X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=974b387a2e3c7fb905a916bfe074734cd45e27c9;hb=199068cbd16767a5d47ef4322793ef62d1e96a1f;hp=9748f42b5c9dc4b8361b13bf442e43d3bbbc259f;hpb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 9748f42..974b387 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,29 +20,45 @@ */ package jalview.gui; -import jalview.analysis.AlignmentSorter; +import jalview.api.FeatureColourI; +import jalview.api.FeatureSettingsControllerI; import jalview.bin.Cache; -import jalview.commands.OrderCommand; import jalview.datamodel.AlignmentI; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.FeatureAttributes; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +import jalview.io.JalviewFileView; +import jalview.schemabinding.version2.JalviewUserColours; +import jalview.schemes.FeatureColour; +import jalview.util.Format; import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.QuickSort; +import jalview.util.ReverseListIterator; +import jalview.util.matcher.Condition; +import jalview.util.matcher.KeyedMatcher; +import jalview.util.matcher.KeyedMatcherI; +import jalview.util.matcher.KeyedMatcherSet; +import jalview.util.matcher.KeyedMatcherSetI; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.DasSequenceFeatureFetcher; import jalview.ws.dbsources.das.api.jalviewSourceI; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; +import java.awt.Dimension; +import java.awt.FlowLayout; import java.awt.Font; import java.awt.Graphics; import java.awt.GridLayout; +import java.awt.LayoutManager; import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.MouseAdapter; @@ -57,47 +73,64 @@ import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashSet; import java.util.Hashtable; import java.util.Iterator; import java.util.List; +import java.util.Map; +import java.util.Set; import java.util.Vector; import javax.help.HelpSetException; import javax.swing.AbstractCellEditor; import javax.swing.BorderFactory; +import javax.swing.BoxLayout; +import javax.swing.ButtonGroup; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; +import javax.swing.JComboBox; import javax.swing.JDialog; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JLayeredPane; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; +import javax.swing.JRadioButton; import javax.swing.JScrollPane; import javax.swing.JSlider; import javax.swing.JTabbedPane; import javax.swing.JTable; +import javax.swing.JTextArea; +import javax.swing.JTextField; import javax.swing.ListSelectionModel; import javax.swing.SwingConstants; import javax.swing.SwingUtilities; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; +import javax.swing.plaf.basic.BasicArrowButton; import javax.swing.table.AbstractTableModel; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; public class FeatureSettings extends JPanel + implements FeatureSettingsControllerI { - DasSourceBrowser dassourceBrowser; + private static final String COLON = ":"; + + private static final int MIN_WIDTH = 400; - jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher; + private static final int MIN_HEIGHT = 400; - JPanel settingsPane = new JPanel(); + private static final int MAX_TOOLTIP_LENGTH = 50; + + DasSourceBrowser dassourceBrowser; + + DasSequenceFeatureFetcher dasFeatureFetcher; JPanel dasSettingsPane = new JPanel(); @@ -105,8 +138,15 @@ public class FeatureSettings extends JPanel 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(); @@ -116,15 +156,71 @@ public class FeatureSettings extends JPanel 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; + + /* + * fields of the feature filters tab + */ + private JPanel filtersPane; + + private JPanel chooseFiltersPanel; - JPanel transPanel = new JPanel(new GridLayout(1, 2)); + private JComboBox filteredFeatureChoice; - public FeatureSettings(AlignFrame af) + private JRadioButton andFilters; + + private JRadioButton orFilters; + + /* + * filters for the currently selected feature type + */ + private List filters; + + private JTextArea filtersAsText; + + // set white normally, black to debug layout + private Color debugBorderColour = Color.white; + + /** + * Constructor + * + * @param af + */ + public FeatureSettings(AlignFrame alignFrame) { - this.af = af; + this.af = alignFrame; fr = af.getFeatureRenderer(); - transparency.setMaximum(100 - (int) (fr.transparency * 100)); + // save transparency for restore on Cancel + originalTransparency = fr.getTransparency(); + int originalTransparencyAsPercent = (int) (originalTransparency * 100); + transparency.setMaximum(100 - originalTransparencyAsPercent); + + originalFilters = fr.getFeatureFilters(); try { @@ -134,15 +230,18 @@ public class FeatureSettings extends JPanel ex.printStackTrace(); } - table = new JTable() { + table = new JTable() + { @Override - public String getToolTipText(MouseEvent e) { - if (table.columnAtPoint(e.getPoint()) == 0) { + public String getToolTipText(MouseEvent e) + { + if (table.columnAtPoint(e.getPoint()) == 0) + { /* * Tooltip for feature name only */ - return JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.feature_settings_click_drag")); + return JvSwingUtils.wrapTooltip(true, MessageManager + .getString("label.feature_settings_click_drag")); } return null; } @@ -153,31 +252,34 @@ public class FeatureSettings extends JPanel table.setDefaultEditor(Color.class, new ColorEditor(this)); - table.setDefaultEditor(GraduatedColor.class, new ColorEditor(this)); - table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer()); + table.setDefaultEditor(FeatureColour.class, new ColorEditor(this)); + table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); - if (SwingUtilities.isRightMouseButton(evt)) + if (evt.isPopupTrigger()) { popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), - table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(), - evt.getY()); + table.getValueAt(selectedRow, 1), fr.getMinMax(), + evt.getX(), evt.getY()); } else if (evt.getClickCount() == 2) { + boolean invertSelection = evt.isAltDown(); + boolean toggleSelection = Platform.isControlDown(evt); + boolean extendSelection = evt.isShiftDown(); fr.ap.alignFrame.avc.markColumnsContainingFeatures( - evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(), - evt.isMetaDown(), + invertSelection, extendSelection, toggleSelection, (String) table.getValueAt(selectedRow, 0)); } } - // isPopupTrigger fires on mouseReleased on Mac + // isPopupTrigger fires on mouseReleased on Windows @Override public void mouseReleased(MouseEvent evt) { @@ -185,54 +287,58 @@ public class FeatureSettings extends JPanel if (evt.isPopupTrigger()) { popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), - table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(), - evt.getY()); + table.getValueAt(selectedRow, 1), fr.getMinMax(), + evt.getX(), evt.getY()); } } }); table.addMouseMotionListener(new MouseMotionAdapter() { + @Override public void mouseDragged(MouseEvent evt) { int newRow = table.rowAtPoint(evt.getPoint()); if (newRow != selectedRow && selectedRow != -1 && newRow != -1) { - Object[] temp = new Object[3]; - temp[0] = table.getValueAt(selectedRow, 0); - temp[1] = table.getValueAt(selectedRow, 1); - temp[2] = table.getValueAt(selectedRow, 2); - - table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0); - table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1); - table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2); - - table.setValueAt(temp[0], newRow, 0); - table.setValueAt(temp[1], newRow, 1); - table.setValueAt(temp[2], newRow, 2); - + /* + * reposition 'selectedRow' to 'newRow' (the dragged to location) + * this could be more than one row away for a very fast drag action + * so just swap it with adjacent rows until we get it there + */ + Object[][] data = ((FeatureTableModel) table.getModel()) + .getData(); + int direction = newRow < selectedRow ? -1 : 1; + for (int i = selectedRow; i != newRow; i += direction) + { + Object[] temp = data[i]; + data[i] = data[i + direction]; + data[i + direction] = temp; + } + updateFeatureRenderer(data); + table.repaint(); selectedRow = newRow; } } }); -// table.setToolTipText(JvSwingUtils.wrapTooltip(true, -// MessageManager.getString("label.feature_settings_click_drag"))); + // table.setToolTipText(JvSwingUtils.wrapTooltip(true, + // MessageManager.getString("label.feature_settings_click_drag"))); scrollPane.setViewportView(table); dassourceBrowser = new DasSourceBrowser(this); dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - if (af.getViewport().featuresDisplayed == null - || fr.renderOrder == null) + if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) { fr.findAllFeatures(true); // display everything! } - setTableData(); + discoverAllFeatureData(); final PropertyChangeListener change; final FeatureSettings fs = this; fr.addPropertyChangeListener(change = new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (!fs.resettingTable && !fs.handlingUpdate) @@ -248,36 +354,43 @@ public class FeatureSettings extends JPanel frame = new JInternalFrame(); frame.setContentPane(this); - if (new jalview.util.Platform().isAMac()) + if (Platform.isAMac()) { Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), - 475, 480); + 600, 480); } else { Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), - 400, 450); + 600, 450); } + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); - frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - fr.removePropertyChangeListener(change); - dassourceBrowser.fs = null; - }; - }); + frame.addInternalFrameListener( + new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + fr.removePropertyChangeListener(change); + dassourceBrowser.fs = null; + }; + }); frame.setLayer(JLayeredPane.PALETTE_LAYER); + inConstruction = false; } protected void popupSort(final int selectedRow, final String type, - final Object typeCol, final Hashtable minmax, int x, int y) + final Object typeCol, final Map minmax, int x, + int y) { - JPopupMenu men = new JPopupMenu(MessageManager.formatMessage( - "label.settings_for_param", new String[] + 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")); @@ -286,10 +399,12 @@ public class FeatureSettings extends JPanel scr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.sortByScore(new String[] - { type }); + me.af.avc + .sortAlignmentByFeatureScore(Arrays.asList(new String[] + { type })); } }); @@ -298,96 +413,77 @@ public class FeatureSettings extends JPanel dens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.sortByDens(new String[] - { type }); + me.af.avc + .sortAlignmentByFeatureDensity(Arrays.asList(new String[] + { type })); } }); men.add(dens); - if (minmax != null) + + /* + * variable colour options include colour by label, by score, + * by selected attribute text, or attribute value + */ + final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( + MessageManager.getString("label.variable_colour")); + mxcol.setSelected(!featureColour.isSimpleColour()); + men.add(mxcol); + mxcol.addActionListener(new ActionListener() { - final Object typeMinMax = minmax.get(type); - /* - * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); // - * this is broken at the moment and isn't that useful anyway! - * chb.setSelected(minmax.get(type) != null); chb.addActionListener(new - * ActionListener() { - * - * public void actionPerformed(ActionEvent e) { - * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type, - * null); } else { minmax.put(type, typeMinMax); } } - * - * }); - * - * men.add(chb); - */ - if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null) - { - // if (table.getValueAt(row, column)); - // graduated colourschemes for those where minmax exists for the - // positional features - final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( - "Graduated Colour"); - mxcol.setSelected(!(typeCol instanceof Color)); - men.add(mxcol); - mxcol.addActionListener(new ActionListener() - { - JColorChooser colorChooser; + JColorChooser colorChooser; - public void actionPerformed(ActionEvent e) + @Override + public void actionPerformed(ActionEvent e) + { + if (e.getSource() == mxcol) + { + if (featureColour.isSimpleColour()) { - if (e.getSource() == mxcol) - { - if (typeCol instanceof Color) - { - FeatureColourChooser fc = new FeatureColourChooser(me.fr, - type); - fc.addActionListener(this); - } - else - { - // bring up simple color chooser - colorChooser = new JColorChooser(); - JDialog dialog = JColorChooser.createDialog(me, - "Select new Colour", true, // modal - colorChooser, this, // OK button handler - null); // no CANCEL button handler - colorChooser.setColor(((GraduatedColor) typeCol) - .getMaxColor()); - dialog.setVisible(true); - } - } - else - { - if (e.getSource() instanceof FeatureColourChooser) - { - FeatureColourChooser fc = (FeatureColourChooser) e - .getSource(); - table.setValueAt(fc.getLastColour(), selectedRow, 1); - table.validate(); - } - else - { - // probably the color chooser! - table.setValueAt(colorChooser.getColor(), selectedRow, 1); - table.validate(); - me.updateFeatureRenderer( - ((FeatureTableModel) table.getModel()).getData(), - false); - } - } + FeatureColourChooser fc = new FeatureColourChooser(me.fr, type); + fc.addActionListener(this); } - - }); + else + { + // bring up simple color chooser + colorChooser = new JColorChooser(); + JDialog dialog = JColorChooser.createDialog(me, + "Select new Colour", true, // modal + colorChooser, this, // OK button handler + null); // no CANCEL button handler + colorChooser.setColor(featureColour.getMaxColour()); + dialog.setVisible(true); + } + } + else + { + if (e.getSource() instanceof FeatureColourChooser) + { + FeatureColourChooser fc = (FeatureColourChooser) e.getSource(); + table.setValueAt(fc.getLastColour(), selectedRow, 1); + table.validate(); + } + else + { + // probably the color chooser! + table.setValueAt(new FeatureColour(colorChooser.getColor()), + selectedRow, 1); + table.validate(); + me.updateFeatureRenderer( + ((FeatureTableModel) table.getModel()).getData(), false); + } + } } - } + + }); + JMenuItem selCols = new JMenuItem( MessageManager.getString("label.select_columns_containing")); selCols.addActionListener(new ActionListener() { - @Override public void actionPerformed(ActionEvent arg0) { @@ -395,11 +491,10 @@ public class FeatureSettings extends JPanel false, type); } }); - JMenuItem clearCols = new JMenuItem( - MessageManager.getString("label.select_columns_not_containing")); + JMenuItem clearCols = new JMenuItem(MessageManager + .getString("label.select_columns_not_containing")); clearCols.addActionListener(new ActionListener() { - @Override public void actionPerformed(ActionEvent arg0) { @@ -407,237 +502,177 @@ public class FeatureSettings extends JPanel false, type); } }); + JMenuItem hideCols = new JMenuItem( + MessageManager.getString("label.hide_columns_containing")); + hideCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + fr.ap.alignFrame.hideFeatureColumns(type, true); + } + }); + JMenuItem hideOtherCols = new JMenuItem( + MessageManager.getString("label.hide_columns_not_containing")); + hideOtherCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + fr.ap.alignFrame.hideFeatureColumns(type, false); + } + }); men.add(selCols); men.add(clearCols); + men.add(hideCols); + men.add(hideOtherCols); men.show(table, x, y); } - /** - * true when Feature Settings are updating from feature renderer - */ - private boolean handlingUpdate = false; - - /** - * contains a float[3] for each feature type string. created by setTableData - */ - Hashtable typeWidth = null; - - synchronized public void setTableData() + @Override + synchronized public void discoverAllFeatureData() { - if (fr.featureGroups == null) - { - fr.featureGroups = new Hashtable(); - } - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); - SequenceFeature[] tmpfeatures; - String group; - for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) - { - if (af.getViewport().getAlignment().getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures() == null) - { - continue; - } - - tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures(); + Set allGroups = new HashSet<>(); + AlignmentI alignment = af.getViewport().getAlignment(); - int index = 0; - while (index < tmpfeatures.length) + for (int i = 0; i < alignment.getHeight(); i++) + { + SequenceI seq = alignment.getSequenceAt(i); + for (String group : seq.getFeatures().getFeatureGroups(true)) { - 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); - if (group != null) - { - checkGroupState(group); - } - } - } - - if (!allFeatures.contains(tmpfeatures[index].getType())) + if (group != null && !allGroups.contains(group)) { - allFeatures.addElement(tmpfeatures[index].getType()); + allGroups.add(group); + checkGroupState(group); } - index++; } } + populateFilterableFeatures(); + 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 - } + boolean visible = fr.checkGroupVisibility(group, true); - if (groupPanel == null) - { - 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; + return visible; } } - if (alreadyAdded) - { - - return true; - } - - 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.setToolTipText(group); check.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent evt) { - fr.featureGroups.put(check.getText(), - new Boolean(check.isSelected())); - af.alignPanel.getSeqPanel().seqCanvas.repaint(); - if (af.alignPanel.overviewPanel != null) - { - af.alignPanel.overviewPanel.updateOverviewImage(); - } - - resetTable(new String[] - { grp }); + fr.setGroupVisibility(check.getText(), check.isSelected()); + resetTable(new String[] { grp }); + af.alignPanel.paintAlignment(true, true); } }); groupPanel.add(check); - return false; + return visible; } - boolean resettingTable = false; - synchronized void resetTable(String[] groupChanged) { - if (resettingTable == true) + if (resettingTable) { return; } resettingTable = true; - typeWidth = new Hashtable(); + 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 + + 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().getAlignment().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; + visibleGroups.add(group); } + } + foundGroups.addAll(groups); - 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()); - } - avWidth[0]++; - if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd()) - { - avWidth[1] += 1 + tmpfeatures[index].getBegin() - - tmpfeatures[index].getEnd(); - } - else + /* + * 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].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()][3]; int dataIndex = 0; - if (fr.renderOrder != null) + if (fr.hasRenderOrder()) { if (!handlingUpdate) - { + { fr.findAllFeatures(groupChanged != null); // prod to update + // colourschemes. but don't + // affect display + // First add the checks in the previous render order, + // in case the window has been closed and reopened } - // 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--) + List frl = fr.getRenderOrder(); + for (int ro = frl.size() - 1; ro > -1; ro--) { - type = fr.renderOrder[ro]; + String type = frl.get(ro); - if (!visibleChecks.contains(type)) + if (!displayableTypes.contains(type)) { continue; } @@ -645,30 +680,32 @@ public class FeatureSettings extends JPanel data[dataIndex][0] = type; data[dataIndex][1] = fr.getFeatureStyle(type); data[dataIndex][2] = new Boolean( - af.getViewport().featuresDisplayed.containsKey(type)); + 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(); + String type = displayableTypes.iterator().next(); data[dataIndex][0] = type; data[dataIndex][1] = fr.getFeatureStyle(type); if (data[dataIndex][1] == null) { // "Colour has been updated in another view!!" - fr.renderOrder = null; + fr.clearRenderOrder(); return; } data[dataIndex][2] = new Boolean(true); dataIndex++; + displayableTypes.remove(type); } if (originalData == null) @@ -679,24 +716,105 @@ public class FeatureSettings extends JPanel System.arraycopy(data[i], 0, originalData[i], 0, 3); } } + 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.validate(); - bigPanel.add(groupPanel, BorderLayout.NORTH); - } + groupPanel.setLayout( + new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4)); + pruneGroups(foundGroups); + groupPanel.validate(); updateFeatureRenderer(data, groupChanged != null); resettingTable = false; } /** + * Updates 'originalData' (used for restore on Cancel) if we detect that + * changes have been made outwith this dialog + *
    + *
  • a new feature type added (and made visible)
    • + *
  • a feature colour changed (in the Amend Features dialog)
    • + *
+ * + * @param foundData + */ + protected void updateOriginalData(Object[][] foundData) + { + // todo LinkedHashMap instead of Object[][] would be nice + + Object[][] currentData = ((FeatureTableModel) table.getModel()) + .getData(); + for (Object[] row : foundData) + { + String type = (String) row[0]; + boolean found = false; + for (Object[] current : currentData) + { + if (type.equals(current[0])) + { + found = true; + /* + * currently dependent on object equality here; + * really need an equals method on FeatureColour + */ + if (!row[1].equals(current[1])) + { + /* + * feature colour has changed externally - update originalData + */ + for (Object[] original : originalData) + { + if (type.equals(original[0])) + { + original[1] = row[1]; + break; + } + } + } + break; + } + } + if (!found) + { + /* + * new feature detected - add to original data (on top) + */ + Object[][] newData = new Object[originalData.length + 1][3]; + for (int i = 0; i < originalData.length; i++) + { + System.arraycopy(originalData[i], 0, newData[i + 1], 0, 3); + } + newData[0] = row; + originalData = newData; + } + } + } + + /** + * Remove from the groups panel any checkboxes for groups that are not in the + * foundGroups set. This enables removing a group from the display when the + * last feature in that group is deleted. + * + * @param foundGroups + */ + protected void pruneGroups(Set foundGroups) + { + for (int g = 0; g < groupPanel.getComponentCount(); g++) + { + JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g); + if (!foundGroups.contains(checkbox.getText())) + { + groupPanel.remove(checkbox); + } + } + } + + /** * reorder data based on the featureRenderers global priority list. * * @param data @@ -725,12 +843,11 @@ public class FeatureSettings extends JPanel 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(MessageManager.getString("label.load_feature_colours")); + 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); @@ -741,12 +858,10 @@ public class FeatureSettings extends JPanel try { - InputStreamReader in = new InputStreamReader(new FileInputStream( - file), "UTF-8"); + InputStreamReader in = new InputStreamReader( + new FileInputStream(file), "UTF-8"); - jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours(); - jucs = jucs - .unmarshal(in); + JalviewUserColours jucs = JalviewUserColours.unmarshal(in); for (int i = jucs.getColourCount() - 1; i >= 0; i--) { @@ -765,7 +880,7 @@ public class FeatureSettings extends JPanel Cache.log.warn("Couldn't parse out graduated feature color.", e); } - GraduatedColor gcol = new GraduatedColor(mincol, maxcol, + FeatureColourI gcol = new FeatureColour(mincol, maxcol, newcol.getMin(), newcol.getMax()); if (newcol.hasAutoScale()) { @@ -777,31 +892,28 @@ public class FeatureSettings extends JPanel } if (newcol.hasThreshold()) { - gcol.setThresh(newcol.getThreshold()); - gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default + gcol.setThreshold(newcol.getThreshold()); } if (newcol.getThreshType().length() > 0) { String ttyp = newcol.getThreshType(); - if (ttyp.equalsIgnoreCase("NONE")) - { - gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); - } if (ttyp.equalsIgnoreCase("ABOVE")) { - gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); + gcol.setAboveThreshold(true); } if (ttyp.equalsIgnoreCase("BELOW")) { - gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); + gcol.setBelowThreshold(true); } } fr.setColour(name = newcol.getName(), gcol); } else { - fr.setColour(name = jucs.getColour(i).getName(), new Color( - Integer.parseInt(jucs.getColour(i).getRGB(), 16))); + Color color = new Color( + Integer.parseInt(jucs.getColour(i).getRGB(), 16)); + fr.setColour(name = jucs.getColour(i).getName(), + new FeatureColour(color)); } fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount()); } @@ -823,12 +935,11 @@ public class FeatureSettings extends JPanel 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(MessageManager.getString("label.save_feature_colours")); + 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); @@ -843,49 +954,40 @@ public class FeatureSettings extends JPanel PrintWriter out = new PrintWriter(new OutputStreamWriter( new FileOutputStream(choice), "UTF-8")); - Iterator e = fr.featureColours.keySet().iterator(); - float[] sortOrder = new float[fr.featureColours.size()]; - String[] sortTypes = new String[fr.featureColours.size()]; + Set fr_colours = fr.getAllFeatureColours(); + Iterator e = fr_colours.iterator(); + float[] sortOrder = new float[fr_colours.size()]; + String[] sortTypes = new String[fr_colours.size()]; int i = 0; while (e.hasNext()) { - sortTypes[i] = e.next().toString(); + sortTypes[i] = e.next(); sortOrder[i] = fr.getOrder(sortTypes[i]); i++; } - jalview.util.QuickSort.sort(sortOrder, sortTypes); + QuickSort.sort(sortOrder, sortTypes); sortOrder = null; - Object fcol; - GraduatedColor gcol; for (i = 0; i < sortTypes.length; i++) { jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setName(sortTypes[i]); - col.setRGB(jalview.util.Format.getHexString(fr.getColour(col - .getName()))); - fcol = fr.getFeatureStyle(sortTypes[i]); - if (fcol instanceof GraduatedColor) + FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]); + if (fcol.isSimpleColour()) { - gcol = (GraduatedColor) fcol; - col.setMin(gcol.getMin()); - col.setMax(gcol.getMax()); - col.setMinRGB(jalview.util.Format.getHexString(gcol - .getMinColor())); - col.setAutoScale(gcol.isAutoScale()); - col.setThreshold(gcol.getThresh()); - col.setColourByLabel(gcol.isColourByLabel()); - switch (gcol.getThreshType()) - { - case AnnotationColourGradient.NO_THRESHOLD: - col.setThreshType("NONE"); - break; - case AnnotationColourGradient.ABOVE_THRESHOLD: - col.setThreshType("ABOVE"); - break; - case AnnotationColourGradient.BELOW_THRESHOLD: - col.setThreshType("BELOW"); - break; - } + col.setRGB(Format.getHexString(fcol.getColour())); + } + else + { + col.setRGB(Format.getHexString(fcol.getMaxColour())); + col.setMin(fcol.getMin()); + col.setMax(fcol.getMax()); + col.setMinRGB( + jalview.util.Format.getHexString(fcol.getMinColour())); + col.setAutoScale(fcol.isAutoScaled()); + col.setThreshold(fcol.getThreshold()); + col.setColourByLabel(fcol.isColourByLabel()); + col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" + : (fcol.isBelowThreshold() ? "BELOW" : "NONE")); } ucs.addColour(col); } @@ -921,7 +1023,7 @@ public class FeatureSettings extends JPanel int num = 0; for (int i = 0; i < data.length; i++) { - awidth = (float[]) typeWidth.get(data[i][0]); + awidth = typeWidth.get(data[i][0]); if (awidth[0] > 0) { width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better @@ -962,9 +1064,9 @@ public class FeatureSettings extends JPanel } } if (sort) - { + { jalview.util.QuickSort.sort(width, data); - // update global priority order + // update global priority order } updateFeatureRenderer(data, false); @@ -987,104 +1089,106 @@ public class FeatureSettings extends JPanel updateFeatureRenderer(data, true); } + /** + * Update the priority order of features; only repaint if this changed the + * order of visible features + * + * @param data + * @param visibleNew + */ private void updateFeatureRenderer(Object[][] data, boolean visibleNew) { - fr.setFeaturePriority(data, visibleNew); - af.alignPanel.paintAlignment(true); + if (fr.setFeaturePriority(data, visibleNew)) + { + af.alignPanel.paintAlignment(true, true); + } } - int selectedRow = -1; - - JTabbedPane tabbedPane = new JTabbedPane(); - - BorderLayout borderLayout1 = new BorderLayout(); - - BorderLayout borderLayout2 = new BorderLayout(); - - BorderLayout borderLayout3 = new BorderLayout(); - - JPanel bigPanel = new JPanel(); - - BorderLayout borderLayout4 = new BorderLayout(); - - JButton invert = new JButton(); - - JPanel buttonPanel = new JPanel(); - - JButton cancel = new JButton(); - - JButton ok = new JButton(); - - JButton loadColours = new JButton(); - - JButton saveColours = new JButton(); - - JPanel dasButtonPanel = new JPanel(); - - JButton fetchDAS = new JButton(); - - JButton saveDAS = new JButton(); - - JButton cancelDAS = new JButton(); + private void jbInit() throws Exception + { + this.setLayout(new BorderLayout()); - JButton optimizeOrder = new JButton(); + JPanel settingsPane = new JPanel(); + settingsPane.setLayout(new BorderLayout()); - JButton sortByScore = new JButton(); + filtersPane = new JPanel(); - JButton sortByDens = new JButton(); + dasSettingsPane.setLayout(new BorderLayout()); - JButton help = new JButton(); + JPanel bigPanel = new JPanel(); + bigPanel.setLayout(new BorderLayout()); - JPanel transbuttons = new JPanel(new GridLayout(5, 1)); + groupPanel = new JPanel(); + bigPanel.add(groupPanel, BorderLayout.NORTH); - private void jbInit() throws Exception - { - this.setLayout(borderLayout1); - settingsPane.setLayout(borderLayout2); - dasSettingsPane.setLayout(borderLayout3); - bigPanel.setLayout(borderLayout4); + JButton invert = new JButton( + MessageManager.getString("label.invert_selection")); invert.setFont(JvSwingUtils.getLabelFont()); - invert.setText(MessageManager.getString("label.invert_selection")); 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.setText(MessageManager.getString("label.optimise_order")); 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 - .setText(MessageManager.getString("label.seq_sort_by_score")); sortByScore.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - sortByScore(null); + af.avc.sortAlignmentByFeatureScore(null); } }); + JButton sortByDens = new JButton( + MessageManager.getString("label.sequence_sort_by_density")); sortByDens.setFont(JvSwingUtils.getLabelFont()); - sortByDens.setText(MessageManager - .getString("label.sequence_sort_by_density")); sortByDens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - sortByDens(null); + 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 @@ -1096,38 +1200,50 @@ public class FeatureSettings extends JPanel } } }); + + JButton cancel = new JButton(MessageManager.getString("action.cancel")); cancel.setFont(JvSwingUtils.getLabelFont()); - cancel.setText(MessageManager.getString("action.cancel")); 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.setText(MessageManager.getString("action.ok")); 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.setText(MessageManager.getString("label.load_colours")); 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.setText(MessageManager.getString("label.save_colours")); saveColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { save(); @@ -1135,19 +1251,24 @@ public class FeatureSettings extends JPanel }); transparency.addChangeListener(new ChangeListener() { + @Override public void stateChanged(ChangeEvent evt) { - fr.setTransparency((100 - transparency.getValue()) / 100f); - af.alignPanel.paintAlignment(true); + if (!inConstruction) + { + fr.setTransparency((100 - transparency.getValue()) / 100f); + af.alignPanel.paintAlignment(true,true); + } } }); transparency.setMaximum(70); - transparency.setToolTipText(MessageManager - .getString("label.transparency_tip")); + transparency.setToolTipText( + MessageManager.getString("label.transparency_tip")); fetchDAS.setText(MessageManager.getString("label.fetch_das_features")); fetchDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { fetchDAS_actionPerformed(e); @@ -1156,171 +1277,499 @@ public class FeatureSettings extends JPanel saveDAS.setText(MessageManager.getString("action.save_as_default")); saveDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { saveDAS_actionPerformed(e); } }); + + JPanel dasButtonPanel = new JPanel(); dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); dasSettingsPane.setBorder(null); cancelDAS.setEnabled(false); cancelDAS.setText(MessageManager.getString("action.cancel_fetch")); cancelDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cancelDAS_actionPerformed(e); } }); - this.add(tabbedPane, java.awt.BorderLayout.CENTER); - tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane); - tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane); - bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); + + JTabbedPane tabbedPane = new JTabbedPane(); + this.add(tabbedPane, BorderLayout.CENTER); + tabbedPane.addTab(MessageManager.getString("label.feature_settings"), + settingsPane); + tabbedPane.addTab(MessageManager.getString("label.filters"), + filtersPane); + // tabbedPane.addTab(MessageManager.getString("label.das_settings"), + // dasSettingsPane); + + 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); - JPanel sliderPanel = new JPanel(); - sliderPanel.add(transparency); 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, java.awt.BorderLayout.CENTER); - dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH); + bigPanel.add(scrollPane, BorderLayout.CENTER); + dasSettingsPane.add(dasButtonPanel, 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); - } + settingsPane.add(bigPanel, BorderLayout.CENTER); + settingsPane.add(buttonPanel, BorderLayout.SOUTH); - protected void sortByDens(String[] typ) - { - sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); + initFiltersTab(); } - protected void sortBy(String[] typ, String methodText, final String method) + /** + * Populates initial layout of the feature attribute filters panel + */ + protected void initFiltersTab() { - if (typ == null) - { - typ = getDisplayedFeatureTypes(); - } - String gps[] = null; - gps = getDisplayedFeatureGroups(); - if (typ != null) + filters = new ArrayList<>(); + + /* + * choose feature type + */ + JPanel chooseTypePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + chooseTypePanel.setBackground(Color.white); + JvSwingUtils.createItalicTitledBorder(chooseTypePanel, + MessageManager.getString("label.feature_type"), true); + filteredFeatureChoice = new JComboBox<>(); + filteredFeatureChoice.addItemListener(new ItemListener() { - ArrayList types = new ArrayList(); - for (int i = 0; i < typ.length; i++) + @Override + public void itemStateChanged(ItemEvent e) { - if (typ[i] != null) - { - types.add(typ[i]); - } - typ = new String[types.size()]; - types.toArray(typ); + refreshFiltersDisplay(); } - } - if (gps != null) + }); + chooseTypePanel.add(new JLabel(MessageManager + .getString("label.feature_to_filter"))); + chooseTypePanel.add(filteredFeatureChoice); + populateFilterableFeatures(); + + /* + * the panel with the filters for the selected feature type + */ + JPanel filtersPanel = new JPanel(); + filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS)); + filtersPanel.setBackground(Color.white); + JvSwingUtils.createItalicTitledBorder(filtersPanel, + MessageManager.getString("label.filters"), true); + + /* + * add AND or OR radio buttons + */ + JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + andOrPanel.setBackground(Color.white); + andOrPanel.setBorder(BorderFactory.createLineBorder(debugBorderColour)); + andFilters = new JRadioButton("And"); + orFilters = new JRadioButton("Or"); + ActionListener actionListener = new ActionListener() { - ArrayList grps = new ArrayList(); - - for (int i = 0; i < gps.length; i++) + @Override + public void actionPerformed(ActionEvent e) { - if (gps[i] != null) - { - grps.add(gps[i]); - } + filtersChanged(); } - gps = new String[grps.size()]; - grps.toArray(gps); - } - AlignmentPanel alignPanel = af.alignPanel; - AlignmentI al = alignPanel.av.getAlignment(); + }; + andFilters.addActionListener(actionListener); + orFilters.addActionListener(actionListener); + ButtonGroup andOr = new ButtonGroup(); + andOr.add(andFilters); + andOr.add(orFilters); + andFilters.setSelected(true); + andOrPanel.add(new JLabel(MessageManager + .getString("label.join_conditions"))); + andOrPanel.add(andFilters); + andOrPanel.add(orFilters); + filtersPanel.add(andOrPanel); + + /* + * panel with filters - populated by refreshFiltersDisplay + */ + chooseFiltersPanel = new JPanel(); + LayoutManager box = new BoxLayout(chooseFiltersPanel, + BoxLayout.Y_AXIS); + chooseFiltersPanel.setLayout(box); + filtersPanel.add(chooseFiltersPanel); + + /* + * a read-only text view of the current filters + */ + JPanel showFiltersPanel = new JPanel(new BorderLayout(5, 5)); + showFiltersPanel.setBackground(Color.white); + JvSwingUtils.createItalicTitledBorder(showFiltersPanel, + MessageManager.getString("label.match_condition"), true); + filtersAsText = new JTextArea(); + filtersAsText.setLineWrap(true); + filtersAsText.setWrapStyleWord(true); + filtersAsText.setEnabled(false); // for display only + showFiltersPanel.add(filtersAsText); + + filtersPane.setLayout(new BorderLayout()); + filtersPane.add(chooseTypePanel, BorderLayout.NORTH); + filtersPane.add(filtersPanel, BorderLayout.CENTER); + filtersPane.add(showFiltersPanel, BorderLayout.SOUTH); + + /* + * update display for initial feature type selection + */ + refreshFiltersDisplay(); + } + + /** + * Adds entries to the 'choose feature to filter' drop-down choice. Only + * feature types which have known attributes (so can be filtered) are + * included, so recall this method to update the list (check for newly added + * attributes). + */ + protected void populateFilterableFeatures() + { + /* + * suppress action handler while updating the list + */ + ItemListener listener = filteredFeatureChoice.getItemListeners()[0]; + filteredFeatureChoice.removeItemListener(listener); + + filteredFeatureChoice.removeAllItems(); + ReverseListIterator types = new ReverseListIterator<>( + fr.getRenderOrder()); - int start, stop; - SequenceGroup sg = alignPanel.av.getSelectionGroup(); - if (sg != null) + boolean found = false; + while (types.hasNext()) { - start = sg.getStartRes(); - stop = sg.getEndRes(); + String type = types.next(); + if (FeatureAttributes.getInstance().hasAttributes(type)) + { + filteredFeatureChoice.addItem(type); + found = true; + } } - else + if (!found) { - start = 0; - stop = al.getWidth(); + filteredFeatureChoice.addItem(MessageManager + .getString("label.no_feature_attributes")); + filteredFeatureChoice.setEnabled(false); } - SequenceI[] oldOrder = al.getSequencesArray(); - AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); - af.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av - .getAlignment())); - alignPanel.paintAlignment(true); + filteredFeatureChoice.addItemListener(listener); } - protected void sortByScore(String[] typ) + /** + * Refreshes the display to show any filters currently configured for the + * selected feature type (editable, with 'remove' option), plus one extra row + * for adding a condition. This should be called on change of selected feature + * type, or after a filter has been removed, added or amended. + */ + protected void refreshFiltersDisplay() { - sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); + /* + * clear the panel and list of filter conditions + */ + chooseFiltersPanel.removeAll(); + filters.clear(); + + /* + * look up attributes known for feature type + */ + String selectedType = (String) filteredFeatureChoice.getSelectedItem(); + List attNames = FeatureAttributes.getInstance() + .getAttributes(selectedType); + + /* + * if this feature type has filters set, load them first + */ + KeyedMatcherSetI featureFilters = fr.getFeatureFilter(selectedType); + filtersAsText.setText(""); + if (featureFilters != null) + { + filtersAsText.setText(featureFilters.toString()); + if (!featureFilters.isAnded()) + { + orFilters.setSelected(true); + } + featureFilters.getMatchers().forEach(matcher -> filters.add(matcher)); + } + + /* + * and an empty filter for the user to populate (add) + */ + KeyedMatcherI noFilter = new KeyedMatcher(Condition.values()[0], "", + (String) null); + filters.add(noFilter); + + /* + * render the conditions in rows, each in its own JPanel + */ + int filterIndex = 0; + for (KeyedMatcherI filter : filters) + { + String[] attName = filter.getKey(); + Condition condition = filter.getMatcher() + .getCondition(); + String pattern = filter.getMatcher().getPattern(); + JPanel row = addFilter(attName, attNames, condition, pattern, filterIndex); + row.setBorder(BorderFactory.createLineBorder(debugBorderColour)); + chooseFiltersPanel.add(row); + filterIndex++; + } + // chooseFiltersPanel.add(Box.createVerticalGlue()); + + filtersPane.validate(); + filtersPane.repaint(); } - private String[] getDisplayedFeatureTypes() + /** + * A helper method that constructs a panel with one filter condition: + *
    + *
  • a drop-down list of attribute names to choose from
    • + *
  • a drop-down list of conditions to choose from
    • + *
  • a text field for input of a match pattern
    • + *
  • optionally, a 'remove' button
    • + *
+ * If attribute, condition or pattern are not null, they are set as defaults for + * the input fields. The 'remove' button is added unless the pattern is null or + * empty (incomplete filter condition). + * + * @param attName + * @param attNames + * @param cond + * @param pattern + * @param filterIndex + * @return + */ + protected JPanel addFilter(String[] attName, List attNames, + Condition cond, String pattern, int filterIndex) { - String[] typ = null; - if (fr != null) + JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT)); + filterRow.setBackground(Color.white); + + /* + * drop-down choice of attribute, with description as a tooltip + * if we can obtain it + */ + String featureType = (String) filteredFeatureChoice.getSelectedItem(); + final JComboBox attCombo = populateAttributesDropdown( + featureType, attNames); + JComboBox condCombo = new JComboBox<>(); + JTextField patternField = new JTextField(8); + + /* + * action handlers that validate and (if valid) apply changes + */ + ActionListener actionListener = new ActionListener() { - synchronized (fr.renderOrder) + @Override + public void actionPerformed(ActionEvent e) { - typ = new String[fr.renderOrder.length]; - System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length); - for (int i = 0; i < typ.length; i++) + if (attCombo.getSelectedItem() != null) { - if (af.viewport.featuresDisplayed.get(typ[i]) == null) + if (validateFilter(patternField, condCombo)) { - typ[i] = null; + updateFilter(attCombo, condCombo, patternField, filterIndex); + filtersChanged(); } } } + }; + ItemListener itemListener = new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + actionListener.actionPerformed(null); + } + }; + + if (attName == null) // the 'add a condition' row + { + attCombo.setSelectedItem(null); } - return typ; - } + else + { + attCombo.setSelectedItem(String.join(COLON, attName)); + } + attCombo.addItemListener(itemListener); - private String[] getDisplayedFeatureGroups() - { - String[] gps = null; - ArrayList _gps = new ArrayList(); - if (fr != null) + filterRow.add(attCombo); + + /* + * drop-down choice of test condition + */ + for (Condition c : Condition.values()) { + condCombo.addItem(c); + } + if (cond != null) + { + condCombo.setSelectedItem(cond); + } + condCombo.addItemListener(itemListener); + filterRow.add(condCombo); - if (fr.featureGroups != null) + /* + * pattern to match against + */ + patternField.setText(pattern); + patternField.addActionListener(actionListener); + patternField.addFocusListener(new FocusAdapter() + { + @Override + public void focusLost(FocusEvent e) { - Iterator en = fr.featureGroups.keySet().iterator(); - int g = 0; - boolean valid = false; - while (en.hasNext()) + actionListener.actionPerformed(null); + } + }); + filterRow.add(patternField); + + /* + * add remove button if filter is populated (non-empty pattern) + */ + if (pattern != null && pattern.trim().length() > 0) + { + // todo: gif for button drawing '-' or 'x' + JButton removeCondition = new BasicArrowButton(SwingConstants.WEST); + removeCondition.setToolTipText(MessageManager + .getString("label.delete_row")); + removeCondition.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - String gp = (String) en.next(); - Boolean on = (Boolean) fr.featureGroups.get(gp); - if (on != null && on.booleanValue()) - { - valid = true; - _gps.add(gp); - } + filters.remove(filterIndex); + filtersChanged(); } - if (!valid) + }); + filterRow.add(removeCondition); + } + + return filterRow; + } + + /** + * A helper method to build the drop-down choice of attributes for a feature. + * Where metadata is available with a description for an attribute, that is + * added as a tooltip. + * + * @param featureType + * @param attNames + */ + protected JComboBox populateAttributesDropdown( + String featureType, List attNames) + { + List displayNames = new ArrayList<>(); + List tooltips = new ArrayList<>(); + FeatureAttributes fa = FeatureAttributes.getInstance(); + for (String[] attName : attNames) + { + String desc = fa.getDescription(featureType, attName); + if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH) + { + desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "..."; + } + displayNames.add(String.join(COLON, attName)); + tooltips.add(desc == null ? "" : desc); + } + + JComboBox attCombo = JvSwingUtils.buildComboWithTooltips( + displayNames, tooltips); + if (attNames.isEmpty()) + { + attCombo.setToolTipText(MessageManager + .getString("label.no_attributes")); + } + return attCombo; + } + + /** + * Action on any change to feature filtering, namely + *
    + *
  • change of selected attribute
    • + *
  • change of selected condition
    • + *
  • change of match pattern
    • + *
  • removal of a condition
    • + *
+ * The action should be to + *
    + *
  • parse and validate the filters
    • + *
  • if valid, update the filter text box
    • + *
  • and apply the filters to the viewport
    • + *
+ */ + protected void filtersChanged() + { + /* + * update the filter conditions for the feature type + */ + String featureType = (String) filteredFeatureChoice.getSelectedItem(); + boolean anded = andFilters.isSelected(); + KeyedMatcherSetI combined = new KeyedMatcherSet(); + + for (KeyedMatcherI filter : filters) + { + String pattern = filter.getMatcher().getPattern(); + if (pattern.trim().length() > 0) + { + if (anded) { - return null; + combined.and(filter); } else { - gps = new String[_gps.size()]; - _gps.toArray(gps); + combined.or(filter); } } } - return gps; + + /* + * save the filter conditions in the FeatureRenderer + * (note this might now be an empty filter with no conditions) + */ + fr.setFeatureFilter(featureType, combined); + + filtersAsText.setText(combined.toString()); + + refreshFiltersDisplay(); + + af.alignPanel.paintAlignment(true, true); + } + + /** + * Constructs a filter condition from the given input fields, and replaces the + * condition at filterIndex with the new one + * + * @param attCombo + * @param condCombo + * @param valueField + * @param filterIndex + */ + protected void updateFilter(JComboBox attCombo, + JComboBox condCombo, JTextField valueField, + int filterIndex) + { + String attName = (String) attCombo.getSelectedItem(); + Condition cond = (Condition) condCombo.getSelectedItem(); + String pattern = valueField.getText(); + KeyedMatcherI km = new KeyedMatcher(cond, pattern, + attName.split(COLON)); + + filters.set(filterIndex, km); } public void fetchDAS_actionPerformed(ActionEvent e) @@ -1328,7 +1777,8 @@ public class FeatureSettings extends JPanel fetchDAS.setEnabled(false); cancelDAS.setEnabled(true); dassourceBrowser.setGuiEnabled(false); - Vector selectedSources = dassourceBrowser.getSelectedSources(); + Vector selectedSources = dassourceBrowser + .getSelectedSources(); doDasFeatureFetch(selectedSources, true, true); } @@ -1344,7 +1794,7 @@ public class FeatureSettings extends JPanel { SequenceI[] dataset, seqs; int iSize; - AlignViewport vp = af.getViewport(); + AlignmentViewport vp = af.getViewport(); if (vp.getSelectionGroup() != null && vp.getSelectionGroup().getSize() > 0) { @@ -1387,7 +1837,7 @@ public class FeatureSettings extends JPanel * Vector of Strings to resolve to DAS source nicknames. * @return sources that are present in source list. */ - public List resolveSourceNicknames(Vector sources) + public List resolveSourceNicknames(Vector sources) { return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); } @@ -1398,7 +1848,7 @@ public class FeatureSettings extends JPanel * * @return vector of selected das source nicknames */ - public Vector getSelectedSources() + public Vector getSelectedSources() { return dassourceBrowser.getSelectedSources(); } @@ -1412,7 +1862,7 @@ public class FeatureSettings extends JPanel * if true then runs in same thread, otherwise passes to the Swing * executor */ - public void fetchDasFeatures(Vector sources, boolean block) + public void fetchDasFeatures(Vector sources, boolean block) { initDasSources(); List resolved = dassourceBrowser.sourceRegistry @@ -1429,6 +1879,7 @@ public class FeatureSettings extends JPanel Runnable fetcher = new Runnable() { + @Override public void run() { doDasFeatureFetch(dassources, true, false); @@ -1472,15 +1923,55 @@ public class FeatureSettings extends JPanel public void noDasSourceActive() { complete(); - JOptionPane - .showInternalConfirmDialog( - Desktop.desktop, - MessageManager - .getString("label.no_das_sources_selected_warn"), - MessageManager - .getString("label.no_das_sources_selected_title"), - JOptionPane.DEFAULT_OPTION, - JOptionPane.INFORMATION_MESSAGE); + JvOptionPane.showInternalConfirmDialog(Desktop.desktop, + MessageManager.getString("label.no_das_sources_selected_warn"), + MessageManager.getString("label.no_das_sources_selected_title"), + JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE); + } + + /** + * Answers true unless a numeric condition has been selected with a + * non-numeric value. Sets the value field to RED with a tooltip if in error. + *

+ * If the pattern entered is empty, this method returns false, but does not + * mark the field as invalid. This supports selecting an attribute for a new + * condition before a match pattern has been entered. + * + * @param value + * @param condCombo + */ + protected boolean validateFilter(JTextField value, + JComboBox condCombo) + { + if (value == null || condCombo == null) + { + return true; // fields not populated + } + + Condition cond = (Condition) condCombo.getSelectedItem(); + value.setBackground(Color.white); + value.setToolTipText(""); + String v1 = value.getText().trim(); + if (v1.length() == 0) + { + return false; + } + + if (cond.isNumeric()) + { + try + { + Float.valueOf(v1); + } catch (NumberFormatException e) + { + value.setBackground(Color.red); + value.setToolTipText(MessageManager + .getString("label.numeric_required")); + return false; + } + } + + return true; } // /////////////////////////////////////////////////////////////////////// @@ -1493,8 +1984,10 @@ public class FeatureSettings extends JPanel this.data = data; } - private String[] columnNames = - { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") }; + private String[] columnNames = { + MessageManager.getString("label.feature_type"), + MessageManager.getString("action.colour"), + MessageManager.getString("label.display") }; private Object[][] data; @@ -1508,6 +2001,7 @@ public class FeatureSettings extends JPanel this.data = data; } + @Override public int getColumnCount() { return columnNames.length; @@ -1518,31 +2012,37 @@ public class FeatureSettings extends JPanel return data[row]; } + @Override public int getRowCount() { return data.length; } + @Override public String getColumnName(int col) { return columnNames[col]; } + @Override public Object getValueAt(int row, int col) { return data[row][col]; } + @Override public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } + @Override public boolean isCellEditable(int row, int col) { return col == 0 ? false : true; } + @Override public void setValueAt(Object value, int row, int col) { data[row][col] = value; @@ -1567,43 +2067,33 @@ public class FeatureSettings extends JPanel 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 color, + boolean isSelected, boolean hasFocus, int row, int column) { - // JLabel comp = new JLabel(); - // comp. + FeatureColourI cellColour = (FeatureColourI) color; setOpaque(true); - // comp. - // setBounds(getBounds()); - Color newColor; setToolTipText(baseTT); - setBackground(table.getBackground()); - if (color instanceof GraduatedColor) + setBackground(tbl.getBackground()); + if (!cellColour.isSimpleColour()) { - Rectangle cr = table.getCellRect(row, column, false); - FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color, + Rectangle cr = tbl.getCellRect(row, column, false); + FeatureSettings.renderGraduatedColor(this, cellColour, (int) cr.getWidth(), (int) cr.getHeight()); - } else { this.setText(""); this.setIcon(null); - newColor = (Color) color; - // comp. - setBackground(newColor); - // comp.setToolTipText("RGB value: " + newColor.getRed() + ", " - // + newColor.getGreen() + ", " + newColor.getBlue()); + setBackground(cellColour.getColour()); } if (isSelected) { if (selectedBorder == null) { selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getSelectionBackground()); + tbl.getSelectionBackground()); } - // comp. setBorder(selectedBorder); } else @@ -1611,9 +2101,8 @@ public class FeatureSettings extends JPanel if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getBackground()); + tbl.getBackground()); } - // comp. setBorder(unselectedBorder); } @@ -1627,7 +2116,7 @@ public class FeatureSettings extends JPanel * @param comp * @param gcol */ - public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol) + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol) { int w = comp.getWidth(), h = comp.getHeight(); if (w < 20) @@ -1643,37 +2132,52 @@ public class FeatureSettings extends JPanel renderGraduatedColor(comp, gcol, w, h); } - public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol, + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol, int w, int h) { boolean thr = false; - String tt = ""; - String tx = ""; - if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) + 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 += ">"; - tt += "Thresholded (Above " + gcol.getThresh() + ") "; + tx.append(">"); + tt.append("Thresholded (Above ").append(gcol.getThreshold()) + .append(") "); } - if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD) + if (gcol.isBelowThreshold()) { thr = true; - tx += "<"; - tt += "Thresholded (Below " + gcol.getThresh() + ") "; + tx.append("<"); + tt.append("Thresholded (Below ").append(gcol.getThreshold()) + .append(") "); } if (gcol.isColourByLabel()) { - tt = "Coloured by label text. " + tt; + tt.append("Coloured by label text. ").append(tt); if (thr) { - tx += " "; + tx.append(" "); + } + if (!gcol.isColourByAttribute()) + { + tx.append("Label"); } - tx += "Label"; comp.setIcon(null); } else { - Color newColor = gcol.getMaxColor(); + Color newColor = gcol.getMaxColour(); comp.setBackground(newColor); // System.err.println("Width is " + w / 2); Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr); @@ -1684,16 +2188,17 @@ public class FeatureSettings extends JPanel // + ", " + minCol.getBlue() + ")"); } comp.setHorizontalAlignment(SwingConstants.CENTER); - comp.setText(tx); + comp.setText(tx.toString()); if (tt.length() > 0) { if (comp.getToolTipText() == null) { - comp.setToolTipText(tt); + comp.setToolTipText(tt.toString()); } else { - comp.setToolTipText(tt + " " + comp.getToolTipText()); + comp.setToolTipText(tt.append(" ").append(comp.getToolTipText()) + .toString()); } } } @@ -1701,7 +2206,7 @@ public class FeatureSettings extends JPanel class FeatureIcon implements Icon { - GraduatedColor gcol; + FeatureColourI gcol; Color backg; @@ -1713,7 +2218,7 @@ class FeatureIcon implements Icon Color mpcolour = Color.white; - FeatureIcon(GraduatedColor gfc, Color bg, int w, int h, boolean mspace) + FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace) { gcol = gfc; backg = bg; @@ -1732,16 +2237,19 @@ class FeatureIcon implements Icon } } + @Override public int getIconWidth() { return width; } + @Override public int getIconHeight() { return height; } + @Override public void paintIcon(Component c, Graphics g, int x, int y) { @@ -1750,7 +2258,7 @@ class FeatureIcon implements Icon g.setColor(backg); g.fillRect(0, 0, width, height); // need an icon here. - g.setColor(gcol.getMaxColor()); + g.setColor(gcol.getMaxColour()); g.setFont(new Font("Verdana", Font.PLAIN, 9)); @@ -1764,7 +2272,7 @@ class FeatureIcon implements Icon } else { - Color minCol = gcol.getMinColor(); + Color minCol = gcol.getMinColour(); g.setColor(minCol); g.fillRect(0, 0, s1, height); if (midspace) @@ -1772,25 +2280,23 @@ class FeatureIcon implements Icon g.setColor(Color.white); g.fillRect(s1, 0, e1 - s1, height); } - g.setColor(gcol.getMaxColor()); + g.setColor(gcol.getMaxColour()); g.fillRect(0, e1, width - e1, height); } } } -class ColorEditor extends AbstractCellEditor implements TableCellEditor, - ActionListener +class ColorEditor extends AbstractCellEditor + implements TableCellEditor, ActionListener { FeatureSettings me; - GraduatedColor currentGColor; + FeatureColourI currentColor; FeatureColourChooser chooser; String type; - Color currentColor; - JButton button; JColorChooser colorChooser; @@ -1814,7 +2320,8 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, button.setBorderPainted(false); // Set up the dialog that the button brings up. colorChooser = new JColorChooser(); - dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal + dialog = JColorChooser.createDialog(button, + MessageManager.getString("label.select_new_colour"), true, // modal colorChooser, this, // OK button handler null); // no CANCEL button handler } @@ -1822,6 +2329,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, /** * Handles events from the editor button and from the dialog's OK button. */ + @Override public void actionPerformed(ActionEvent e) { @@ -1829,11 +2337,11 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { // The user has clicked the cell, so // bring up the dialog. - if (currentColor != null) + if (currentColor.isSimpleColour()) { // bring up simple color chooser - button.setBackground(currentColor); - colorChooser.setColor(currentColor); + button.setBackground(currentColor.getColour()); + colorChooser.setColor(currentColor.getColour()); dialog.setVisible(true); } else @@ -1850,15 +2358,13 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, } else { // User pressed dialog's "OK" button. - if (currentColor != null) + if (currentColor.isSimpleColour()) { - currentColor = colorChooser.getColor(); + currentColor = new FeatureColour(colorChooser.getColor()); } else { - // class cast exceptions may be raised if the chooser created on a - // non-graduated color - currentGColor = (GraduatedColor) chooser.getLastColour(); + currentColor = chooser.getLastColour(); } me.table.setValueAt(getCellEditorValue(), selectedRow, 1); fireEditingStopped(); @@ -1867,31 +2373,27 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, } // Implement the one CellEditor method that AbstractCellEditor doesn't. + @Override public Object getCellEditorValue() { - if (currentColor == null) - { - return currentGColor; - } return currentColor; } // Implement the one method defined by TableCellEditor. + @Override public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row, int column) { - currentGColor = null; - currentColor = null; + currentColor = (FeatureColourI) value; this.selectedRow = row; type = me.table.getValueAt(row, 0).toString(); button.setOpaque(true); button.setBackground(me.getBackground()); - if (value instanceof GraduatedColor) + if (!currentColor.isSimpleColour()) { - currentGColor = (GraduatedColor) value; JLabel btn = new JLabel(); btn.setSize(button.getSize()); - FeatureSettings.renderGraduatedColor(btn, currentGColor); + FeatureSettings.renderGraduatedColor(btn, currentColor); button.setBackground(btn.getBackground()); button.setIcon(btn.getIcon()); button.setText(btn.getText()); @@ -1900,8 +2402,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { button.setText(""); button.setIcon(null); - currentColor = (Color) value; - button.setBackground(currentColor); + button.setBackground(currentColor.getColour()); } return button; }