X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=2bd98d5e2945cf85dba3509ff9933d9876d9e08f;hb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;hp=895c23586204b66c8969a5e92f615b3f0688ff67;hpb=a920a78c4c63ebb211a221dcbce9db2dd98923fb;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java old mode 100755 new mode 100644 index 895c235..dedbba0 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,570 +1,1112 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; +import jalview.api.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.AlignmentViewport; +import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; +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.Font; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Point; +import java.awt.Rectangle; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.event.MouseMotionAdapter; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.util.Arrays; +import java.util.Comparator; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.Vector; + +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.JCheckBoxMenuItem; +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.SwingUtilities; +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 +{ + private static final String SEQUENCE_FEATURE_COLOURS = MessageManager + .getString("label.sequence_feature_colours"); + + /* + * column indices of fields in Feature Settings table + */ + static final int TYPE_COLUMN = 0; -import javax.swing.*; -import javax.swing.event.*; -import javax.swing.table.*; + static final int COLOUR_COLUMN = 1; -import jalview.datamodel.*; -import jalview.io.*; + static final int FILTER_COLUMN = 2; + + static final int SHOW_COLUMN = 3; + + private static final int COLUMN_COUNT = 4; + + private static final int MIN_WIDTH = 400; + + private static final int MIN_HEIGHT = 400; -public class FeatureSettings - extends JPanel -{ DasSourceBrowser dassourceBrowser; - jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher; - JPanel settingsPane = new JPanel(); + + DasSequenceFeatureFetcher dasFeatureFetcher; + JPanel dasSettingsPane = new JPanel(); 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(); + JTable table; + JPanel groupPanel; + 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; - public FeatureSettings(AlignFrame af) + /* + * true when Feature Settings are updating from feature renderer + */ + private boolean handlingUpdate = false; + + /* + * holds {featureCount, totalExtent} for each feature type + */ + Map typeWidth = null; + + /** + * Constructor + * + * @param af + */ + public FeatureSettings(AlignFrame 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 { jbInit(); - } - catch (Exception ex) + } catch (Exception ex) { 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.filters_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) + 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(); + dassourceBrowser = new DasSourceBrowser(this); dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null) + if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) { fr.findAllFeatures(true); // display everything! } - setTableData(); + discoverAllFeatureData(); final PropertyChangeListener change; - final FeatureSettings fs=this; - fr.addPropertyChangeListener(change=new PropertyChangeListener() { - private boolean firing=false; + final FeatureSettings fs = this; + fr.addPropertyChangeListener(change = new PropertyChangeListener() + { + @Override public void propertyChange(PropertyChangeEvent evt) { - if (!fs.resettingTable && !firing) { - firing=true; - resetTable(null); - firing=false; + if (!fs.resettingTable && !fs.handlingUpdate) + { + fs.handlingUpdate = true; + fs.resetTable(null); + // new groups may be added with new sequence feature types only + fs.handlingUpdate = false; } } - + }); - + frame = new JInternalFrame(); frame.setContentPane(this); - Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450); - frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + if (Platform.isAMac()) { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - fr.removePropertyChangeListener(change); - } - ; - }); + 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) + { + fr.removePropertyChangeListener(change); + dassourceBrowser.fs = null; + }; + }); frame.setLayer(JLayeredPane.PALETTE_LAYER); + inConstruction = 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); + + /* + * variable colour options include colour by label, by score, + * by selected attribute text, or attribute value + */ + final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( + MessageManager.getString("label.variable_colour")); + mxcol.setSelected(!featureColour.isSimpleColour()); + men.add(mxcol); + mxcol.addActionListener(new ActionListener() + { + JColorChooser colorChooser; - int index = 0; - while (index < tmpfeatures.length) + @Override + public void actionPerformed(ActionEvent e) { - if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) + if (e.getSource() == mxcol) { - index++; - continue; + if (featureColour.isSimpleColour()) + { + FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type); + fc.addActionListener(this); + } + else + { + // bring up simple color chooser + colorChooser = new JColorChooser(); + String title = MessageManager + .getString("label.select_colour"); + JDialog dialog = JColorChooser.createDialog(me, + title, true, // modal + colorChooser, this, // OK button handler + null); // no CANCEL button handler + colorChooser.setColor(featureColour.getMaxColour()); + dialog.setVisible(true); + } } - - if (tmpfeatures[index].getFeatureGroup() != null) + else { - group = tmpfeatures[index].featureGroup; - if (!allGroups.contains(group)) + if (e.getSource() instanceof FeatureTypeSettings) { - allGroups.addElement(group); - - boolean visible; - if (fr.featureGroups.containsKey(group)) - { - visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue(); - } else { - visible=true; //initGroups || fr.av.featuresDisplayed.containsKey(tmpfeatures[index].getType()); - } - - if (groupPanel == null) - { - groupPanel = new JPanel(); - } + /* + * update after OK in feature colour dialog; the updated + * colour will have already been set in the FeatureRenderer + */ + FeatureColourI fci = fr.getFeatureColours().get(type); + table.setValueAt(fci, rowSelected, 1); + table.validate(); + } + else + { + // probably the color chooser! + table.setValueAt(new FeatureColour(colorChooser.getColor()), + rowSelected, 1); + table.validate(); + me.updateFeatureRenderer( + ((FeatureTableModel) table.getModel()).getData(), + false); + } + } + } - boolean alreadyAdded = false; - for (int g = 0; g < groupPanel.getComponentCount(); g++) - { - if ( ( (JCheckBox) groupPanel.getComponent(g)) - .getText().equals(group)) - { - alreadyAdded = true; - break; - } - } + }); - if (alreadyAdded) - { - - continue; - } + JMenuItem selCols = new JMenuItem( + MessageManager.getString("label.select_columns_containing")); + selCols.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + 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); + } - fr.featureGroups.put(group, new Boolean(visible)); - final String grp = group; - final JCheckBox check = new JCheckBox(group, visible); - check.setFont(new Font("Serif", Font.BOLD, 12)); - check.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent evt) - { - fr.featureGroups.put(check.getText(), - new Boolean(check.isSelected())); - af.alignPanel.seqPanel.seqCanvas.repaint(); - if (af.alignPanel.overviewPanel != null) - { - af.alignPanel.overviewPanel.updateOverviewImage(); - } - - resetTable(new String[] { grp } ); - } - }); - groupPanel.add(check); - } - } + @Override + synchronized public void discoverAllFeatureData() + { + Set allGroups = new HashSet<>(); + AlignmentI alignment = af.getViewport().getAlignment(); - if (!allFeatures.contains(tmpfeatures[index].getType())) + for (int i = 0; i < alignment.getHeight(); i++) + { + SequenceI seq = alignment.getSequenceAt(i); + for (String group : seq.getFeatures().getFeatureGroups(true)) + { + if (group != null && !allGroups.contains(group)) { - allFeatures.addElement(tmpfeatures[index].getType()); + allGroups.add(group); + checkGroupState(group); } - index++; } } - + resetTable(null); validate(); } - boolean resettingTable=false; - void resetTable(String[] groupChanged) + + /** + * Synchronise gui group list and check visibility of group + * + * @param group + * @return true if group is visible + */ + private boolean checkGroupState(String group) { - resettingTable=true; - typeWidth=new Hashtable(); - Vector groupchanged = new Vector(); - // 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(); + boolean visible = fr.checkGroupVisibility(group, true); - //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++) + for (int g = 0; g < groupPanel.getComponentCount(); g++) { - - tmpfeatures = af.getViewport().alignment.getSequenceAt(i). - getDatasetSequence().getSequenceFeatures(); - if (tmpfeatures == null) + if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group)) { - continue; + ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible); + return visible; } + } - int index = 0; - while (index < tmpfeatures.length) + 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) { - group = tmpfeatures[index].featureGroup; + fr.setGroupVisibility(check.getText(), check.isSelected()); + resetTable(new String[] { grp }); + af.alignPanel.paintAlignment(true, true); + } + }); + groupPanel.add(check); + return visible; + } - if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) - { - index++; - continue; - } + synchronized void resetTable(String[] groupChanged) + { + if (resettingTable) + { + return; + } + resettingTable = true; + typeWidth = new Hashtable<>(); + // TODO: change avWidth calculation to 'per-sequence' average and use long + // rather than float + + Set displayableTypes = new HashSet<>(); + Set foundGroups = new HashSet<>(); + + /* + * determine which feature types may be visible depending on + * which groups are selected, and recompute average width data + */ + for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) + { + + SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i); - if (group == null || fr.featureGroups.get(group) == null || - ( (Boolean) fr.featureGroups.get(group)).booleanValue()) + /* + * 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) + { + if (group == null || checkGroupState(group)) { - type = tmpfeatures[index].getType(); - if (groupchanged==null || groupchanged.contains(group)) { - //af.getViewport().featuresDisplayed.put(type, fr.getColour(type)); - } - if (!visibleChecks.contains(type)) - { - visibleChecks.addElement(type); - } + visibleGroups.add(group); } - 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()) + } + foundGroups.addAll(groups); + + /* + * get distinct feature types for visible groups + * record distinct visible types, and their count and total length + */ + Set types = seq.getFeatures().getFeatureTypesForGroups(true, + visibleGroups.toArray(new String[visibleGroups.size()])); + for (String type : types) + { + displayableTypes.add(type); + float[] avWidth = typeWidth.get(type); + if (avWidth == null) { - avWidth[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd(); - } else { - avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin(); + avWidth = new float[2]; + typeWidth.put(type, avWidth); } - index++; + // todo this could include features with a non-visible group + // - do we greatly care? + // todo should we include non-displayable features here, and only + // update when features are added? + avWidth[0] += seq.getFeatures().getFeatureCount(true, type); + avWidth[1] += seq.getFeatures().getTotalFeatureLength(type); } } - int fSize = visibleChecks.size(); - Object[][] data = new Object[fSize][3]; + Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT]; int dataIndex = 0; - if (fr.renderOrder != null) + if (fr.hasRenderOrder()) { - 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--) + 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 + } + 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; + // "Colour has been updated in another view!!" + fr.clearRenderOrder(); return; } - - data[dataIndex][2] = new Boolean(true); + FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); + data[dataIndex][FILTER_COLUMN] = featureFilter == null + ? new FeatureMatcherSet() + : featureFilter; + data[dataIndex][SHOW_COLUMN] = 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.setLayout( + new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4)); + pruneGroups(foundGroups); + groupPanel.validate(); - groupPanel.validate(); - bigPanel.add(groupPanel, BorderLayout.NORTH); + 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; + } } + } - updateFeatureRenderer(data, groupChanged!=null); - resettingTable=false; + /** + * Remove from the groups panel any checkboxes for groups that are not in the + * foundGroups set. This enables removing a group from the display when the last + * feature in that group is deleted. + * + * @param foundGroups + */ + protected void pruneGroups(Set foundGroups) + { + for (int g = 0; g < groupPanel.getComponentCount(); g++) + { + JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g); + if (!foundGroups.contains(checkbox.getText())) + { + groupPanel.remove(checkbox); + } + } } + /** * reorder data based on the featureRenderers global priority list. + * * @param data */ private void ensureOrder(Object[][] data) { - boolean sort=false; + boolean sort = false; float[] order = new float[data.length]; - for (int i=0;i1) - sort = sort || order[i-1]>order[i]; + if (order[i] < 0) + { + order[i] = fr.setOrder(data[i][0].toString(), i / order.length); + } + if (i > 1) + { + sort = sort || order[i - 1] > order[i]; + } } if (sort) + { jalview.util.QuickSort.sort(order, data); + } } + /** + * Offers a file chooser dialog, and then loads the feature colours and + * filters from file in XML format and unmarshals to Jalview feature settings + */ void load() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY"), new String[] - {"fc"}, - new String[] - {"Sequence Feature Colours"}, "Sequence Feature Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Load Feature Colours"); - chooser.setToolTipText("Load"); + JalviewFileChooser chooser = new JalviewFileChooser("fc", + SEQUENCE_FEATURE_COLOURS); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle( + MessageManager.getString("label.load_feature_colours")); + chooser.setToolTipText(MessageManager.getString("action.load")); int value = chooser.showOpenDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { File file = chooser.getSelectedFile(); + load(file); + } + } - try - { - 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"); + + JalviewUserColours jucs = JalviewUserColours.unmarshal(in); - jalview.binding.JalviewUserColours jucs = new jalview.binding. - JalviewUserColours(); - jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in); + /* + * 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()); + } - for (int i = 0; i < jucs.getColourCount(); i++) + /* + * load feature filters; loaded filters will replace any that are + * currently defined, other defined filters are left unchanged + */ + for (int i = 0; i < jucs.getFilterCount(); i++) + { + jalview.schemabinding.version2.Filter filterModel = jucs + .getFilter(i); + String featureType = filterModel.getFeatureType(); + FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType, + filterModel.getMatcherSet()); + if (!filter.isEmpty()) { - String name; - fr.setColour(name=jucs.getColour(i).getName(), - new Color(Integer.parseInt(jucs.getColour(i).getRGB(), - 16))); - fr.setOrder(name,i/jucs.getColourCount()); + fr.setFeatureFilter(featureType, filter); } - - setTableData(); - af.alignPanel.paintAlignment(true); } - 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(); - 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) { - jalview.binding.Colour col = new jalview.binding.Colour(); - col.setName(e.nextElement().toString()); - col.setRGB(jalview.util.Format.getHexString( - fr.getColour(col.getName()))); - ucs.addColour(col); + return Float.compare(fr.getOrder(type1), fr.getOrder(type2)); } + }); - ucs.marshal(out); - out.close(); + /* + * save feature colours + */ + for (String featureType : sortedTypes) + { + FeatureColourI fcol = fr.getFeatureStyle(featureType); + jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour( + featureType, fcol); + ucs.addColour(col); } - catch (Exception ex) + + /* + * save any feature filters + */ + for (String featureType : sortedTypes) { - ex.printStackTrace(); + FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); + if (filter != null && !filter.isEmpty()) + { + 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(); } } 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][2] = !(Boolean) data[i][2]; } + af.alignPanel.paintAlignment(true, true); } - public void orderByAvWidth() { - if (table==null || table.getModel()==null) + + public void orderByAvWidth() + { + if (table == null || table.getModel() == null) + { return; + } Object[][] data = ((FeatureTableModel) table.getModel()).getData(); float[] width = new float[data.length]; float[] awidth; - float max=0; - int num=0; - for (int i=0;i0) { - width[i] = awidth[1]/awidth[0];// *awidth[0]*awidth[2]; - better weight - but have to make per sequence, too (awidth[2]) - //if (width[i]==1) // hack to distinguish single width sequences. - num++; - } else { - width[i]=0; - } - if (max0) - sort = sort || width[i-1]>width[i]; + float max = 0; + + for (int i = 0; i < data.length; i++) + { + awidth = typeWidth.get(data[i][TYPE_COLUMN]); + if (awidth[0] > 0) + { + width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better + // weight - but have to make per + // sequence, too (awidth[2]) + // if (width[i]==1) // hack to distinguish single width sequences. + } + else + { + width[i] = 0; + } + if (max < width[i]) + { + max = width[i]; + } + } + boolean sort = false; + for (int i = 0; i < width.length; i++) + { + // awidth = (float[]) typeWidth.get(data[i][0]); + if (width[i] == 0) + { + width[i] = fr.getOrder(data[i][TYPE_COLUMN].toString()); + if (width[i] < 0) + { + width[i] = fr.setOrder(data[i][TYPE_COLUMN].toString(), + i / data.length); + } + } + else + { + width[i] /= max; // normalize + fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later + } + if (i > 0) + { + sort = sort || width[i - 1] > width[i]; + } } if (sort) + { jalview.util.QuickSort.sort(width, data); - // update global priority order - - updateFeatureRenderer(data,false); + // update global priority order + } + + updateFeatureRenderer(data, false); table.repaint(); } + public void close() { try { frame.setClosed(true); + } catch (Exception exe) + { } - catch (Exception exe) - {} } @@ -572,91 +1114,184 @@ public class FeatureSettings { 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); + FeatureSettingsBean[] rowData = getTableAsBeans(data); + + if (fr.setFeaturePriority(rowData, visibleNew)) + { + af.alignPanel.paintAlignment(true, true); + } + } + + /** + * 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; + } + + private void jbInit() throws Exception + { + this.setLayout(new BorderLayout()); + + JPanel settingsPane = new JPanel(); + settingsPane.setLayout(new BorderLayout()); + + dasSettingsPane.setLayout(new BorderLayout()); + + JPanel bigPanel = new JPanel(); + bigPanel.setLayout(new BorderLayout()); - if (af.alignPanel.overviewPanel != null) + groupPanel = new JPanel(); + bigPanel.add(groupPanel, BorderLayout.NORTH); + + JButton invert = new JButton( + MessageManager.getString("label.invert_selection")); + invert.setFont(JvSwingUtils.getLabelFont()); + invert.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + invertSelection(); + } + }); + + JButton optimizeOrder = new JButton( + MessageManager.getString("label.optimise_order")); + optimizeOrder.setFont(JvSwingUtils.getLabelFont()); + optimizeOrder.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + orderByAvWidth(); + } + }); + + JButton sortByScore = new JButton( + MessageManager.getString("label.seq_sort_by_score")); + sortByScore.setFont(JvSwingUtils.getLabelFont()); + sortByScore.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + af.avc.sortAlignmentByFeatureScore(null); + } + }); + JButton sortByDens = new JButton( + MessageManager.getString("label.sequence_sort_by_density")); + sortByDens.setFont(JvSwingUtils.getLabelFont()); + sortByDens.addActionListener(new ActionListener() { - af.alignPanel.overviewPanel.updateOverviewImage(); - } - } + @Override + public void actionPerformed(ActionEvent e) + { + af.avc.sortAlignmentByFeatureDensity(null); + } + }); - int selectedRow = -1; - JTabbedPane tabbedPane = new JTabbedPane(); - BorderLayout borderLayout1 = new BorderLayout(); - BorderLayout borderLayout2 = new BorderLayout(); - BorderLayout borderLayout3 = new BorderLayout(); - JPanel bigPanel = new JPanel(); - BorderLayout borderLayout4 = new BorderLayout(); - JButton invert = new JButton(); - JPanel buttonPanel = new JPanel(); - JButton cancel = new JButton(); - JButton ok = new JButton(); - JButton loadColours = new JButton(); - JButton saveColours = new JButton(); - JPanel dasButtonPanel = new JPanel(); - JButton fetchDAS = new JButton(); - JButton saveDAS = new JButton(); - JButton cancelDAS = new JButton(); - JButton optimizeOrder = new JButton(); - JPanel transbuttons = new JPanel(new BorderLayout()); - private void jbInit() - throws Exception - { - this.setLayout(borderLayout1); - settingsPane.setLayout(borderLayout2); - dasSettingsPane.setLayout(borderLayout3); - bigPanel.setLayout(borderLayout4); - invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - invert.setText("Invert Selection"); - invert.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) { - invertSelection(); + try + { + Help.showHelpWindow(HelpId.SequenceFeatureSettings); + } catch (HelpSetException e1) + { + e1.printStackTrace(); + } } }); - optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - optimizeOrder.setText("Optimise Order"); - optimizeOrder.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - orderByAvWidth(); + help.setFont(JvSwingUtils.getLabelFont()); + help.setText(MessageManager.getString("action.help")); + help.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + Help.showHelpWindow(HelpId.SequenceFeatureSettings); + } catch (HelpSetException e1) + { + e1.printStackTrace(); + } } }); - cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - cancel.setText("Cancel"); + + JButton cancel = new JButton(MessageManager.getString("action.cancel")); + cancel.setFont(JvSwingUtils.getLabelFont()); cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { + fr.setTransparency(originalTransparency); + fr.setFeatureFilters(originalFilters); updateFeatureRenderer(originalData); close(); } }); - ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - ok.setText("OK"); + + JButton ok = new JButton(MessageManager.getString("action.ok")); + ok.setFont(JvSwingUtils.getLabelFont()); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { close(); } }); - loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - loadColours.setText("Load Colours"); + + JButton loadColours = new JButton( + MessageManager.getString("label.load_colours")); + loadColours.setFont(JvSwingUtils.getLabelFont()); + loadColours.setToolTipText( + MessageManager.getString("label.load_colours_tooltip")); loadColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { load(); } }); - saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - saveColours.setText("Save Colours"); + + JButton saveColours = new JButton( + MessageManager.getString("label.save_colours")); + saveColours.setFont(JvSwingUtils.getLabelFont()); + saveColours.setToolTipText( + MessageManager.getString("label.save_colours_tooltip")); saveColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { save(); @@ -664,84 +1299,114 @@ public class FeatureSettings }); transparency.addChangeListener(new ChangeListener() { + @Override public void stateChanged(ChangeEvent evt) { - fr.setTransparency( (float) (100 - transparency.getValue()) / 100f); - af.alignPanel.paintAlignment(true); + if (!inConstruction) + { + fr.setTransparency((100 - transparency.getValue()) / 100f); + af.alignPanel.paintAlignment(true, true); + } } }); transparency.setMaximum(70); - fetchDAS.setText("Fetch DAS Features"); + transparency.setToolTipText( + MessageManager.getString("label.transparency_tip")); + fetchDAS.setText(MessageManager.getString("label.fetch_das_features")); fetchDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { fetchDAS_actionPerformed(e); } }); - saveDAS.setText("Save as default"); + saveDAS.setText(MessageManager.getString("action.save_as_default")); saveDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { saveDAS_actionPerformed(e); } }); + + JPanel dasButtonPanel = new JPanel(); dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); dasSettingsPane.setBorder(null); cancelDAS.setEnabled(false); - cancelDAS.setText("Cancel Fetch"); + cancelDAS.setText(MessageManager.getString("action.cancel_fetch")); cancelDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cancelDAS_actionPerformed(e); } }); - this.add(tabbedPane, java.awt.BorderLayout.CENTER); - tabbedPane.addTab("Feature Settings", settingsPane); - tabbedPane.addTab("DAS Settings", dasSettingsPane); - bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); + + JPanel transPanel = new JPanel(new GridLayout(1, 2)); + bigPanel.add(transPanel, BorderLayout.SOUTH); + + JPanel transbuttons = new JPanel(new GridLayout(5, 1)); + transbuttons.add(optimizeOrder); + transbuttons.add(invert); + transbuttons.add(sortByScore); + transbuttons.add(sortByDens); + transbuttons.add(help); transPanel.add(transparency); - transbuttons.add(invert, java.awt.BorderLayout.NORTH); - transbuttons.add(optimizeOrder,java.awt.BorderLayout.SOUTH); transPanel.add(transbuttons); + + JPanel buttonPanel = new JPanel(); buttonPanel.add(ok); buttonPanel.add(cancel); buttonPanel.add(loadColours); buttonPanel.add(saveColours); - bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER); - dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH); + bigPanel.add(scrollPane, BorderLayout.CENTER); + dasSettingsPane.add(dasButtonPanel, BorderLayout.SOUTH); dasButtonPanel.add(fetchDAS); dasButtonPanel.add(cancelDAS); dasButtonPanel.add(saveDAS); - settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER); - settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH); + settingsPane.add(bigPanel, BorderLayout.CENTER); + settingsPane.add(buttonPanel, BorderLayout.SOUTH); + this.add(settingsPane); } public void fetchDAS_actionPerformed(ActionEvent e) { fetchDAS.setEnabled(false); cancelDAS.setEnabled(true); - Vector selectedSources = dassourceBrowser.getSelectedSources(); + dassourceBrowser.setGuiEnabled(false); + 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(List selectedSources, + boolean checkDbRefs, boolean promptFetchDbRefs) + { SequenceI[] dataset, seqs; int iSize; - - if (af.getViewport().getSelectionGroup() != null - && af.getViewport().getSelectionGroup().getSize() > 0) + AlignmentViewport vp = af.getViewport(); + if (vp.getSelectionGroup() != null + && vp.getSelectionGroup().getSize() > 0) { - iSize = af.getViewport().getSelectionGroup().getSize(); + iSize = vp.getSelectionGroup().getSize(); dataset = new SequenceI[iSize]; - seqs = af.getViewport().getSelectionGroup(). - getSequencesInOrder( - af.getViewport().getAlignment()); + seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment()); } else { - iSize = af.getViewport().getAlignment().getHeight(); - seqs = af.getViewport().getAlignment().getSequencesArray(); + iSize = vp.getAlignment().getHeight(); + seqs = vp.getAlignment().getSequencesArray(); } dataset = new SequenceI[iSize]; @@ -750,50 +1415,139 @@ public class FeatureSettings dataset[i] = seqs[i].getDatasetSequence(); } - dasFeatureFetcher = - new jalview.io.DasSequenceFeatureFetcher( - dataset, - this, - selectedSources); cancelDAS.setEnabled(true); + dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset, + this, selectedSources, checkDbRefs, promptFetchDbRefs); af.getViewport().setShowSequenceFeatures(true); af.showSeqFeatures.setSelected(true); } + /** + * blocking call to initialise the das source browser + */ + public void initDasSources() + { + dassourceBrowser.initDasSources(); + } + + /** + * examine the current list of das sources and return any matching the given + * nicknames in sources + * + * @param sources + * Vector of Strings to resolve to DAS source nicknames. + * @return sources that are present in source list. + */ + public List resolveSourceNicknames(Vector sources) + { + return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); + } + + /** + * get currently selected das sources. ensure you have called initDasSources + * before calling this. + * + * @return vector of selected das source nicknames + */ + public Vector getSelectedSources() + { + return dassourceBrowser.getSelectedSources(); + } + + /** + * 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 + * @param block + * if true then runs in same thread, otherwise passes to the Swing + * executor + */ + public void fetchDasFeatures(Vector sources, boolean block) + { + initDasSources(); + List resolved = dassourceBrowser.sourceRegistry + .resolveSourceNicknames(sources); + if (resolved.size() == 0) + { + resolved = dassourceBrowser.getSelectedSources(); + } + if (resolved.size() > 0) + { + final List dassources = resolved; + fetchDAS.setEnabled(false); + // cancelDAS.setEnabled(true); doDasFetch does this. + Runnable fetcher = new Runnable() + { + + @Override + public void run() + { + doDasFeatureFetch(dassources, true, false); + + } + }; + if (block) + { + fetcher.run(); + } + else + { + SwingUtilities.invokeLater(fetcher); + } + } + } + public void saveDAS_actionPerformed(ActionEvent e) { - dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties); + dassourceBrowser + .saveProperties(jalview.bin.Cache.applicationProperties); } public void complete() { fetchDAS.setEnabled(true); cancelDAS.setEnabled(false); + dassourceBrowser.setGuiEnabled(true); + } public void cancelDAS_actionPerformed(ActionEvent e) { - dasFeatureFetcher.cancel(); - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); + if (dasFeatureFetcher != null) + { + dasFeatureFetcher.cancel(); + } + complete(); + } + + public void noDasSourceActive() + { + complete(); + 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); } - ///////////////////////////////////////////////////////////////////////// + // /////////////////////////////////////////////////////////////////////// // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html - ///////////////////////////////////////////////////////////////////////// - class FeatureTableModel - extends AbstractTableModel + // /////////////////////////////////////////////////////////////////////// + class FeatureTableModel extends AbstractTableModel { + private String[] columnNames = { + MessageManager.getString("label.feature_type"), + MessageManager.getString("action.colour"), + MessageManager.getString("label.filter"), + 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; @@ -804,6 +1558,7 @@ public class FeatureSettings this.data = data; } + @Override public int getColumnCount() { return columnNames.length; @@ -814,31 +1569,41 @@ public class FeatureSettings return data[row]; } + @Override public int getRowCount() { return data.length; } + @Override public String getColumnName(int col) { return columnNames[col]; } + @Override public Object getValueAt(int row, int col) { return data[row][col]; } - public Class getColumnClass(int c) + /** + * Answers the class of 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; @@ -848,30 +1613,47 @@ public class FeatureSettings } - class ColorRenderer - extends JLabel implements TableCellRenderer + class ColorRenderer extends JLabel implements TableCellRenderer { javax.swing.border.Border unselectedBorder = null; + 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. + 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); } @@ -880,88 +1662,474 @@ public class FeatureSettings if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getBackground()); + tbl.getBackground()); } setBorder(unselectedBorder); } - setToolTipText("RGB value: " + newColor.getRed() + ", " - + newColor.getGreen() + ", " - + newColor.getBlue()); return this; } } -} -class ColorEditor - extends AbstractCellEditor implements TableCellEditor, - ActionListener -{ - Color currentColor; - JButton button; - JColorChooser colorChooser; - JDialog dialog; - protected static final String EDIT = "edit"; - - public ColorEditor() - { - //Set up the editor (from the table's point of view), - //which is a button. - //This button brings up the color chooser dialog, - //which is the editor from the user's point of view. - button = new JButton(); - button.setActionCommand(EDIT); - button.addActionListener(this); - button.setBorderPainted(false); - //Set up the dialog that the button brings up. - colorChooser = new JColorChooser(); - dialog = JColorChooser.createDialog(button, - "Select new Colour", - true, //modal - colorChooser, - this, //OK button handler - null); //no CANCEL button handler + class FilterRenderer extends JLabel implements TableCellRenderer + { + javax.swing.border.Border unselectedBorder = null; + + javax.swing.border.Border selectedBorder = null; + + public FilterRenderer() + { + setOpaque(true); // MUST do this for background to show up. + setHorizontalTextPosition(SwingConstants.CENTER); + setVerticalTextPosition(SwingConstants.CENTER); + } + + @Override + public Component getTableCellRendererComponent(JTable tbl, + Object filter, boolean isSelected, boolean hasFocus, int row, + int column) + { + FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter; + setOpaque(true); + String asText = theFilter.toString(); + setBackground(tbl.getBackground()); + this.setText(asText); + this.setIcon(null); + + if (isSelected) + { + if (selectedBorder == null) + { + selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + tbl.getSelectionBackground()); + } + setBorder(selectedBorder); + } + else + { + if (unselectedBorder == null) + { + unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + tbl.getBackground()); + } + setBorder(unselectedBorder); + } + + return this; + } + } + + /** + * update comp using rendering settings from gcol + * + * @param comp + * @param gcol + */ + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol) + { + int w = comp.getWidth(), h = comp.getHeight(); + if (w < 20) + { + w = (int) comp.getPreferredSize().getWidth(); + h = (int) comp.getPreferredSize().getHeight(); + if (w < 20) + { + w = 80; + h = 12; + } + } + renderGraduatedColor(comp, gcol, w, h); + } + + 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); + chooser.setRequestFocusEnabled(true); + chooser.requestFocus(); + chooser.addActionListener(this); + chooser.showTab(true); + } + // Make the renderer reappear. + fireEditingStopped(); + + } + else + { + if (currentColor.isSimpleColour()) + { + /* + * read off colour picked in colour chooser after OK pressed + */ + currentColor = new FeatureColour(colorChooser.getColor()); + me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN); + } + else + { + /* + * after OK in variable colour dialog, any changes to colour + * (or filters!) are already set in FeatureRenderer, so just + * update table data without triggering updateFeatureRenderer + */ + currentColor = fr.getFeatureColours().get(type); + 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(); + } + chooser.showTab(false); + fireEditingStopped(); + } + else if (e.getSource() instanceof Component) + { + + /* + * after OK in variable colour dialog, any changes to filter + * (or colours!) are already set in FeatureRenderer, so just + * update table data without triggering updateFeatureRenderer + */ + FeatureColourI currentColor = fr.getFeatureColours().get(type); + currentFilter = me.fr.getFeatureFilter(type); + if (currentFilter == null) + { + currentFilter = new FeatureMatcherSet(); + } + Object[] data = ((FeatureTableModel) table.getModel()) + .getData()[rowSelected]; + data[COLOUR_COLUMN] = currentColor; + data[FILTER_COLUMN] = currentFilter; + fireEditingStopped(); + me.table.validate(); + } + } + + @Override + public Object getCellEditorValue() + { + return currentFilter; + } - if (EDIT.equals(e.getActionCommand())) + @Override + public Component getTableCellEditorComponent(JTable theTable, Object value, + boolean isSelected, int row, int column) { - //The user has clicked the cell, so - //bring up the dialog. - button.setBackground(currentColor); - colorChooser.setColor(currentColor); - dialog.setVisible(true); + 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; + } + } +} - //Make the renderer reappear. - fireEditingStopped(); +class FeatureIcon implements Icon +{ + FeatureColourI gcol; + + Color backg; + + boolean midspace = false; + + int width = 50, height = 20; + int s1, e1; // start and end of midpoint band for thresholded symbol + + Color mpcolour = Color.white; + + FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace) + { + gcol = gfc; + backg = bg; + width = w; + height = h; + midspace = mspace; + if (midspace) + { + s1 = width / 3; + e1 = s1 * 2; } else - { //User pressed dialog's "OK" button. - currentColor = colorChooser.getColor(); + { + s1 = width / 2; + e1 = s1; } } - //Implement the one CellEditor method that AbstractCellEditor doesn't. - public Object getCellEditorValue() + @Override + public int getIconWidth() + { + return width; + } + + @Override + public int getIconHeight() { - return currentColor; + return height; } - //Implement the one method defined by TableCellEditor. - public Component getTableCellEditorComponent(JTable table, - Object value, - boolean isSelected, - int row, - int column) + @Override + public void paintIcon(Component c, Graphics g, int x, int y) { - currentColor = (Color) value; - return button; + + if (gcol.isColourByLabel()) + { + g.setColor(backg); + g.fillRect(0, 0, width, height); + // need an icon here. + g.setColor(gcol.getMaxColour()); + + g.setFont(new Font("Verdana", Font.PLAIN, 9)); + + // g.setFont(g.getFont().deriveFont( + // AffineTransform.getScaleInstance( + // width/g.getFontMetrics().stringWidth("Label"), + // height/g.getFontMetrics().getHeight()))); + + g.drawString(MessageManager.getString("label.label"), 0, 0); + + } + else + { + Color minCol = gcol.getMinColour(); + g.setColor(minCol); + g.fillRect(0, 0, s1, height); + if (midspace) + { + g.setColor(Color.white); + g.fillRect(s1, 0, e1 - s1, height); + } + g.setColor(gcol.getMaxColour()); + g.fillRect(0, e1, width - e1, height); + } } }