionGroup().getSize(); - dataset = new SequenceI[iSize]; - seqs = af.getViewport().getSelectionGroup(). - getSequencesInOrder( - af.getViewport().getAlignment()); + return null; } - else + if (fcol.isSimpleColour()) { - iSize = af.getViewport().getAlignment().getHeight(); - seqs = af.getViewport().getAlignment().getSequencesArray(); + return withHint ? BASE_TOOLTIP : null; } - - dataset = new SequenceI[iSize]; - for (int i = 0; i < iSize; i++) + String description = fcol.getDescription(); + description = description.replaceAll("<", "<"); + description = description.replaceAll(">", ">"); + StringBuilder tt = new StringBuilder(description); + if (withHint) { - dataset[i] = seqs[i].getDatasetSequence(); + tt.append("
").append(BASE_TOOLTIP).append("
"); } - - dasFeatureFetcher = - new jalview.io.DasSequenceFeatureFetcher( - dataset, - this, - selectedSources); - cancelDAS.setEnabled(true); - af.getViewport().setShowSequenceFeatures(true); - af.showSeqFeatures.setSelected(true); + return JvSwingUtils.wrapTooltip(true, tt.toString()); } - public void saveDAS_actionPerformed(ActionEvent e) + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol, + int w, int h) { - dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties); + boolean thr = false; + StringBuilder tx = new StringBuilder(); + + if (gcol.isColourByAttribute()) + { + tx.append(FeatureMatcher + .toAttributeDisplayName(gcol.getAttributeName())); + } + else if (!gcol.isColourByLabel()) + { + tx.append(MessageManager.getString("label.score")); + } + tx.append(" "); + if (gcol.isAboveThreshold()) + { + thr = true; + tx.append(">"); + } + if (gcol.isBelowThreshold()) + { + thr = true; + tx.append("<"); + } + if (gcol.isColourByLabel()) + { + if (thr) + { + tx.append(" "); + } + if (!gcol.isColourByAttribute()) + { + tx.append("Label"); + } + comp.setIcon(null); + } + else + { + Color newColor = gcol.getMaxColour(); + comp.setBackground(newColor); + // 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()); } - public void complete() + // /////////////////////////////////////////////////////////////////////// + // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html + // /////////////////////////////////////////////////////////////////////// + class FeatureTableModel extends AbstractTableModel { - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); - } + private String[] columnNames = { + MessageManager.getString("label.feature_type"), + MessageManager.getString("action.colour"), + MessageManager.getString("label.configuration"), + MessageManager.getString("label.show") }; - public void cancelDAS_actionPerformed(ActionEvent e) - { - dasFeatureFetcher.cancel(); - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); - } + private Object[][] data; - ///////////////////////////////////////////////////////////////////////// - // 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; @@ -832,6 +1636,7 @@ public class FeatureSettings this.data = data; } + @Override public int getColumnCount() { return columnNames.length; @@ -842,31 +1647,50 @@ public class FeatureSettings 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]; } - public Class getColumnClass(int c) + /** + * Answers the class of column c of the table + */ + @Override + public Class getColumnClass(int c) { - return getValueAt(0, c).getClass(); + switch (c) + { + case TYPE_COLUMN: + return String.class; + case COLOUR_COLUMN: + return FeatureColour.class; + case FILTER_COLUMN: + return FeatureMatcherSet.class; + default: + return Boolean.class; + } } + @Override public boolean isCellEditable(int row, int col) { return col == 0 ? false : true; } + @Override public void setValueAt(Object value, int row, int col) { data[row][col] = value; @@ -876,30 +1700,92 @@ public class FeatureSettings } - class ColorRenderer - extends JLabel implements TableCellRenderer + class ColorRenderer extends JLabel implements TableCellRenderer + { + Border unselectedBorder = null; + + Border selectedBorder = null; + + public ColorRenderer() + { + setOpaque(true); // MUST do this for background to show up. + setHorizontalTextPosition(SwingConstants.CENTER); + setVerticalTextPosition(SwingConstants.CENTER); + } + + @Override + public Component getTableCellRendererComponent(JTable tbl, Object color, + boolean isSelected, boolean hasFocus, int row, int column) + { + FeatureColourI cellColour = (FeatureColourI) color; + setOpaque(true); + setBackground(tbl.getBackground()); + if (!cellColour.isSimpleColour()) + { + Rectangle cr = tbl.getCellRect(row, column, false); + FeatureSettings.renderGraduatedColor(this, cellColour, + (int) cr.getWidth(), (int) cr.getHeight()); + } + else + { + this.setText(""); + this.setIcon(null); + setBackground(cellColour.getColour()); + } + if (isSelected) + { + if (selectedBorder == null) + { + selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + tbl.getSelectionBackground()); + } + setBorder(selectedBorder); + } + else + { + if (unselectedBorder == null) + { + unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + tbl.getBackground()); + } + setBorder(unselectedBorder); + } + + return this; + } + } + + class FilterRenderer extends JLabel implements TableCellRenderer { javax.swing.border.Border unselectedBorder = null; + javax.swing.border.Border selectedBorder = null; - public ColorRenderer() + public FilterRenderer() { - setOpaque(true); //MUST do this for background to show up. + setOpaque(true); // MUST do this for background to show up. + setHorizontalTextPosition(SwingConstants.CENTER); + setVerticalTextPosition(SwingConstants.CENTER); } - public Component getTableCellRendererComponent( - JTable table, Object color, - boolean isSelected, boolean hasFocus, - int row, int column) + @Override + public Component getTableCellRendererComponent(JTable tbl, + Object filter, boolean isSelected, boolean hasFocus, int row, + int column) { - Color newColor = (Color) color; - setBackground(newColor); + 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, - table.getSelectionBackground()); + tbl.getSelectionBackground()); } setBorder(selectedBorder); } @@ -908,88 +1794,377 @@ public class FeatureSettings if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getBackground()); + tbl.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 + /** + * 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); + } + + 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; + } } /** - * Handles events from the editor button and from - * the dialog's OK 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. */ - public void actionPerformed(ActionEvent e) + 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.setIcon(null); + return button; + } + } - if (EDIT.equals(e.getActionCommand())) + public boolean isOpen() + { + if (af.getSplitViewContainer() != null) { - //The user has clicked the cell, so - //bring up the dialog. - button.setBackground(currentColor); - colorChooser.setColor(currentColor); - dialog.setVisible(true); + return af.getSplitViewContainer().isFeatureSettingsOpen(); + } + return frame != null && !frame.isClosed(); + } + + @Override + public void revert() + { + fr.setTransparency(originalTransparency); + fr.setFeatureFilters(originalFilters); + updateFeatureRenderer(originalData); + af.getViewport().setViewStyle(originalViewStyle); + updateTransparencySliderFromFR(); + updateComplementButtons(); + refreshDisplay(); + } +} - //Make the renderer reappear. - fireEditingStopped(); +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 - { //User pressed dialog's "OK" button. - currentColor = colorChooser.getColor(); + { + s1 = width / 2; + e1 = s1; } } - //Implement the one CellEditor method that AbstractCellEditor doesn't. - public Object getCellEditorValue() + @Override + public int getIconWidth() + { + return width; + } + + @Override + public int getIconHeight() { - return currentColor; + return height; } - //Implement the one method defined by TableCellEditor. - public Component getTableCellEditorComponent(JTable table, - Object value, - boolean isSelected, - int row, - int column) + @Override + public void paintIcon(Component c, Graphics g, int x, int y) { - currentColor = (Color) value; - return button; + + 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); + } } }