X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=d30f5a066721148ae3827d51fd06deaa94eb3aa6;hb=3f62f10ab0f8985945e460c70c89b530446d6afa;hp=632ad00cc611b36cccfb7c3ea766083050552d06;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java old mode 100755 new mode 100644 index 632ad00..132bb2b --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,54 +1,139 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; +import jalview.api.FeatureColourI; +import jalview.api.FeatureSettingsControllerI; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; +import jalview.datamodel.features.FeatureMatcherI; +import jalview.datamodel.features.FeatureMatcherSet; +import jalview.datamodel.features.FeatureMatcherSetI; +import jalview.gui.Help.HelpId; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.schemabinding.version2.Filter; +import jalview.schemabinding.version2.JalviewUserColours; +import jalview.schemabinding.version2.MatcherSet; +import jalview.schemes.FeatureColour; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Point; +import java.awt.Rectangle; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.event.MouseMotionAdapter; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; - -import javax.swing.*; -import javax.swing.event.*; -import javax.swing.table.*; - -import jalview.datamodel.*; -import jalview.io.*; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.util.Arrays; +import java.util.Comparator; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import javax.help.HelpSetException; +import javax.swing.AbstractCellEditor; +import javax.swing.BorderFactory; +import javax.swing.Icon; +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JColorChooser; +import javax.swing.JDialog; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.JScrollPane; +import javax.swing.JSlider; +import javax.swing.JTable; +import javax.swing.ListSelectionModel; +import javax.swing.SwingConstants; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; +import javax.swing.table.AbstractTableModel; +import javax.swing.table.TableCellEditor; +import javax.swing.table.TableCellRenderer; +import javax.swing.table.TableColumn; public class FeatureSettings extends JPanel + implements FeatureSettingsControllerI { - DasSourceBrowser dassourceBrowser; + private static final String SEQUENCE_FEATURE_COLOURS = MessageManager + .getString("label.sequence_feature_colours"); + + /* + * column indices of fields in Feature Settings table + */ + static final int TYPE_COLUMN = 0; + + static final int COLOUR_COLUMN = 1; - jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher; + static final int FILTER_COLUMN = 2; - JPanel settingsPane = new JPanel(); + static final int SHOW_COLUMN = 3; - JPanel dasSettingsPane = new JPanel(); + private static final int COLUMN_COUNT = 4; + + private static final int MIN_WIDTH = 400; + + private static final int MIN_HEIGHT = 400; final FeatureRenderer fr; public final AlignFrame af; + /* + * 'original' fields hold settings to restore on Cancel + */ Object[][] originalData; + private float originalTransparency; + + private Map originalFilters; + final JInternalFrame frame; JScrollPane scrollPane = new JScrollPane(); @@ -59,14 +144,47 @@ public class FeatureSettings extends JPanel JSlider transparency = new JSlider(); - JPanel transPanel = new JPanel(new FlowLayout()); + /* + * 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; - public FeatureSettings(AlignFrame af) + /** + * 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 = new HashMap<>(fr.getFeatureFilters()); // shallow copy try { @@ -76,71 +194,144 @@ public class FeatureSettings extends JPanel ex.printStackTrace(); } - table = new JTable(); + table = new JTable() + { + @Override + public String getToolTipText(MouseEvent e) + { + String tip = null; + int column = table.columnAtPoint(e.getPoint()); + switch (column) + { + case TYPE_COLUMN: + tip = JvSwingUtils.wrapTooltip(true, MessageManager + .getString("label.feature_settings_click_drag")); + break; + case FILTER_COLUMN: + int row = table.rowAtPoint(e.getPoint()); + FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row, + column); + tip = o.isEmpty() + ? MessageManager + .getString("label.configure_feature_tooltip") + : o.toString(); + break; + default: + break; + } + return tip; + } + }; table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); table.setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setDefaultRenderer(Color.class, new ColorRenderer()); - table.setDefaultEditor(Color.class, new ColorEditor()); + // table.setDefaultRenderer(Color.class, new ColorRenderer()); + // table.setDefaultEditor(Color.class, new ColorEditor(this)); + // + table.setDefaultEditor(FeatureColour.class, new ColorEditor(this)); + table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); + + table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this)); + table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer()); + + TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75, + new ColorRenderer(), new ColorEditor(this)); + table.addColumn(colourColumn); + + TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75, + new FilterRenderer(), new FilterEditor(this)); + table.addColumn(filterColumn); table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); + String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); + if (evt.isPopupTrigger()) + { + Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); + popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(), + evt.getY()); + } + else if (evt.getClickCount() == 2) + { + boolean invertSelection = evt.isAltDown(); + boolean toggleSelection = Platform.isControlDown(evt); + boolean extendSelection = evt.isShiftDown(); + fr.ap.alignFrame.avc.markColumnsContainingFeatures( + invertSelection, extendSelection, toggleSelection, type); + } + } + + // isPopupTrigger fires on mouseReleased on Windows + @Override + public void mouseReleased(MouseEvent evt) + { + selectedRow = table.rowAtPoint(evt.getPoint()); + if (evt.isPopupTrigger()) + { + String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); + Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); + popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(), + evt.getY()); + } } }); table.addMouseMotionListener(new MouseMotionAdapter() { + @Override public void mouseDragged(MouseEvent evt) { int newRow = table.rowAtPoint(evt.getPoint()); if (newRow != selectedRow && selectedRow != -1 && newRow != -1) { - Object[] temp = new Object[3]; - temp[0] = table.getValueAt(selectedRow, 0); - temp[1] = table.getValueAt(selectedRow, 1); - temp[2] = table.getValueAt(selectedRow, 2); - - table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0); - table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1); - table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2); - - table.setValueAt(temp[0], newRow, 0); - table.setValueAt(temp[1], newRow, 1); - table.setValueAt(temp[2], newRow, 2); - + /* + * reposition 'selectedRow' to 'newRow' (the dragged to location) + * this could be more than one row away for a very fast drag action + * so just swap it with adjacent rows until we get it there + */ + Object[][] data = ((FeatureTableModel) table.getModel()) + .getData(); + int direction = newRow < selectedRow ? -1 : 1; + for (int i = selectedRow; i != newRow; i += direction) + { + Object[] temp = data[i]; + data[i] = data[i + direction]; + data[i + direction] = temp; + } + updateFeatureRenderer(data); + table.repaint(); selectedRow = newRow; } } }); - + // table.setToolTipText(JvSwingUtils.wrapTooltip(true, + // MessageManager.getString("label.feature_settings_click_drag"))); scrollPane.setViewportView(table); - dassourceBrowser = new DasSourceBrowser(); - dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - - if (af.getViewport().featuresDisplayed == null - || fr.renderOrder == null) + if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) { fr.findAllFeatures(true); // display everything! } - setTableData(); + discoverAllFeatureData(); final PropertyChangeListener change; final FeatureSettings fs = this; fr.addPropertyChangeListener(change = new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (!fs.resettingTable && !fs.handlingUpdate) { fs.handlingUpdate = true; - fs.resetTable(null); // new groups may be added with new seuqence - // feature types only + fs.resetTable(null); + // new groups may be added with new sequence feature types only fs.handlingUpdate = false; } } @@ -149,10 +340,24 @@ public class FeatureSettings extends JPanel frame = new JInternalFrame(); frame.setContentPane(this); - Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450); - frame - .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + if (Platform.isAMac()) + { + Desktop.addInternalFrame(frame, + MessageManager.getString("label.sequence_feature_settings"), + 600, 480); + } + else + { + Desktop.addInternalFrame(frame, + MessageManager.getString("label.sequence_feature_settings"), + 600, 450); + } + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); + + frame.addInternalFrameListener( + new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -160,66 +365,115 @@ public class FeatureSettings extends JPanel }; }); frame.setLayer(JLayeredPane.PALETTE_LAYER); + inConstruction = false; } - /** - * true when Feature Settings are updating from feature renderer - */ - private boolean handlingUpdate = false; - - /** - * contains a float[3] for each feature type string. created by setTableData - */ - Hashtable typeWidth = null; - - synchronized public void setTableData() + protected void popupSort(final int rowSelected, final String type, + final Object typeCol, final Map minmax, int x, + int y) { - if (fr.featureGroups == null) + final FeatureColourI featureColour = (FeatureColourI) typeCol; + + JPopupMenu men = new JPopupMenu(MessageManager + .formatMessage("label.settings_for_param", new String[] + { type })); + JMenuItem scr = new JMenuItem( + MessageManager.getString("label.sort_by_score")); + men.add(scr); + final FeatureSettings me = this; + scr.addActionListener(new ActionListener() { - fr.featureGroups = new Hashtable(); - } - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); - SequenceFeature[] tmpfeatures; - String group; - for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) + + @Override + public void actionPerformed(ActionEvent e) + { + me.af.avc + .sortAlignmentByFeatureScore(Arrays.asList(new String[] + { type })); + } + + }); + JMenuItem dens = new JMenuItem( + MessageManager.getString("label.sort_by_density")); + dens.addActionListener(new ActionListener() { - if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence() - .getSequenceFeatures() == null) + + @Override + public void actionPerformed(ActionEvent e) { - continue; + me.af.avc + .sortAlignmentByFeatureDensity(Arrays.asList(new String[] + { type })); } - tmpfeatures = af.getViewport().alignment.getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures(); + }); + men.add(dens); - int index = 0; - while (index < tmpfeatures.length) + JMenuItem selCols = new JMenuItem( + MessageManager.getString("label.select_columns_containing")); + selCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) { - if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) - { - index++; - continue; - } + fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, + false, type); + } + }); + JMenuItem clearCols = new JMenuItem(MessageManager + .getString("label.select_columns_not_containing")); + clearCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, + false, type); + } + }); + JMenuItem hideCols = new JMenuItem( + MessageManager.getString("label.hide_columns_containing")); + hideCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + fr.ap.alignFrame.hideFeatureColumns(type, true); + } + }); + JMenuItem hideOtherCols = new JMenuItem( + MessageManager.getString("label.hide_columns_not_containing")); + hideOtherCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + fr.ap.alignFrame.hideFeatureColumns(type, false); + } + }); + men.add(selCols); + men.add(clearCols); + men.add(hideCols); + men.add(hideOtherCols); + men.show(table, x, y); + } - if (tmpfeatures[index].getFeatureGroup() != null) - { - group = tmpfeatures[index].featureGroup; - if (!allGroups.contains(group)) - { - allGroups.addElement(group); - if (group != null) - { - checkGroupState(group); - } - } - } + @Override + synchronized public void discoverAllFeatureData() + { + Set allGroups = new HashSet<>(); + AlignmentI alignment = af.getViewport().getAlignment(); - if (!allFeatures.contains(tmpfeatures[index].getType())) + for (int i = 0; i < alignment.getHeight(); i++) + { + SequenceI seq = alignment.getSequenceAt(i); + for (String group : seq.getFeatures().getFeatureGroups(true)) + { + if (group != null && !allGroups.contains(group)) { - allFeatures.addElement(tmpfeatures[index].getType()); + allGroups.add(group); + checkGroupState(group); } - index++; } } @@ -229,217 +483,274 @@ public class FeatureSettings extends JPanel } /** + * 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 - } - - if (groupPanel == null) - { - groupPanel = new JPanel(); - } + boolean visible = fr.checkGroupVisibility(group, true); - 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.seqPanel.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 - for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) + Set displayableTypes = new HashSet<>(); + Set foundGroups = new HashSet<>(); + + /* + * determine which feature types may be visible depending on + * which groups are selected, and recompute average width data + */ + for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) { - tmpfeatures = af.getViewport().alignment.getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures(); - if (tmpfeatures == null) - { - continue; - } + SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i); - int index = 0; - while (index < tmpfeatures.length) + /* + * get the sequence's groups for positional features + * and keep track of which groups are visible + */ + Set groups = seq.getFeatures().getFeatureGroups(true); + Set visibleGroups = new HashSet<>(); + for (String group : groups) { - group = tmpfeatures[index].featureGroup; - - if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) - { - index++; - continue; - } - - if (group == null || fr.featureGroups.get(group) == null - || ((Boolean) fr.featureGroups.get(group)).booleanValue()) - { - if (group != null) - checkGroupState(group); - type = tmpfeatures[index].getType(); - if (!visibleChecks.contains(type)) - { - visibleChecks.addElement(type); - } - } - if (!typeWidth.containsKey(tmpfeatures[index].getType())) - { - typeWidth.put(tmpfeatures[index].getType(), - avWidth = new float[3]); - } - else - { - avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType()); - } - avWidth[0]++; - if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd()) + if (group == null || checkGroupState(group)) { - 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()][COLUMN_COUNT]; int dataIndex = 0; - if (fr.renderOrder != null) + if (fr.hasRenderOrder()) { if (!handlingUpdate) + { fr.findAllFeatures(groupChanged != null); // prod to update - // colourschemes. but don't - // affect display - // First add the checks in the previous render order, - // in case the window has been closed and reopened - for (int ro = fr.renderOrder.length - 1; ro > -1; ro--) + // colourschemes. but don't + // affect display + // First add the checks in the previous render order, + // in case the window has been closed and reopened + } + List frl = fr.getRenderOrder(); + for (int ro = frl.size() - 1; ro > -1; ro--) { - type = fr.renderOrder[ro]; + String type = frl.get(ro); - if (!visibleChecks.contains(type)) + if (!displayableTypes.contains(type)) { continue; } - data[dataIndex][0] = type; - data[dataIndex][1] = fr.getColour(type); - data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed - .containsKey(type)); + data[dataIndex][TYPE_COLUMN] = type; + data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); + FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); + data[dataIndex][FILTER_COLUMN] = featureFilter == null + ? new FeatureMatcherSet() + : featureFilter; + data[dataIndex][SHOW_COLUMN] = 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(); - data[dataIndex][0] = type; + String type = displayableTypes.iterator().next(); + data[dataIndex][TYPE_COLUMN] = type; - data[dataIndex][1] = fr.getColour(type); - if (data[dataIndex][1] == null) + data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); + if (data[dataIndex][COLOUR_COLUMN] == null) { // "Colour has been updated in another view!!" - fr.renderOrder = null; + fr.clearRenderOrder(); return; } - - data[dataIndex][2] = new Boolean(true); + FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); + data[dataIndex][FILTER_COLUMN] = featureFilter == null + ? new FeatureMatcherSet() + : featureFilter; + data[dataIndex][SHOW_COLUMN] = new Boolean(true); dataIndex++; + displayableTypes.remove(type); } if (originalData == null) { - originalData = new Object[data.length][3]; - System.arraycopy(data, 0, originalData, 0, data.length); + originalData = new Object[data.length][COLUMN_COUNT]; + for (int i = 0; i < data.length; i++) + { + System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT); + } + } + else + { + updateOriginalData(data); } table.setModel(new FeatureTableModel(data)); table.getColumnModel().getColumn(0).setPreferredWidth(200); - if (groupPanel != null) - { - groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1, - 4)); - - groupPanel.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[TYPE_COLUMN]; + boolean found = false; + for (Object[] current : currentData) + { + if (type.equals(current[TYPE_COLUMN])) + { + found = true; + /* + * currently dependent on object equality here; + * really need an equals method on FeatureColour + */ + if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN])) + { + /* + * feature colour has changed externally - update originalData + */ + for (Object[] original : originalData) + { + if (type.equals(original[TYPE_COLUMN])) + { + original[COLOUR_COLUMN] = row[COLOUR_COLUMN]; + break; + } + } + } + break; + } + } + if (!found) + { + /* + * new feature detected - add to original data (on top) + */ + Object[][] newData = new Object[originalData.length + + 1][COLUMN_COUNT]; + for (int i = 0; i < originalData.length; i++) + { + System.arraycopy(originalData[i], 0, newData[i + 1], 0, + COLUMN_COUNT); + } + newData[0] = row; + originalData = newData; + } + } + } + + /** + * Remove from the groups panel any checkboxes for groups that are not in the + * foundGroups set. This enables removing a group from the display when the last + * feature in that group is deleted. + * + * @param foundGroups + */ + protected void pruneGroups(Set foundGroups) + { + for (int g = 0; g < groupPanel.getComponentCount(); g++) + { + JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g); + if (!foundGroups.contains(checkbox.getText())) + { + groupPanel.remove(checkbox); + } + } + } + + /** * reorder data based on the featureRenderers global priority list. * * @param data @@ -452,148 +763,231 @@ public class FeatureSettings extends JPanel { order[i] = fr.getOrder(data[i][0].toString()); if (order[i] < 0) + { order[i] = fr.setOrder(data[i][0].toString(), i / order.length); + } if (i > 1) + { sort = sort || order[i - 1] > order[i]; + } } if (sort) + { jalview.util.QuickSort.sort(order, data); + } } + /** + * Offers a file chooser dialog, and then loads the feature colours and + * filters from file in XML format and unmarshals to Jalview feature settings + */ void load() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), new String[] - { "fc" }, new String[] - { "Sequence Feature Colours" }, "Sequence Feature Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Load Feature Colours"); - chooser.setToolTipText("Load"); + JalviewFileChooser chooser = new JalviewFileChooser("fc", + SEQUENCE_FEATURE_COLOURS); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle( + MessageManager.getString("label.load_feature_colours")); + chooser.setToolTipText(MessageManager.getString("action.load")); int value = chooser.showOpenDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { File file = chooser.getSelectedFile(); + load(file); + } + } - try - { - InputStreamReader in = new InputStreamReader(new FileInputStream( - file), "UTF-8"); + /** + * Loads feature colours and filters from XML stored in the given file + * + * @param file + */ + void load(File file) + { + try + { + InputStreamReader in = new InputStreamReader( + new FileInputStream(file), "UTF-8"); - jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours(); - jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in); + JalviewUserColours jucs = JalviewUserColours.unmarshal(in); - for (int i = jucs.getColourCount() - 1; i >= 0; i--) - { - String name; - fr.setColour(name = jucs.getColour(i).getName(), new Color( - Integer.parseInt(jucs.getColour(i).getRGB(), 16))); - fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount()); - } - if (table != null) + /* + * load feature colours + */ + for (int i = jucs.getColourCount() - 1; i >= 0; i--) + { + jalview.schemabinding.version2.Colour newcol = jucs.getColour(i); + FeatureColourI colour = Jalview2XML.unmarshalColour(newcol); + fr.setColour(newcol.getName(), colour); + fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount()); + } + + /* + * load feature filters; loaded filters will replace any that are + * currently defined, other defined filters are left unchanged + */ + for (int i = 0; i < jucs.getFilterCount(); i++) + { + jalview.schemabinding.version2.Filter filterModel = jucs + .getFilter(i); + String featureType = filterModel.getFeatureType(); + FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType, + filterModel.getMatcherSet()); + if (!filter.isEmpty()) { - resetTable(null); - Object[][] data = ((FeatureTableModel) table.getModel()) - .getData(); - ensureOrder(data); - updateFeatureRenderer(data, false); - table.repaint(); + fr.setFeatureFilter(featureType, filter); } - } catch (Exception ex) + } + + /* + * update feature settings table + */ + if (table != null) { - System.out.println("Error loading User Colour File\n" + ex); + resetTable(null); + Object[][] data = ((FeatureTableModel) table.getModel()) + .getData(); + ensureOrder(data); + updateFeatureRenderer(data, false); + table.repaint(); } + } catch (Exception ex) + { + System.out.println("Error loading User Colour File\n" + ex); } } + /** + * Offers a file chooser dialog, and then saves the current feature colours + * and any filters to the selected file in XML format + */ void save() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), new String[] - { "fc" }, new String[] - { "Sequence Feature Colours" }, "Sequence Feature Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Save Feature Colour Scheme"); - chooser.setToolTipText("Save"); + JalviewFileChooser chooser = new JalviewFileChooser("fc", + SEQUENCE_FEATURE_COLOURS); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle( + MessageManager.getString("label.save_feature_colours")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours(); - ucs.setSchemeName("Sequence Features"); - try - { - PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(choice), "UTF-8")); + save(chooser.getSelectedFile()); + } + } - Enumeration e = fr.featureColours.keys(); - float[] sortOrder = new float[fr.featureColours.size()]; - String[] sortTypes = new String[fr.featureColours.size()]; - int i = 0; - while (e.hasMoreElements()) + /** + * Saves feature colours and filters to the given file + * + * @param file + */ + void save(File file) + { + JalviewUserColours ucs = new JalviewUserColours(); + ucs.setSchemeName("Sequence Features"); + try + { + PrintWriter out = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(file), "UTF-8")); + + /* + * sort feature types by colour order, from 0 (highest) + * to 1 (lowest) + */ + Set fr_colours = fr.getAllFeatureColours(); + String[] sortedTypes = fr_colours + .toArray(new String[fr_colours.size()]); + Arrays.sort(sortedTypes, new Comparator() + { + @Override + public int compare(String type1, String type2) { - sortTypes[i] = e.nextElement().toString(); - sortOrder[i] = fr.getOrder(sortTypes[i]); - i++; + return Float.compare(fr.getOrder(type1), fr.getOrder(type2)); } - jalview.util.QuickSort.sort(sortOrder, sortTypes); - sortOrder = null; - for (i = 0; i < sortTypes.length; i++) + }); + + /* + * save feature colours + */ + for (String featureType : sortedTypes) + { + FeatureColourI fcol = fr.getFeatureStyle(featureType); + jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour( + featureType, fcol); + ucs.addColour(col); + } + + /* + * save any feature filters + */ + for (String featureType : sortedTypes) + { + FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); + if (filter != null && !filter.isEmpty()) { - jalview.binding.Colour col = new jalview.binding.Colour(); - col.setName(sortTypes[i]); - col.setRGB(jalview.util.Format.getHexString(fr.getColour(col - .getName()))); - ucs.addColour(col); + Iterator iterator = filter.getMatchers().iterator(); + FeatureMatcherI firstMatcher = iterator.next(); + MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator, + filter.isAnded()); + Filter filterModel = new Filter(); + filterModel.setFeatureType(featureType); + filterModel.setMatcherSet(ms); + ucs.addFilter(filterModel); } - ucs.marshal(out); - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); } + + ucs.marshal(out); + out.close(); + } catch (Exception ex) + { + ex.printStackTrace(); } } public void invertSelection() { - for (int i = 0; i < table.getRowCount(); i++) + Object[][] data = ((FeatureTableModel) table.getModel()).getData(); + for (int i = 0; i < data.length; i++) { - Boolean value = (Boolean) table.getValueAt(i, 2); - - table.setValueAt(new Boolean(!value.booleanValue()), i, 2); + data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN]; } + updateFeatureRenderer(data, true); + table.repaint(); } public void orderByAvWidth() { if (table == null || table.getModel() == null) + { return; + } Object[][] data = ((FeatureTableModel) table.getModel()).getData(); float[] width = new float[data.length]; float[] awidth; float max = 0; - int num = 0; + for (int i = 0; i < data.length; i++) { - awidth = (float[]) 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]) + // weight - but have to make per + // sequence, too (awidth[2]) // if (width[i]==1) // hack to distinguish single width sequences. - num++; } else { width[i] = 0; } if (max < width[i]) + { max = width[i]; + } } boolean sort = false; for (int i = 0; i < width.length; i++) @@ -601,23 +995,28 @@ 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) + { sort = sort || width[i - 1] > width[i]; + } } if (sort) + { jalview.util.QuickSort.sort(width, data); - // update global priority order + // update global priority order + } updateFeatureRenderer(data, false); table.repaint(); @@ -639,309 +1038,224 @@ 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); - } - - 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(); + FeatureSettingsBean[] rowData = getTableAsBeans(data); - JButton cancel = new JButton(); - - JButton ok = new JButton(); - - JButton loadColours = new JButton(); - - JButton saveColours = new JButton(); - - JPanel dasButtonPanel = new JPanel(); + if (fr.setFeaturePriority(rowData, visibleNew)) + { + af.alignPanel.paintAlignment(true, true); + } + } - JButton fetchDAS = new JButton(); + /** + * Converts table data into an array of data beans + */ + private FeatureSettingsBean[] getTableAsBeans(Object[][] data) + { + FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length]; + for (int i = 0; i < data.length; i++) + { + String type = (String) data[i][TYPE_COLUMN]; + FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN]; + FeatureMatcherSetI theFilter = (FeatureMatcherSetI) data[i][FILTER_COLUMN]; + Boolean isShown = (Boolean) data[i][SHOW_COLUMN]; + rowData[i] = new FeatureSettingsBean(type, colour, theFilter, + isShown); + } + return rowData; + } - JButton saveDAS = new JButton(); + private void jbInit() throws Exception + { + this.setLayout(new BorderLayout()); - JButton cancelDAS = new JButton(); + JPanel settingsPane = new JPanel(); + settingsPane.setLayout(new BorderLayout()); - JButton optimizeOrder = new JButton(); + JPanel bigPanel = new JPanel(); + bigPanel.setLayout(new BorderLayout()); - JPanel transbuttons = new JPanel(new BorderLayout()); + 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); - invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - invert.setText("Invert Selection"); + JButton invert = new JButton( + MessageManager.getString("label.invert_selection")); + invert.setFont(JvSwingUtils.getLabelFont()); invert.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { invertSelection(); } }); - optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - optimizeOrder.setText("Optimise Order"); + + JButton optimizeOrder = new JButton( + MessageManager.getString("label.optimise_order")); + optimizeOrder.setFont(JvSwingUtils.getLabelFont()); optimizeOrder.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { orderByAvWidth(); } }); - cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - cancel.setText("Cancel"); - cancel.addActionListener(new ActionListener() + + JButton sortByScore = new JButton( + MessageManager.getString("label.seq_sort_by_score")); + sortByScore.setFont(JvSwingUtils.getLabelFont()); + sortByScore.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - updateFeatureRenderer(originalData); - close(); + af.avc.sortAlignmentByFeatureScore(null); } }); - ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - ok.setText("OK"); - ok.addActionListener(new ActionListener() + JButton sortByDens = new JButton( + MessageManager.getString("label.sequence_sort_by_density")); + sortByDens.setFont(JvSwingUtils.getLabelFont()); + sortByDens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - close(); + af.avc.sortAlignmentByFeatureDensity(null); } }); - loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - loadColours.setText("Load Colours"); - loadColours.addActionListener(new ActionListener() + + JButton help = new JButton(MessageManager.getString("action.help")); + help.setFont(JvSwingUtils.getLabelFont()); + help.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - load(); + try + { + Help.showHelpWindow(HelpId.SequenceFeatureSettings); + } catch (HelpSetException e1) + { + e1.printStackTrace(); + } } }); - saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - saveColours.setText("Save Colours"); - saveColours.addActionListener(new ActionListener() + help.setFont(JvSwingUtils.getLabelFont()); + help.setText(MessageManager.getString("action.help")); + help.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - save(); - } - }); - transparency.addChangeListener(new ChangeListener() - { - public void stateChanged(ChangeEvent evt) - { - fr.setTransparency((float) (100 - transparency.getValue()) / 100f); - af.alignPanel.paintAlignment(true); + try + { + Help.showHelpWindow(HelpId.SequenceFeatureSettings); + } catch (HelpSetException e1) + { + e1.printStackTrace(); + } } }); - transparency.setMaximum(70); - fetchDAS.setText("Fetch DAS Features"); - fetchDAS.addActionListener(new ActionListener() + JButton cancel = new JButton(MessageManager.getString("action.cancel")); + cancel.setFont(JvSwingUtils.getLabelFont()); + cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - fetchDAS_actionPerformed(e); + fr.setTransparency(originalTransparency); + fr.setFeatureFilters(originalFilters); + updateFeatureRenderer(originalData); + close(); } }); - saveDAS.setText("Save as default"); - saveDAS.addActionListener(new ActionListener() + + JButton ok = new JButton(MessageManager.getString("action.ok")); + ok.setFont(JvSwingUtils.getLabelFont()); + ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - saveDAS_actionPerformed(e); + close(); } }); - dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); - dasSettingsPane.setBorder(null); - cancelDAS.setEnabled(false); - cancelDAS.setText("Cancel Fetch"); - cancelDAS.addActionListener(new ActionListener() + + JButton loadColours = new JButton( + MessageManager.getString("label.load_colours")); + loadColours.setFont(JvSwingUtils.getLabelFont()); + loadColours.setToolTipText( + MessageManager.getString("label.load_colours_tooltip")); + loadColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - cancelDAS_actionPerformed(e); + load(); } }); - this.add(tabbedPane, java.awt.BorderLayout.CENTER); - tabbedPane.addTab("Feature Settings", settingsPane); - tabbedPane.addTab("DAS Settings", dasSettingsPane); - bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); - transPanel.add(transparency); - transbuttons.add(invert, java.awt.BorderLayout.NORTH); - transbuttons.add(optimizeOrder, java.awt.BorderLayout.SOUTH); - transPanel.add(transbuttons); - buttonPanel.add(ok); - buttonPanel.add(cancel); - buttonPanel.add(loadColours); - buttonPanel.add(saveColours); - bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER); - dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH); - dasButtonPanel.add(fetchDAS); - dasButtonPanel.add(cancelDAS); - dasButtonPanel.add(saveDAS); - settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER); - settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH); - } - - public void fetchDAS_actionPerformed(ActionEvent e) - { - fetchDAS.setEnabled(false); - cancelDAS.setEnabled(true); - Vector selectedSources = dassourceBrowser.getSelectedSources(); - doDasFeatureFetch(selectedSources, true, true); - } - /** - * get the features from selectedSources for all or the current selection - * - * @param selectedSources - * @param checkDbRefs - * @param promptFetchDbRefs - */ - private void doDasFeatureFetch(Vector selectedSources, - boolean checkDbRefs, boolean promptFetchDbRefs) - { - SequenceI[] dataset, seqs; - int iSize; - AlignViewport vp = af.getViewport(); - if (vp.getSelectionGroup() != null - && vp.getSelectionGroup().getSize() > 0) - { - iSize = vp.getSelectionGroup().getSize(); - dataset = new SequenceI[iSize]; - seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment()); - } - else - { - iSize = vp.getAlignment().getHeight(); - seqs = vp.getAlignment().getSequencesArray(); - } - - dataset = new SequenceI[iSize]; - for (int i = 0; i < iSize; i++) - { - dataset[i] = seqs[i].getDatasetSequence(); - } - - cancelDAS.setEnabled(true); - dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset, - this, selectedSources, checkDbRefs, promptFetchDbRefs); - af.getViewport().setShowSequenceFeatures(true); - af.showSeqFeatures.setSelected(true); - } - - /** - * properly initialise DAS fetcher and then initiate a new thread to fetch - * features from the named sources (rather than any turned on by default) - * - * @param sources - */ - public void fetchDasFeatures(Vector sources) - { - Thread thr = new Thread(new Runnable() + JButton saveColours = new JButton( + MessageManager.getString("label.save_colours")); + saveColours.setFont(JvSwingUtils.getLabelFont()); + saveColours.setToolTipText( + MessageManager.getString("label.save_colours_tooltip")); + saveColours.addActionListener(new ActionListener() { - public void run() + @Override + public void actionPerformed(ActionEvent e) { - // this actually initialises the das source list - dassourceBrowser.paintComponent(null); // yuk + save(); } }); - thr.start(); - while (dassourceBrowser.loadingDasSources - || dassourceBrowser.dasSources == null) - { - try - { - Thread.sleep(10); - } catch (Exception e) - { - } - ; - } - Vector resolved = new Vector(); - if (sources != null) + transparency.addChangeListener(new ChangeListener() { - for (int i = 0; i < dassourceBrowser.dasSources.length; i++) + @Override + public void stateChanged(ChangeEvent evt) { - if (sources.contains(dassourceBrowser.dasSources[i].getNickname())) + if (!inConstruction) { - if (!resolved.contains(dassourceBrowser.dasSources[i])) - { - resolved.addElement(dassourceBrowser.dasSources[i]); - } + fr.setTransparency((100 - transparency.getValue()) / 100f); + af.alignPanel.paintAlignment(true, true); } } - } - if (resolved.size() == 0) - { - resolved = dassourceBrowser.getSelectedSources(); - } - if (resolved.size() > 0) - { - final Vector dassources = resolved; - SwingUtilities.invokeLater(new Runnable() - { - - public void run() - { - fetchDAS.setEnabled(false); - cancelDAS.setEnabled(true); - doDasFeatureFetch(dassources, true, false); - - } - }); - } - } - - public void saveDAS_actionPerformed(ActionEvent e) - { - dassourceBrowser - .saveProperties(jalview.bin.Cache.applicationProperties); - } - - public void complete() - { - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); - } + }); - public void cancelDAS_actionPerformed(ActionEvent e) - { - if (dasFeatureFetcher != null) - { - dasFeatureFetcher.cancel(); - } - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); - } + transparency.setMaximum(70); + transparency.setToolTipText( + MessageManager.getString("label.transparency_tip")); + + JPanel transPanel = new JPanel(new GridLayout(1, 2)); + bigPanel.add(transPanel, BorderLayout.SOUTH); + + JPanel transbuttons = new JPanel(new GridLayout(5, 1)); + transbuttons.add(optimizeOrder); + transbuttons.add(invert); + transbuttons.add(sortByScore); + transbuttons.add(sortByDens); + transbuttons.add(help); + transPanel.add(transparency); + transPanel.add(transbuttons); - public void noDasSourceActive() - { - complete(); - JOptionPane.showInternalConfirmDialog(Desktop.desktop, - "No das sources were selected.\n" - + "Please select some sources and\n" + " try again.", - "No Sources Selected", JOptionPane.DEFAULT_OPTION, - JOptionPane.INFORMATION_MESSAGE); + JPanel buttonPanel = new JPanel(); + buttonPanel.add(ok); + buttonPanel.add(cancel); + buttonPanel.add(loadColours); + buttonPanel.add(saveColours); + bigPanel.add(scrollPane, BorderLayout.CENTER); + settingsPane.add(bigPanel, BorderLayout.CENTER); + settingsPane.add(buttonPanel, BorderLayout.SOUTH); + this.add(settingsPane); } // /////////////////////////////////////////////////////////////////////// @@ -949,16 +1263,19 @@ public class FeatureSettings extends JPanel // /////////////////////////////////////////////////////////////////////// class FeatureTableModel extends AbstractTableModel { + private String[] columnNames = { + MessageManager.getString("label.feature_type"), + MessageManager.getString("action.colour"), + MessageManager.getString("label.configuration"), + MessageManager.getString("label.show") }; + + private Object[][] data; + FeatureTableModel(Object[][] data) { this.data = data; } - private String[] columnNames = - { "Feature Type", "Colour", "Display" }; - - private Object[][] data; - public Object[][] getData() { return data; @@ -969,6 +1286,7 @@ public class FeatureSettings extends JPanel this.data = data; } + @Override public int getColumnCount() { return columnNames.length; @@ -979,31 +1297,41 @@ 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]; } - public Class getColumnClass(int c) + /** + * Answers the class of the object in column c of the first row of the table + */ + @Override + public Class getColumnClass(int c) { - return getValueAt(0, c).getClass(); + Object v = getValueAt(0, c); + return v == null ? null : v.getClass(); } + @Override public boolean isCellEditable(int row, int col) { return col == 0 ? false : true; } + @Override public void setValueAt(Object value, int row, int col) { data[row][col] = value; @@ -1019,23 +1347,41 @@ public class FeatureSettings extends JPanel javax.swing.border.Border selectedBorder = null; + final String baseTT = "Click to edit, right/apple click for menu."; + public ColorRenderer() { setOpaque(true); // MUST do this for background to show up. + setHorizontalTextPosition(SwingConstants.CENTER); + setVerticalTextPosition(SwingConstants.CENTER); } - 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) { - Color newColor = (Color) color; - setBackground(newColor); + FeatureColourI cellColour = (FeatureColourI) color; + setOpaque(true); + setToolTipText(baseTT); + setBackground(tbl.getBackground()); + if (!cellColour.isSimpleColour()) + { + Rectangle cr = tbl.getCellRect(row, column, false); + FeatureSettings.renderGraduatedColor(this, cellColour, + (int) cr.getWidth(), (int) cr.getHeight()); + } + else + { + this.setText(""); + this.setIcon(null); + setBackground(cellColour.getColour()); + } if (isSelected) { if (selectedBorder == null) { selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getSelectionBackground()); + tbl.getSelectionBackground()); } setBorder(selectedBorder); } @@ -1044,83 +1390,476 @@ public class FeatureSettings extends JPanel if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getBackground()); + tbl.getBackground()); } setBorder(unselectedBorder); } - setToolTipText("RGB value: " + newColor.getRed() + ", " - + newColor.getGreen() + ", " + newColor.getBlue()); return this; } } -} -class ColorEditor extends AbstractCellEditor implements TableCellEditor, - ActionListener -{ - Color currentColor; + class FilterRenderer extends JLabel implements TableCellRenderer + { + javax.swing.border.Border unselectedBorder = null; - JButton button; + javax.swing.border.Border selectedBorder = null; - JColorChooser colorChooser; + public FilterRenderer() + { + setOpaque(true); // MUST do this for background to show up. + setHorizontalTextPosition(SwingConstants.CENTER); + setVerticalTextPosition(SwingConstants.CENTER); + } - JDialog dialog; + @Override + public Component getTableCellRendererComponent(JTable tbl, + Object filter, boolean isSelected, boolean hasFocus, int row, + int column) + { + FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter; + setOpaque(true); + String asText = theFilter.toString(); + setBackground(tbl.getBackground()); + this.setText(asText); + this.setIcon(null); - protected static final String EDIT = "edit"; + 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; + } + } - public ColorEditor() + /** + * update comp using rendering settings from gcol + * + * @param comp + * @param gcol + */ + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol) { - // 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 + int w = comp.getWidth(), h = comp.getHeight(); + if (w < 20) + { + w = (int) comp.getPreferredSize().getWidth(); + h = (int) comp.getPreferredSize().getHeight(); + if (w < 20) + { + w = 80; + h = 12; + } + } + renderGraduatedColor(comp, gcol, w, h); + } + + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol, + int w, int h) + { + boolean thr = false; + StringBuilder tt = new StringBuilder(); + StringBuilder tx = new StringBuilder(); + + if (gcol.isColourByAttribute()) + { + tx.append(String.join(":", gcol.getAttributeName())); + } + else if (!gcol.isColourByLabel()) + { + tx.append(MessageManager.getString("label.score")); + } + tx.append(" "); + if (gcol.isAboveThreshold()) + { + thr = true; + tx.append(">"); + tt.append("Thresholded (Above ").append(gcol.getThreshold()) + .append(") "); + } + if (gcol.isBelowThreshold()) + { + thr = true; + tx.append("<"); + tt.append("Thresholded (Below ").append(gcol.getThreshold()) + .append(") "); + } + if (gcol.isColourByLabel()) + { + tt.append("Coloured by label text. ").append(tt); + if (thr) + { + tx.append(" "); + } + if (!gcol.isColourByAttribute()) + { + tx.append("Label"); + } + comp.setIcon(null); + } + else + { + Color newColor = gcol.getMaxColour(); + comp.setBackground(newColor); + // System.err.println("Width is " + w / 2); + Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr); + comp.setIcon(ficon); + // tt+="RGB value: Max (" + newColor.getRed() + ", " + // + newColor.getGreen() + ", " + newColor.getBlue() + // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen() + // + ", " + minCol.getBlue() + ")"); + } + comp.setHorizontalAlignment(SwingConstants.CENTER); + comp.setText(tx.toString()); + if (tt.length() > 0) + { + if (comp.getToolTipText() == null) + { + comp.setToolTipText(tt.toString()); + } + else + { + comp.setToolTipText( + tt.append(" ").append(comp.getToolTipText()).toString()); + } + } + } + + class ColorEditor extends AbstractCellEditor + implements TableCellEditor, ActionListener + { + FeatureSettings me; + + FeatureColourI currentColor; + + FeatureTypeSettings chooser; + + String type; + + JButton button; + + JColorChooser colorChooser; + + JDialog dialog; + + protected static final String EDIT = "edit"; + + int rowSelected = 0; + + public ColorEditor(FeatureSettings me) + { + this.me = me; + // Set up the editor (from the table's point of view), + // which is a button. + // This button brings up the color chooser dialog, + // which is the editor from the user's point of view. + button = new JButton(); + button.setActionCommand(EDIT); + button.addActionListener(this); + button.setBorderPainted(false); + // Set up the dialog that the button brings up. + colorChooser = new JColorChooser(); + dialog = JColorChooser.createDialog(button, + MessageManager.getString("label.select_colour"), true, // modal + colorChooser, this, // OK button handler + null); // no CANCEL button handler + } + + /** + * Handles events from the editor button and from the dialog's OK button. + */ + @Override + public void actionPerformed(ActionEvent e) + { + // todo test e.getSource() instead here + if (EDIT.equals(e.getActionCommand())) + { + // The user has clicked the cell, so + // bring up the dialog. + if (currentColor.isSimpleColour()) + { + // bring up simple color chooser + button.setBackground(currentColor.getColour()); + colorChooser.setColor(currentColor.getColour()); + dialog.setVisible(true); + } + else + { + // bring up graduated chooser. + chooser = new FeatureTypeSettings(me.fr, type); + /** + * @j2sNative + */ + { + chooser.setRequestFocusEnabled(true); + chooser.requestFocus(); + } + chooser.addActionListener(this); + // Make the renderer reappear. + fireEditingStopped(); + } + } + else + { + if (currentColor.isSimpleColour()) + { + /* + * read off colour picked in colour chooser after OK pressed + */ + currentColor = new FeatureColour(colorChooser.getColor()); + me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN); + } + else + { + /* + * after OK in variable colour dialog, any changes to colour + * (or filters!) are already set in FeatureRenderer, so just + * update table data without triggering updateFeatureRenderer + */ + currentColor = fr.getFeatureColours().get(type); + FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type); + if (currentFilter == null) + { + currentFilter = new FeatureMatcherSet(); + } + Object[] data = ((FeatureTableModel) table.getModel()) + .getData()[rowSelected]; + data[COLOUR_COLUMN] = currentColor; + data[FILTER_COLUMN] = currentFilter; + } + fireEditingStopped(); + me.table.validate(); + } + } + + // Implement the one CellEditor method that AbstractCellEditor doesn't. + @Override + public Object getCellEditorValue() + { + return currentColor; + } + + // Implement the one method defined by TableCellEditor. + @Override + public Component getTableCellEditorComponent(JTable theTable, Object value, + boolean isSelected, int row, int column) + { + currentColor = (FeatureColourI) value; + this.rowSelected = row; + type = me.table.getValueAt(row, TYPE_COLUMN).toString(); + button.setOpaque(true); + button.setBackground(me.getBackground()); + if (!currentColor.isSimpleColour()) + { + JLabel btn = new JLabel(); + btn.setSize(button.getSize()); + FeatureSettings.renderGraduatedColor(btn, currentColor); + button.setBackground(btn.getBackground()); + button.setIcon(btn.getIcon()); + button.setText(btn.getText()); + } + else + { + button.setText(""); + button.setIcon(null); + button.setBackground(currentColor.getColour()); + } + return button; + } } /** - * Handles events from the editor button and from the dialog's OK button. + * The cell editor for the Filter column. It displays the text of any filters + * for the feature type in that row (in full as a tooltip, possible abbreviated + * as display text). On click in the cell, opens the Feature Display Settings + * dialog at the Filters tab. */ - public void actionPerformed(ActionEvent e) + class FilterEditor extends AbstractCellEditor + implements TableCellEditor, ActionListener { + FeatureSettings me; + + FeatureMatcherSetI currentFilter; + + Point lastLocation; + + String type; + + JButton button; + + protected static final String EDIT = "edit"; + + int rowSelected = 0; + + public FilterEditor(FeatureSettings me) + { + this.me = me; + button = new JButton(); + button.setActionCommand(EDIT); + button.addActionListener(this); + button.setBorderPainted(false); + } + + /** + * Handles events from the editor button + */ + @Override + public void actionPerformed(ActionEvent e) + { + if (button == e.getSource()) + { + FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type); + chooser.addActionListener(this); + chooser.setRequestFocusEnabled(true); + chooser.requestFocus(); + if (lastLocation != null) + { + // todo open at its last position on screen + chooser.setBounds(lastLocation.x, lastLocation.y, + chooser.getWidth(), chooser.getHeight()); + chooser.validate(); + } + fireEditingStopped(); + } + else if (e.getSource() instanceof Component) + { + + /* + * after OK in variable colour dialog, any changes to filter + * (or colours!) are already set in FeatureRenderer, so just + * update table data without triggering updateFeatureRenderer + */ + FeatureColourI currentColor = fr.getFeatureColours().get(type); + currentFilter = me.fr.getFeatureFilter(type); + if (currentFilter == null) + { + currentFilter = new FeatureMatcherSet(); + } + Object[] data = ((FeatureTableModel) table.getModel()) + .getData()[rowSelected]; + data[COLOUR_COLUMN] = currentColor; + data[FILTER_COLUMN] = currentFilter; + fireEditingStopped(); + me.table.validate(); + } + } - if (EDIT.equals(e.getActionCommand())) + @Override + public Object getCellEditorValue() { - // The user has clicked the cell, so - // bring up the dialog. - button.setBackground(currentColor); - colorChooser.setColor(currentColor); - dialog.setVisible(true); + return currentFilter; + } + + @Override + public Component getTableCellEditorComponent(JTable theTable, Object value, + boolean isSelected, int row, int column) + { + currentFilter = (FeatureMatcherSetI) value; + this.rowSelected = row; + type = me.table.getValueAt(row, TYPE_COLUMN).toString(); + button.setOpaque(true); + button.setBackground(me.getBackground()); + button.setText(currentFilter.toString()); + button.setToolTipText(currentFilter.toString()); + button.setIcon(null); + return button; + } + } +} + +class FeatureIcon implements Icon +{ + FeatureColourI gcol; + + Color backg; + + boolean midspace = false; - // Make the renderer reappear. - fireEditingStopped(); + int width = 50, height = 20; + int s1, e1; // start and end of midpoint band for thresholded symbol + + Color mpcolour = Color.white; + + FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace) + { + gcol = gfc; + backg = bg; + width = w; + height = h; + midspace = mspace; + if (midspace) + { + s1 = width / 3; + e1 = s1 * 2; } else - { // User pressed dialog's "OK" button. - currentColor = colorChooser.getColor(); + { + s1 = width / 2; + e1 = s1; } } - // Implement the one CellEditor method that AbstractCellEditor doesn't. - public Object getCellEditorValue() + @Override + public int getIconWidth() { - return currentColor; + return width; } - // Implement the one method defined by TableCellEditor. - public Component getTableCellEditorComponent(JTable table, Object value, - boolean isSelected, int row, int column) + @Override + public int getIconHeight() { - currentColor = (Color) value; - return button; + return height; + } + + @Override + public void paintIcon(Component c, Graphics g, int x, int y) + { + + if (gcol.isColourByLabel()) + { + g.setColor(backg); + g.fillRect(0, 0, width, height); + // need an icon here. + g.setColor(gcol.getMaxColour()); + + g.setFont(new Font("Verdana", Font.PLAIN, 9)); + + // g.setFont(g.getFont().deriveFont( + // AffineTransform.getScaleInstance( + // width/g.getFontMetrics().stringWidth("Label"), + // height/g.getFontMetrics().getHeight()))); + + g.drawString(MessageManager.getString("label.label"), 0, 0); + + } + else + { + Color minCol = gcol.getMinColour(); + g.setColor(minCol); + g.fillRect(0, 0, s1, height); + if (midspace) + { + g.setColor(Color.white); + g.fillRect(s1, 0, e1 - s1, height); + } + g.setColor(gcol.getMaxColour()); + g.fillRect(0, e1, width - e1, height); + } } }