X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=d724b8c51dd6809402dd4cb85b9f881bf2140742;hb=baa077bd19420018433d78927aad3ad139e47351;hp=cf7bdb3cc8949e907f380bd3bc05aa894f191ec8;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index cf7bdb3..d724b8c 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -23,28 +23,41 @@ package jalview.gui; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; import jalview.bin.Cache; -import jalview.datamodel.SequenceFeature; +import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.FeatureAttributes; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; import jalview.schemabinding.version2.JalviewUserColours; import jalview.schemes.FeatureColour; import jalview.util.Format; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.QuickSort; +import jalview.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.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; @@ -58,6 +71,9 @@ import java.io.FileOutputStream; 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; @@ -68,40 +84,47 @@ import java.util.Vector; import javax.help.HelpSetException; import javax.swing.AbstractCellEditor; import javax.swing.BorderFactory; +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 +public class FeatureSettings extends JPanel + implements FeatureSettingsControllerI { - DasSourceBrowser dassourceBrowser; + private static final int MIN_WIDTH = 400; + + private static final int MIN_HEIGHT = 400; - jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher; + DasSourceBrowser dassourceBrowser; - JPanel settingsPane = new JPanel(); + DasSequenceFeatureFetcher dasFeatureFetcher; JPanel dasSettingsPane = new JPanel(); @@ -109,10 +132,15 @@ public class FeatureSettings extends JPanel implements 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(); @@ -122,16 +150,68 @@ public class FeatureSettings extends JPanel implements JPanel groupPanel; JSlider transparency = new JSlider(); + + /* + * when true, constructor is still executing - so ignore UI events + */ + protected volatile boolean inConstruction = true; - JPanel transPanel = new JPanel(new GridLayout(1, 2)); + int selectedRow = -1; + + JButton fetchDAS = new JButton(); - public FeatureSettings(AlignFrame af) + 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; + + private JComboBox filteredFeatureChoice; + + private JRadioButton andFilters; + + private JRadioButton orFilters; + + /* + * filters for the currently selected feature type + */ + private List filters; + + private JTextArea filtersAsText; + + /** + * Constructor + * + * @param 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 { @@ -173,7 +253,7 @@ public class FeatureSettings extends JPanel implements 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.getMinMax(), @@ -181,14 +261,16 @@ public class FeatureSettings extends JPanel implements } 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) { @@ -210,19 +292,22 @@ public class FeatureSettings extends JPanel implements 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; } } @@ -264,36 +349,40 @@ public class FeatureSettings extends JPanel implements { 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() - { - @Override - 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 row, final String type, + protected void popupSort(final int selectedRow, final String type, final Object typeCol, final Map minmax, int x, int y) { final FeatureColourI featureColour = (FeatureColourI) typeCol; - JPopupMenu men = new JPopupMenu(MessageManager.formatMessage( - "label.settings_for_param", new String[] { type })); + JPopupMenu men = new JPopupMenu(MessageManager + .formatMessage("label.settings_for_param", new String[] + { type })); JMenuItem scr = new JMenuItem( MessageManager.getString("label.sort_by_score")); men.add(scr); @@ -304,7 +393,9 @@ public class FeatureSettings extends JPanel implements @Override public void actionPerformed(ActionEvent e) { - me.af.avc.sortAlignmentByFeatureScore(new String[] { type }); + me.af.avc + .sortAlignmentByFeatureScore(Arrays.asList(new String[] + { type })); } }); @@ -316,7 +407,9 @@ public class FeatureSettings extends JPanel implements @Override public void actionPerformed(ActionEvent e) { - me.af.avc.sortAlignmentByFeatureDensity(new String[] { type }); + me.af.avc + .sortAlignmentByFeatureDensity(Arrays.asList(new String[] + { type })); } }); @@ -380,13 +473,14 @@ public class FeatureSettings extends JPanel implements { FeatureColourChooser fc = (FeatureColourChooser) e .getSource(); - table.setValueAt(fc.getLastColour(), row, 1); + table.setValueAt(fc.getLastColour(), selectedRow, 1); table.validate(); } else { // probably the color chooser! - table.setValueAt(colorChooser.getColor(), row, 1); + table.setValueAt(new FeatureColour(colorChooser.getColor()), + selectedRow, 1); table.validate(); me.updateFeatureRenderer( ((FeatureTableModel) table.getModel()).getData(), @@ -402,7 +496,6 @@ public class FeatureSettings extends JPanel implements MessageManager.getString("label.select_columns_containing")); selCols.addActionListener(new ActionListener() { - @Override public void actionPerformed(ActionEvent arg0) { @@ -410,11 +503,10 @@ public class FeatureSettings extends JPanel implements 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) { @@ -422,64 +514,54 @@ public class FeatureSettings extends JPanel implements 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 - */ - Map typeWidth = null; - @Override synchronized public void discoverAllFeatureData() { - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); - SequenceFeature[] tmpfeatures; - String group; - for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) - { - tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) - .getSequenceFeatures(); - if (tmpfeatures == null) - { - continue; - } + 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); - 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(); @@ -495,124 +577,96 @@ public class FeatureSettings extends JPanel implements { 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 visible; - } final String grp = group; final JCheckBox check = new JCheckBox(group, visible); check.setFont(new Font("Serif", Font.BOLD, 12)); + check.setToolTipText(group); check.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent evt) { fr.setGroupVisibility(check.getText(), check.isSelected()); - af.alignPanel.getSeqPanel().seqCanvas.repaint(); - if (af.alignPanel.overviewPanel != null) - { - af.alignPanel.overviewPanel.updateOverviewImage(); - } - resetTable(new String[] { grp }); + af.alignPanel.paintAlignment(true, true); } }); groupPanel.add(check); 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) - .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) - { - index++; - continue; - } - 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 = typeWidth.get(tmpfeatures[index].getType()); - } - avWidth[0]++; - if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd()) - { - avWidth[1] += 1 + tmpfeatures[index].getBegin() - - tmpfeatures[index].getEnd(); + visibleGroups.add(group); } - else + } + foundGroups.addAll(groups); + + /* + * get distinct feature types for visible groups + * record distinct visible types, and their count and total length + */ + Set types = seq.getFeatures().getFeatureTypesForGroups(true, + visibleGroups.toArray(new String[visibleGroups.size()])); + for (String type : types) + { + displayableTypes.add(type); + float[] avWidth = typeWidth.get(type); + if (avWidth == null) { - avWidth[1] += 1 + tmpfeatures[index].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.hasRenderOrder()) @@ -628,28 +682,29 @@ public class FeatureSettings extends JPanel implements List frl = fr.getRenderOrder(); for (int ro = frl.size() - 1; ro > -1; ro--) { - type = frl.get(ro); + String type = frl.get(ro); - if (!visibleChecks.contains(type)) + if (!displayableTypes.contains(type)) { continue; } data[dataIndex][0] = type; data[dataIndex][1] = fr.getFeatureStyle(type); - data[dataIndex][2] = new Boolean(af.getViewport() - .getFeaturesDisplayed().isVisible(type)); + data[dataIndex][2] = new Boolean( + 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); @@ -662,6 +717,7 @@ public class FeatureSettings extends JPanel implements data[dataIndex][2] = new Boolean(true); dataIndex++; + displayableTypes.remove(type); } if (originalData == null) @@ -672,24 +728,105 @@ public class FeatureSettings extends JPanel implements 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.getFeatureGroupsSize() / 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 @@ -718,14 +855,11 @@ public class FeatureSettings extends JPanel implements void load() { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - new String[] { "fc" }, - new String[] { "Sequence Feature Colours" }, + JalviewFileChooser chooser = new JalviewFileChooser("fc", "Sequence Feature Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.load_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); @@ -736,8 +870,8 @@ public class FeatureSettings extends JPanel implements try { - InputStreamReader in = new InputStreamReader(new FileInputStream( - file), "UTF-8"); + InputStreamReader in = new InputStreamReader( + new FileInputStream(file), "UTF-8"); JalviewUserColours jucs = JalviewUserColours.unmarshal(in); @@ -813,14 +947,11 @@ public class FeatureSettings extends JPanel implements void save() { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - new String[] { "fc" }, - new String[] { "Sequence Feature Colours" }, + JalviewFileChooser chooser = new JalviewFileChooser("fc", "Sequence Feature Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.save_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); @@ -862,13 +993,13 @@ public class FeatureSettings extends JPanel implements col.setRGB(Format.getHexString(fcol.getMaxColour())); col.setMin(fcol.getMin()); col.setMax(fcol.getMax()); - col.setMinRGB(jalview.util.Format.getHexString(fcol - .getMinColour())); + 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")); + col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" + : (fcol.isBelowThreshold() ? "BELOW" : "NONE")); } ucs.addColour(col); } @@ -970,64 +1101,41 @@ public class FeatureSettings extends JPanel implements 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 @@ -1036,8 +1144,10 @@ public class FeatureSettings extends JPanel implements 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 @@ -1046,9 +1156,10 @@ public class FeatureSettings extends JPanel implements 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 @@ -1057,9 +1168,9 @@ public class FeatureSettings extends JPanel implements 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 @@ -1068,8 +1179,9 @@ public class FeatureSettings extends JPanel implements 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 @@ -1100,20 +1212,23 @@ public class FeatureSettings extends JPanel implements } } }); + + 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 @@ -1122,8 +1237,10 @@ public class FeatureSettings extends JPanel implements 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 @@ -1132,8 +1249,10 @@ public class FeatureSettings extends JPanel implements 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 @@ -1147,14 +1266,17 @@ public class FeatureSettings extends JPanel implements @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() { @@ -1173,6 +1295,8 @@ public class FeatureSettings extends JPanel implements saveDAS_actionPerformed(e); } }); + + JPanel dasButtonPanel = new JPanel(); dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); dasSettingsPane.setBorder(null); cancelDAS.setEnabled(false); @@ -1185,32 +1309,455 @@ public class FeatureSettings extends JPanel implements cancelDAS_actionPerformed(e); } }); - this.add(tabbedPane, java.awt.BorderLayout.CENTER); + + JTabbedPane tabbedPane = new JTabbedPane(); + this.add(tabbedPane, 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); + 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); + + initFiltersTab(); + } + + /** + * Populates initial layout of the feature attribute filters panel + */ + protected void initFiltersTab() + { + filters = new ArrayList<>(); + + /* + * choose feature type + */ + JPanel chooseTypePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + chooseTypePanel.setBackground(Color.white); + chooseTypePanel.setBorder(BorderFactory + .createTitledBorder(MessageManager + .getString("label.feature_type"))); + filteredFeatureChoice = new JComboBox<>(); + filteredFeatureChoice.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + refreshFiltersDisplay(); + } + }); + 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(new GridLayout(0, 1)); + filtersPanel.setBackground(Color.white); + filtersPanel.setBorder(BorderFactory + .createTitledBorder(MessageManager.getString("label.filters"))); + + /* + * add AND or OR radio buttons + */ + JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + andOrPanel.setBackground(Color.white); + andFilters = new JRadioButton("And"); + orFilters = new JRadioButton("Or"); + ActionListener actionListener = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + filtersChanged(); + } + }; + 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(new GridLayout(0, 1)); + filtersPanel.add(chooseFiltersPanel); + + /* + * a read-only text view of the current filters + */ + JPanel showFiltersPanel = new JPanel(new BorderLayout(5, 5)); + showFiltersPanel.setBackground(Color.white); + showFiltersPanel.setBorder(BorderFactory + .createTitledBorder(MessageManager + .getString("label.match_condition"))); + filtersAsText = new JTextArea(); + filtersAsText.setLineWrap(true); + filtersAsText.setWrapStyleWord(true); + 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()); + + boolean found = false; + while (types.hasNext()) + { + String type = types.next(); + if (FeatureAttributes.getInstance().hasAttributes(type)) + { + filteredFeatureChoice.addItem(type); + found = true; + } + } + if (!found) + { + filteredFeatureChoice + .addItem("No filterable feature attributes known"); + } + + filteredFeatureChoice.addItemListener(listener); + + } + + /** + * 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() + { + /* + * clear the panel and list of filter conditions + */ + chooseFiltersPanel.removeAll(); + + String selectedType = (String) filteredFeatureChoice.getSelectedItem(); + + filters.clear(); + + /* + * look up attributes known for feature type + */ + 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); + } + Iterator matchers = featureFilters.getMatchers(); + while (matchers.hasNext()) + { + filters.add(matchers.next()); + } + } + + /* + * and an empty filter for the user to populate (add) + */ + KeyedMatcherI noFilter = new KeyedMatcher("", Condition.values()[0], ""); + filters.add(noFilter); + + /* + * render the conditions in rows, each in its own JPanel + */ + int i = 0; + for (KeyedMatcherI filter : filters) + { + String key = filter.getKey(); + Condition condition = filter.getMatcher() + .getCondition(); + String pattern = filter.getMatcher().getPattern(); + JPanel row = addFilter(key, attNames, condition, pattern, i); + chooseFiltersPanel.add(row); + i++; + } + + filtersPane.validate(); + filtersPane.repaint(); + } + + /** + * 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 attribute + * @param attNames + * @param cond + * @param pattern + * @param i + * @return + */ + protected JPanel addFilter(String attribute, List attNames, + Condition cond, String pattern, int i) + { + JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT)); + filterRow.setBackground(Color.white); + + /* + * inputs for attribute, condition, pattern + */ + JComboBox attCombo = new JComboBox<>(); + JComboBox condCombo = new JComboBox<>(); + JTextField patternField = new JTextField(8); + + /* + * action handlers that validate and (if valid) apply changes + */ + ActionListener actionListener = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (attCombo.getSelectedItem() != null) + { + if (validateFilter(patternField, condCombo)) + { + updateFilter(attCombo, condCombo, patternField, i); + filtersChanged(); + } + } + } + }; + ItemListener itemListener = new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + actionListener.actionPerformed(null); + } + }; + + /* + * drop-down choice of attribute + */ + if (attNames.isEmpty()) + { + attCombo.addItem("---"); + attCombo.setToolTipText(MessageManager + .getString("label.no_attributes_known")); + } + else + { + attCombo.setToolTipText(""); + for (String attName : attNames) + { + attCombo.addItem(attName); + } + if ("".equals(attribute)) + { + attCombo.setSelectedItem(null); + } + else + { + attCombo.setSelectedItem(attribute); + } + attCombo.addItemListener(itemListener); + } + 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); + + /* + * pattern to match against + */ + patternField.setText(pattern); + patternField.addActionListener(actionListener); + patternField.addFocusListener(new FocusAdapter() + { + @Override + public void focusLost(FocusEvent e) + { + 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 + JButton removeCondition = new BasicArrowButton(SwingConstants.WEST); + removeCondition.setToolTipText(MessageManager + .getString("label.delete_row")); + removeCondition.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + filters.remove(i); + filtersChanged(); + } + }); + filterRow.add(removeCondition); + } + + return filterRow; + } + + /** + * 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) + { + combined.and(filter); + } + else + { + combined.or(filter); + } + } + } + + /* + * 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(attName, cond, pattern); + + filters.set(filterIndex, km); } public void fetchDAS_actionPerformed(ActionEvent e) @@ -1364,15 +1911,55 @@ public class FeatureSettings extends JPanel implements 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; } // /////////////////////////////////////////////////////////////////////// @@ -1469,9 +2056,8 @@ public class FeatureSettings extends JPanel implements } @Override - public Component getTableCellRendererComponent(JTable tbl, - Object color, boolean isSelected, boolean hasFocus, int row, - int column) + public Component getTableCellRendererComponent(JTable tbl, Object color, + boolean isSelected, boolean hasFocus, int row, int column) { FeatureColourI cellColour = (FeatureColourI) color; // JLabel comp = new JLabel(); @@ -1679,8 +2265,8 @@ class FeatureIcon implements Icon } } -class ColorEditor extends AbstractCellEditor implements TableCellEditor, - ActionListener +class ColorEditor extends AbstractCellEditor + implements TableCellEditor, ActionListener { FeatureSettings me;