X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=fedfe3fc851015f42cdd6490d54fe29b151d809e;hb=e16e9699b56f3db4e42dc694aaafad76dae66c4b;hp=151ae9b594e58b9c4146cd6db32f5aeabb20c5b5;hpb=6efcc6b872e24abc34363d37577eac99a8756614;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 151ae9b..fedfe3f 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,6 +20,11 @@ */ package jalview.gui; +import static jalview.viewmodel.seqfeatures.FeatureRendererModel.COLOUR_COLUMN; +import static jalview.viewmodel.seqfeatures.FeatureRendererModel.FILTER_COLUMN; +import static jalview.viewmodel.seqfeatures.FeatureRendererModel.SHOW_COLUMN; +import static jalview.viewmodel.seqfeatures.FeatureRendererModel.TYPE_COLUMN; + import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; import jalview.bin.Cache; @@ -34,7 +39,10 @@ import jalview.util.Format; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.QuickSort; +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; @@ -44,6 +52,7 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; import java.awt.GridLayout; +import java.awt.Point; import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; @@ -86,7 +95,6 @@ import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JScrollPane; import javax.swing.JSlider; -import javax.swing.JTabbedPane; import javax.swing.JTable; import javax.swing.ListSelectionModel; import javax.swing.SwingConstants; @@ -96,15 +104,24 @@ import javax.swing.event.ChangeListener; import javax.swing.table.AbstractTableModel; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; +import javax.swing.table.TableColumn; public class FeatureSettings extends JPanel implements FeatureSettingsControllerI { - DasSourceBrowser dassourceBrowser; + private static final int COLUMN_COUNT = 4; + + private static final String COLON = ":"; - jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher; + private static final int MIN_WIDTH = 400; + + 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(); @@ -112,10 +129,15 @@ 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(); @@ -126,29 +148,47 @@ public class FeatureSettings extends JPanel JSlider transparency = new JSlider(); - JPanel transPanel = new JPanel(new GridLayout(1, 2)); - - private static final int MIN_WIDTH = 400; - - private static final int MIN_HEIGHT = 400; - - /** + /* * when true, constructor is still executing - so ignore UI events */ protected volatile boolean inConstruction = true; + int selectedRow = -1; + + JButton fetchDAS = new JButton(); + + JButton saveDAS = new JButton(); + + JButton cancelDAS = new JButton(); + + boolean resettingTable = false; + + /* + * true when Feature Settings are updating from feature renderer + */ + private boolean handlingUpdate = false; + + /* + * holds {featureCount, totalExtent} for each feature type + */ + Map typeWidth = null; + /** * Constructor * * @param af */ - public FeatureSettings(AlignFrame af) + public FeatureSettings(AlignFrame alignFrame) { - this.af = af; + this.af = alignFrame; fr = af.getFeatureRenderer(); - // allow transparency to be recovered - transparency.setMaximum(100 - - (int) ((originalTransparency = fr.getTransparency()) * 100)); + + // save transparency for restore on Cancel + originalTransparency = fr.getTransparency(); + int originalTransparencyAsPercent = (int) (originalTransparency * 100); + transparency.setMaximum(100 - originalTransparencyAsPercent); + + originalFilters = fr.getFeatureFilters(); try { @@ -163,25 +203,48 @@ public class FeatureSettings extends JPanel @Override public String getToolTipText(MouseEvent e) { - if (table.columnAtPoint(e.getPoint()) == 0) + String tip = null; + int column = table.columnAtPoint(e.getPoint()); + switch (column) { - /* - * Tooltip for feature name only - */ - return JvSwingUtils.wrapTooltip(true, MessageManager + case TYPE_COLUMN: + tip = JvSwingUtils.wrapTooltip(true, MessageManager .getString("label.feature_settings_click_drag")); + break; + case FILTER_COLUMN: + int row = table.rowAtPoint(e.getPoint()); + KeyedMatcherSet o = (KeyedMatcherSet) table.getValueAt(row, + column); + tip = o.isEmpty() + ? MessageManager.getString("label.filters_tooltip") + : o.toString(); + break; + default: + break; } - return null; + return tip; } }; table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); table.setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setDefaultRenderer(Color.class, new ColorRenderer()); - - table.setDefaultEditor(Color.class, new ColorEditor(this)); + // table.setDefaultRenderer(Color.class, new ColorRenderer()); + // table.setDefaultEditor(Color.class, new ColorEditor(this)); + // table.setDefaultEditor(FeatureColour.class, new ColorEditor(this)); table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); + + table.setDefaultEditor(KeyedMatcherSet.class, new FilterEditor(this)); + table.setDefaultRenderer(KeyedMatcherSet.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() @@ -190,11 +253,12 @@ public class FeatureSettings extends JPanel public void mousePressed(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); + String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); if (evt.isPopupTrigger()) { - popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), - table.getValueAt(selectedRow, 1), fr.getMinMax(), - evt.getX(), evt.getY()); + Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); + popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(), + evt.getY()); } else if (evt.getClickCount() == 2) { @@ -202,8 +266,7 @@ public class FeatureSettings extends JPanel boolean toggleSelection = Platform.isControlDown(evt); boolean extendSelection = evt.isShiftDown(); fr.ap.alignFrame.avc.markColumnsContainingFeatures( - invertSelection, extendSelection, toggleSelection, - (String) table.getValueAt(selectedRow, 0)); + invertSelection, extendSelection, toggleSelection, type); } } @@ -214,9 +277,10 @@ public class FeatureSettings extends JPanel selectedRow = table.rowAtPoint(evt.getPoint()); if (evt.isPopupTrigger()) { - popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), - table.getValueAt(selectedRow, 1), fr.getMinMax(), - evt.getX(), evt.getY()); + 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()); } } }); @@ -272,8 +336,8 @@ public class FeatureSettings extends JPanel if (!fs.resettingTable && !fs.handlingUpdate) { fs.handlingUpdate = true; - fs.resetTable(null); // new groups may be added with new seuqence - // feature types only + fs.resetTable(null); + // new groups may be added with new sequence feature types only fs.handlingUpdate = false; } } @@ -286,13 +350,13 @@ public class FeatureSettings extends JPanel { 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)); @@ -311,7 +375,7 @@ public class FeatureSettings extends JPanel inConstruction = false; } - protected void popupSort(final int selectedRow, final String type, + protected void popupSort(final int rowSelected, final String type, final Object typeCol, final Map minmax, int x, int y) { @@ -351,84 +415,70 @@ public class FeatureSettings extends JPanel }); 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 float[][] typeMinMax = minmax.get(type); - /* - * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); // - * this is broken at the moment and isn't that useful anyway! - * chb.setSelected(minmax.get(type) != null); chb.addActionListener(new - * ActionListener() { - * - * public void actionPerformed(ActionEvent e) { - * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type, - * null); } else { minmax.put(type, typeMinMax); } } - * - * }); - * - * men.add(chb); - */ - if (typeMinMax != null && typeMinMax[0] != null) - { - // if (table.getValueAt(row, column)); - // graduated colourschemes for those where minmax exists for the - // positional features - final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( - "Graduated Colour"); - mxcol.setSelected(!featureColour.isSimpleColour()); - men.add(mxcol); - mxcol.addActionListener(new ActionListener() - { - JColorChooser colorChooser; + JColorChooser colorChooser; - @Override - public void actionPerformed(ActionEvent e) + @Override + public void actionPerformed(ActionEvent e) + { + if (e.getSource() == mxcol) + { + if (featureColour.isSimpleColour()) { - if (e.getSource() == mxcol) - { - if (featureColour.isSimpleColour()) - { - FeatureColourChooser fc = new FeatureColourChooser(me.fr, - type); - fc.addActionListener(this); - } - else - { - // bring up simple color chooser - colorChooser = new JColorChooser(); - JDialog dialog = JColorChooser.createDialog(me, - "Select new Colour", true, // modal - colorChooser, this, // OK button handler - null); // no CANCEL button handler - colorChooser.setColor(featureColour.getMaxColour()); - dialog.setVisible(true); - } - } - else - { - if (e.getSource() instanceof FeatureColourChooser) - { - FeatureColourChooser fc = (FeatureColourChooser) e - .getSource(); - table.setValueAt(fc.getLastColour(), selectedRow, 1); - table.validate(); - } - else - { - // probably the color chooser! - table.setValueAt(new FeatureColour(colorChooser.getColor()), - selectedRow, 1); - table.validate(); - me.updateFeatureRenderer( - ((FeatureTableModel) table.getModel()).getData(), - false); - } - } + FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type); + fc.addActionListener(this); } - - }); + else + { + // bring up simple color chooser + colorChooser = new JColorChooser(); + String title = MessageManager + .getString("label.select_colour"); + JDialog dialog = JColorChooser.createDialog(me, + title, true, // modal + colorChooser, this, // OK button handler + null); // no CANCEL button handler + colorChooser.setColor(featureColour.getMaxColour()); + dialog.setVisible(true); + } + } + else + { + if (e.getSource() instanceof FeatureTypeSettings) + { + /* + * update after OK in feature colour dialog; the updated + * colour will have already been set in the FeatureRenderer + */ + FeatureColourI fci = fr.getFeatureColours().get(type); + table.setValueAt(fci, rowSelected, 1); + table.validate(); + } + else + { + // probably the color chooser! + table.setValueAt(new FeatureColour(colorChooser.getColor()), + rowSelected, 1); + table.validate(); + me.updateFeatureRenderer( + ((FeatureTableModel) table.getModel()).getData(), + false); + } + } } - } + + }); + JMenuItem selCols = new JMenuItem( MessageManager.getString("label.select_columns_containing")); selCols.addActionListener(new ActionListener() @@ -478,20 +528,10 @@ public class FeatureSettings extends JPanel men.show(table, x, y); } - /** - * true when Feature Settings are updating from feature renderer - */ - private boolean handlingUpdate = false; - - /** - * holds {featureCount, totalExtent} for each feature type - */ - Map typeWidth = null; - @Override synchronized public void discoverAllFeatureData() { - Set allGroups = new HashSet(); + Set allGroups = new HashSet<>(); AlignmentI alignment = af.getViewport().getAlignment(); for (int i = 0; i < alignment.getHeight(); i++) @@ -541,21 +581,14 @@ public class FeatureSettings extends JPanel public void itemStateChanged(ItemEvent evt) { fr.setGroupVisibility(check.getText(), check.isSelected()); - af.alignPanel.getSeqPanel().seqCanvas.repaint(); - if (af.alignPanel.overviewPanel != null) - { - af.alignPanel.overviewPanel.updateOverviewImage(); - } - resetTable(new String[] { grp }); + af.alignPanel.paintAlignment(true, true); } }); groupPanel.add(check); return visible; } - boolean resettingTable = false; - synchronized void resetTable(String[] groupChanged) { if (resettingTable) @@ -563,12 +596,12 @@ public class FeatureSettings extends JPanel return; } resettingTable = true; - typeWidth = new Hashtable(); + 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(); + Set displayableTypes = new HashSet<>(); + Set foundGroups = new HashSet<>(); /* * determine which feature types may be visible depending on @@ -584,7 +617,7 @@ public class FeatureSettings extends JPanel * and keep track of which groups are visible */ Set groups = seq.getFeatures().getFeatureGroups(true); - Set visibleGroups = new HashSet(); + Set visibleGroups = new HashSet<>(); for (String group : groups) { if (group == null || checkGroupState(group)) @@ -618,7 +651,8 @@ public class FeatureSettings extends JPanel } } - Object[][] data = new Object[displayableTypes.size()][3]; + int columnCount = COLUMN_COUNT; + Object[][] data = new Object[displayableTypes.size()][columnCount]; int dataIndex = 0; if (fr.hasRenderOrder()) @@ -641,9 +675,13 @@ public class FeatureSettings extends JPanel continue; } - data[dataIndex][0] = type; - data[dataIndex][1] = fr.getFeatureStyle(type); - data[dataIndex][2] = new Boolean( + data[dataIndex][TYPE_COLUMN] = type; + data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); + KeyedMatcherSetI featureFilter = fr.getFeatureFilter(type); + data[dataIndex][FILTER_COLUMN] = featureFilter == null + ? new KeyedMatcherSet() + : featureFilter; + data[dataIndex][SHOW_COLUMN] = new Boolean( af.getViewport().getFeaturesDisplayed().isVisible(type)); dataIndex++; displayableTypes.remove(type); @@ -657,27 +695,31 @@ public class FeatureSettings extends JPanel while (!displayableTypes.isEmpty()) { String type = displayableTypes.iterator().next(); - data[dataIndex][0] = type; + data[dataIndex][TYPE_COLUMN] = type; - data[dataIndex][1] = fr.getFeatureStyle(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.clearRenderOrder(); return; } - - data[dataIndex][2] = new Boolean(true); + KeyedMatcherSetI featureFilter = fr.getFeatureFilter(type); + data[dataIndex][FILTER_COLUMN] = featureFilter == null + ? new KeyedMatcherSet() + : featureFilter; + data[dataIndex][SHOW_COLUMN] = new Boolean(true); dataIndex++; displayableTypes.remove(type); } if (originalData == null) { - originalData = new Object[data.length][3]; + int size = data[0].length; + originalData = new Object[data.length][size]; for (int i = 0; i < data.length; i++) { - System.arraycopy(data[i], 0, originalData[i], 0, 3); + System.arraycopy(data[i], 0, originalData[i], 0, size); } } else @@ -698,8 +740,8 @@ public class FeatureSettings extends JPanel } /** - * Updates 'originalData' (used for restore on Cancel) if we detect that - * changes have been made outwith this dialog + * 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)
    • @@ -715,27 +757,27 @@ public class FeatureSettings extends JPanel .getData(); for (Object[] row : foundData) { - String type = (String) row[0]; + String type = (String) row[TYPE_COLUMN]; boolean found = false; for (Object[] current : currentData) { - if (type.equals(current[0])) + if (type.equals(current[TYPE_COLUMN])) { found = true; /* * currently dependent on object equality here; * really need an equals method on FeatureColour */ - if (!row[1].equals(current[1])) + if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN])) { /* * feature colour has changed externally - update originalData */ for (Object[] original : originalData) { - if (type.equals(original[0])) + if (type.equals(original[TYPE_COLUMN])) { - original[1] = row[1]; + original[COLOUR_COLUMN] = row[COLOUR_COLUMN]; break; } } @@ -748,10 +790,11 @@ public class FeatureSettings extends JPanel /* * new feature detected - add to original data (on top) */ - Object[][] newData = new Object[originalData.length + 1][3]; + int size = currentData[0].length; + Object[][] newData = new Object[originalData.length + 1][size]; for (int i = 0; i < originalData.length; i++) { - System.arraycopy(originalData[i], 0, newData[i + 1], 0, 3); + System.arraycopy(originalData[i], 0, newData[i + 1], 0, size); } newData[0] = row; originalData = newData; @@ -761,8 +804,8 @@ public class FeatureSettings extends JPanel /** * 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. + * foundGroups set. This enables removing a group from the display when the last + * feature in that group is deleted. * * @param foundGroups */ @@ -968,9 +1011,9 @@ public class FeatureSettings extends JPanel { for (int i = 0; i < table.getRowCount(); i++) { - Boolean value = (Boolean) table.getValueAt(i, 2); + Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN); - table.setValueAt(new Boolean(!value.booleanValue()), i, 2); + table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN); } } @@ -984,17 +1027,16 @@ public class FeatureSettings extends JPanel float[] width = new float[data.length]; float[] awidth; float max = 0; - int num = 0; + for (int i = 0; i < data.length; i++) { - awidth = typeWidth.get(data[i][0]); + 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. - num++; } else { @@ -1011,16 +1053,17 @@ public class FeatureSettings extends JPanel // awidth = (float[]) typeWidth.get(data[i][0]); if (width[i] == 0) { - width[i] = fr.getOrder(data[i][0].toString()); + width[i] = fr.getOrder(data[i][TYPE_COLUMN].toString()); if (width[i] < 0) { - width[i] = fr.setOrder(data[i][0].toString(), i / data.length); + width[i] = fr.setOrder(data[i][TYPE_COLUMN].toString(), + i / data.length); } } else { width[i] /= max; // normalize - fr.setOrder(data[i][0].toString(), width[i]); // store for later + fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later } if (i > 0) { @@ -1054,8 +1097,8 @@ public class FeatureSettings extends JPanel } /** - * Update the priority order of features; only repaint if this changed the - * order of visible features + * Update the priority order of features; only repaint if this changed the order + * of visible features * * @param data * @param visibleNew @@ -1064,66 +1107,28 @@ public class FeatureSettings extends JPanel { if (fr.setFeaturePriority(data, visibleNew)) { - af.alignPanel.paintAlignment(true); + 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(); - - JButton optimizeOrder = new JButton(); - - JButton sortByScore = new JButton(); - - JButton sortByDens = new JButton(); + private void jbInit() throws Exception + { + this.setLayout(new BorderLayout()); - JButton help = new JButton(); + JPanel settingsPane = new JPanel(); + settingsPane.setLayout(new BorderLayout()); - JPanel transbuttons = new JPanel(new GridLayout(5, 1)); + dasSettingsPane.setLayout(new BorderLayout()); - private void jbInit() throws Exception - { - this.setLayout(borderLayout1); - settingsPane.setLayout(borderLayout2); - dasSettingsPane.setLayout(borderLayout3); - bigPanel.setLayout(borderLayout4); + 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.setText(MessageManager.getString("label.invert_selection")); invert.addActionListener(new ActionListener() { @Override @@ -1132,8 +1137,10 @@ public class FeatureSettings extends JPanel 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 @@ -1142,9 +1149,10 @@ public class FeatureSettings extends JPanel 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 @@ -1153,9 +1161,9 @@ public class FeatureSettings extends JPanel af.avc.sortAlignmentByFeatureScore(null); } }); - sortByDens.setFont(JvSwingUtils.getLabelFont()); - sortByDens.setText( + JButton sortByDens = new JButton( MessageManager.getString("label.sequence_sort_by_density")); + sortByDens.setFont(JvSwingUtils.getLabelFont()); sortByDens.addActionListener(new ActionListener() { @Override @@ -1164,8 +1172,9 @@ public class FeatureSettings extends JPanel af.avc.sortAlignmentByFeatureDensity(null); } }); + + JButton help = new JButton(MessageManager.getString("action.help")); help.setFont(JvSwingUtils.getLabelFont()); - help.setText(MessageManager.getString("action.help")); help.addActionListener(new ActionListener() { @Override @@ -1196,20 +1205,23 @@ 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 @@ -1218,8 +1230,10 @@ public class FeatureSettings extends JPanel 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 @@ -1228,8 +1242,10 @@ public class FeatureSettings extends JPanel 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 @@ -1243,11 +1259,10 @@ public class FeatureSettings extends JPanel @Override public void stateChanged(ChangeEvent evt) { - fr.setTransparency((100 - transparency.getValue()) / 100f); if (!inConstruction) { fr.setTransparency((100 - transparency.getValue()) / 100f); - af.alignPanel.paintAlignment(true); + af.alignPanel.paintAlignment(true, true); } } }); @@ -1273,6 +1288,8 @@ public class FeatureSettings extends JPanel saveDAS_actionPerformed(e); } }); + + JPanel dasButtonPanel = new JPanel(); dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); dasSettingsPane.setBorder(null); cancelDAS.setEnabled(false); @@ -1285,32 +1302,32 @@ public class FeatureSettings extends JPanel 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); + + 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); + this.add(settingsPane); } public void fetchDAS_actionPerformed(ActionEvent e) @@ -1475,18 +1492,20 @@ public class FeatureSettings extends JPanel // /////////////////////////////////////////////////////////////////////// class FeatureTableModel extends AbstractTableModel { - FeatureTableModel(Object[][] data) - { - this.data = data; - } private String[] columnNames = { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), - MessageManager.getString("label.display") }; + MessageManager.getString("label.filter"), + MessageManager.getString("label.show") }; private Object[][] data; + FeatureTableModel(Object[][] data) + { + this.data = data; + } + public Object[][] getData() { return data; @@ -1526,10 +1545,14 @@ public class FeatureSettings extends JPanel return data[row][col]; } + /** + * Answers the class of the object in column c of the first row of the table + */ @Override - public Class getColumnClass(int c) + public Class getColumnClass(int c) { - return getValueAt(0, c).getClass(); + Object v = getValueAt(0, c); + return v == null ? null : v.getClass(); } @Override @@ -1568,12 +1591,7 @@ public class FeatureSettings extends JPanel boolean isSelected, boolean hasFocus, int row, int column) { FeatureColourI cellColour = (FeatureColourI) color; - // JLabel comp = new JLabel(); - // comp. setOpaque(true); - // comp. - // setBounds(getBounds()); - Color newColor; setToolTipText(baseTT); setBackground(tbl.getBackground()); if (!cellColour.isSimpleColour()) @@ -1581,15 +1599,61 @@ public class FeatureSettings extends JPanel Rectangle cr = tbl.getCellRect(row, column, false); FeatureSettings.renderGraduatedColor(this, cellColour, (int) cr.getWidth(), (int) cr.getHeight()); - } else { this.setText(""); this.setIcon(null); - newColor = cellColour.getColour(); - setBackground(newColor); + setBackground(cellColour.getColour()); + } + if (isSelected) + { + if (selectedBorder == null) + { + selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + tbl.getSelectionBackground()); + } + setBorder(selectedBorder); + } + else + { + if (unselectedBorder == null) + { + unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + tbl.getBackground()); + } + setBorder(unselectedBorder); } + + return this; + } + } + + class FilterRenderer extends JLabel implements TableCellRenderer + { + javax.swing.border.Border unselectedBorder = null; + + javax.swing.border.Border selectedBorder = null; + + public FilterRenderer() + { + setOpaque(true); // MUST do this for background to show up. + setHorizontalTextPosition(SwingConstants.CENTER); + setVerticalTextPosition(SwingConstants.CENTER); + } + + @Override + public Component getTableCellRendererComponent(JTable tbl, + Object filter, boolean isSelected, boolean hasFocus, int row, + int column) + { + KeyedMatcherSetI theFilter = (KeyedMatcherSetI) filter; + setOpaque(true); + String asText = theFilter.toString(); + setBackground(tbl.getBackground()); + this.setText(asText); + this.setIcon(null); + if (isSelected) { if (selectedBorder == null) @@ -1639,28 +1703,43 @@ public class FeatureSettings extends JPanel int w, int h) { boolean thr = false; - String tt = ""; - String tx = ""; + 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.getThreshold() + ") "; + tx.append(">"); + tt.append("Thresholded (Above ").append(gcol.getThreshold()) + .append(") "); } if (gcol.isBelowThreshold()) { thr = true; - tx += "<"; - tt += "Thresholded (Below " + gcol.getThreshold() + ") "; + 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 @@ -1676,19 +1755,259 @@ 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()); } } } + + 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); + chooser.setRequestFocusEnabled(true); + chooser.requestFocus(); + chooser.addActionListener(this); + chooser.showTab(true); + } + // 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); + KeyedMatcherSetI currentFilter = me.fr.getFeatureFilter(type); + if (currentFilter == null) + { + currentFilter = new KeyedMatcherSet(); + } + Object[] data = ((FeatureTableModel) table.getModel()) + .getData()[rowSelected]; + data[COLOUR_COLUMN] = currentColor; + data[FILTER_COLUMN] = currentFilter; + } + fireEditingStopped(); + me.table.validate(); + } + } + + // Implement the one CellEditor method that AbstractCellEditor doesn't. + @Override + public Object getCellEditorValue() + { + return currentColor; + } + + // Implement the one method defined by TableCellEditor. + @Override + public Component getTableCellEditorComponent(JTable theTable, Object value, + boolean isSelected, int row, int column) + { + currentColor = (FeatureColourI) value; + this.rowSelected = row; + type = me.table.getValueAt(row, TYPE_COLUMN).toString(); + button.setOpaque(true); + button.setBackground(me.getBackground()); + if (!currentColor.isSimpleColour()) + { + JLabel btn = new JLabel(); + btn.setSize(button.getSize()); + FeatureSettings.renderGraduatedColor(btn, currentColor); + button.setBackground(btn.getBackground()); + button.setIcon(btn.getIcon()); + button.setText(btn.getText()); + } + else + { + button.setText(""); + button.setIcon(null); + button.setBackground(currentColor.getColour()); + } + return button; + } + } + + /** + * The cell editor for the Filter column. It displays the text of any filters + * for the feature type in that row (in full as a tooltip, possible abbreviated + * as display text). On click in the cell, opens the Feature Display Settings + * dialog at the Filters tab. + */ + class FilterEditor extends AbstractCellEditor + implements TableCellEditor, ActionListener + { + FeatureSettings me; + + KeyedMatcherSetI 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(); + } + chooser.showTab(false); + 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 KeyedMatcherSet(); + } + 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 = (KeyedMatcherSetI) value; + this.rowSelected = row; + type = me.table.getValueAt(row, TYPE_COLUMN).toString(); + button.setOpaque(true); + button.setBackground(me.getBackground()); + button.setText(currentFilter.toString()); + button.setToolTipText(currentFilter.toString()); + button.setIcon(null); + return button; + } + } } class FeatureIcon implements Icon @@ -1772,124 +2091,3 @@ class FeatureIcon implements Icon } } } - -class ColorEditor extends AbstractCellEditor - implements TableCellEditor, ActionListener -{ - FeatureSettings me; - - FeatureColourI currentColor; - - FeatureColourChooser chooser; - - String type; - - JButton button; - - JColorChooser colorChooser; - - JDialog dialog; - - protected static final String EDIT = "edit"; - - int selectedRow = 0; - - public ColorEditor(FeatureSettings me) - { - this.me = me; - // Set up the editor (from the table's point of view), - // which is a button. - // This button brings up the color chooser dialog, - // which is the editor from the user's point of view. - button = new JButton(); - button.setActionCommand(EDIT); - button.addActionListener(this); - button.setBorderPainted(false); - // Set up the dialog that the button brings up. - colorChooser = new JColorChooser(); - dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal - colorChooser, this, // OK button handler - null); // no CANCEL button handler - } - - /** - * Handles events from the editor button and from the dialog's OK button. - */ - @Override - public void actionPerformed(ActionEvent e) - { - - if (EDIT.equals(e.getActionCommand())) - { - // The user has clicked the cell, so - // bring up the dialog. - if (currentColor.isSimpleColour()) - { - // bring up simple color chooser - button.setBackground(currentColor.getColour()); - colorChooser.setColor(currentColor.getColour()); - dialog.setVisible(true); - } - else - { - // bring up graduated chooser. - chooser = new FeatureColourChooser(me.fr, type); - chooser.setRequestFocusEnabled(true); - chooser.requestFocus(); - chooser.addActionListener(this); - } - // Make the renderer reappear. - fireEditingStopped(); - - } - else - { // User pressed dialog's "OK" button. - if (currentColor.isSimpleColour()) - { - currentColor = new FeatureColour(colorChooser.getColor()); - } - else - { - currentColor = chooser.getLastColour(); - } - me.table.setValueAt(getCellEditorValue(), selectedRow, 1); - fireEditingStopped(); - me.table.validate(); - } - } - - // Implement the one CellEditor method that AbstractCellEditor doesn't. - @Override - public Object getCellEditorValue() - { - return currentColor; - } - - // Implement the one method defined by TableCellEditor. - @Override - public Component getTableCellEditorComponent(JTable table, Object value, - boolean isSelected, int row, int column) - { - currentColor = (FeatureColourI) value; - this.selectedRow = row; - type = me.table.getValueAt(row, 0).toString(); - button.setOpaque(true); - button.setBackground(me.getBackground()); - if (!currentColor.isSimpleColour()) - { - JLabel btn = new JLabel(); - btn.setSize(button.getSize()); - FeatureSettings.renderGraduatedColor(btn, currentColor); - button.setBackground(btn.getBackground()); - button.setIcon(btn.getIcon()); - button.setText(btn.getText()); - } - else - { - button.setText(""); - button.setIcon(null); - button.setBackground(currentColor.getColour()); - } - return button; - } -}