X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=63f1b137853a8af84f0f6133616d324222623264;hb=ad79fcf0705b71f2504b1ed4092d54a8c45ef09f;hp=db93724bd332f22bed87db6c18a160fcc66ea5d9;hpb=79912985d2d21c7d456bbd2281ed84fdfe2e99e7;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java old mode 100755 new mode 100644 index db93724..63f1b13 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,41 +1,104 @@ /* - * 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.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; +import jalview.gui.Help.HelpId; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.schemabinding.version2.JalviewUserColours; +import jalview.schemes.FeatureColour; +import jalview.util.Format; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.QuickSort; +import jalview.viewmodel.AlignmentViewport; +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.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.analysis.AlignmentSorter; -import jalview.commands.OrderCommand; -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.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.JTabbedPane; +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; public class FeatureSettings extends JPanel + implements FeatureSettingsControllerI { DasSourceBrowser dassourceBrowser; @@ -51,6 +114,8 @@ public class FeatureSettings extends JPanel Object[][] originalData; + private float originalTransparency; + final JInternalFrame frame; JScrollPane scrollPane = new JScrollPane(); @@ -61,14 +126,29 @@ public class FeatureSettings extends JPanel JSlider transparency = new JSlider(); - JPanel transPanel = new JPanel(new FlowLayout()); + JPanel transPanel = new JPanel(new GridLayout(1, 2)); + + private static final int MIN_WIDTH = 400; + private static final int MIN_HEIGHT = 400; + + /** + * when true, constructor is still executing - so ignore UI events + */ + protected volatile boolean inConstruction = true; + + /** + * Constructor + * + * @param af + */ public FeatureSettings(AlignFrame af) { this.af = af; fr = af.getFeatureRenderer(); - - transparency.setMaximum(100 - (int) (fr.transparency * 100)); + // allow transparency to be recovered + transparency.setMaximum(100 + - (int) ((originalTransparency = fr.getTransparency()) * 100)); try { @@ -78,23 +158,64 @@ public class FeatureSettings extends JPanel ex.printStackTrace(); } - table = new JTable(); + table = new JTable() + { + @Override + public String getToolTipText(MouseEvent e) + { + if (table.columnAtPoint(e.getPoint()) == 0) + { + /* + * Tooltip for feature name only + */ + return JvSwingUtils.wrapTooltip(true, MessageManager + .getString("label.feature_settings_click_drag")); + } + return null; + } + }; 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.setDefaultEditor(Color.class, new ColorEditor(this)); + table.setDefaultEditor(FeatureColour.class, new ColorEditor(this)); + table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); - if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + if (evt.isPopupTrigger()) { - popupSort((String) table.getValueAt(selectedRow, 0), fr.minmax, + popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), + table.getValueAt(selectedRow, 1), fr.getMinMax(), + evt.getX(), evt.getY()); + } + else if (evt.getClickCount() == 2) + { + boolean invertSelection = evt.isAltDown(); + boolean toggleSelection = Platform.isControlDown(evt); + boolean extendSelection = evt.isShiftDown(); + fr.ap.alignFrame.avc.markColumnsContainingFeatures( + invertSelection, extendSelection, toggleSelection, + (String) table.getValueAt(selectedRow, 0)); + } + } + + // isPopupTrigger fires on mouseReleased on Windows + @Override + public void mouseReleased(MouseEvent evt) + { + selectedRow = table.rowAtPoint(evt.getPoint()); + if (evt.isPopupTrigger()) + { + popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), + table.getValueAt(selectedRow, 1), fr.getMinMax(), evt.getX(), evt.getY()); } } @@ -102,45 +223,50 @@ public class FeatureSettings extends JPanel 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(); + dassourceBrowser = new DasSourceBrowser(this); dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - if (af.getViewport().featuresDisplayed == null - || fr.renderOrder == null) + if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) { fr.findAllFeatures(true); // display everything! } - setTableData(); + discoverAllFeatureData(); final PropertyChangeListener change; final FeatureSettings fs = this; fr.addPropertyChangeListener(change = new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (!fs.resettingTable && !fs.handlingUpdate) @@ -156,72 +282,199 @@ 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"), + 475, 480); + } + else + { + Desktop.addInternalFrame(frame, + MessageManager.getString("label.sequence_feature_settings"), + 400, 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; } - protected void popupSort(final String type, final Hashtable minmax, - int x, int y) + protected void popupSort(final int selectedRow, final String type, + final Object typeCol, final Map minmax, int x, + int y) { - JPopupMenu men = new JPopupMenu("Settings for " + type); - JMenuItem scr = new JMenuItem("Sort by Score"); + 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() { + @Override public void actionPerformed(ActionEvent e) { - me.sortByScore(new String[] - { type }); + me.af.avc + .sortAlignmentByFeatureScore(Arrays.asList(new String[] + { type })); } }); - JMenuItem dens = new JMenuItem("Sort by Density"); + JMenuItem dens = new JMenuItem( + MessageManager.getString("label.sort_by_density")); dens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.sortByDens(new String[] - { type }); + me.af.avc + .sortAlignmentByFeatureDensity(Arrays.asList(new String[] + { type })); } }); men.add(dens); if (minmax != null) { - final Object typeMinMax = minmax.get(type); - final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); - chb.setSelected(minmax.get(type) != null); - chb.addActionListener(new ActionListener() + final float[][] typeMinMax = minmax.get(type); + /* + * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); // + * this is broken at the moment and isn't that useful anyway! + * chb.setSelected(minmax.get(type) != null); chb.addActionListener(new + * ActionListener() { + * + * public void actionPerformed(ActionEvent e) { + * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type, + * null); } else { minmax.put(type, typeMinMax); } } + * + * }); + * + * men.add(chb); + */ + if (typeMinMax != null && typeMinMax[0] != null) { - - public void actionPerformed(ActionEvent e) + // if (table.getValueAt(row, column)); + // graduated colourschemes for those where minmax exists for the + // positional features + final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( + "Graduated Colour"); + mxcol.setSelected(!featureColour.isSimpleColour()); + men.add(mxcol); + mxcol.addActionListener(new ActionListener() { - chb.setState(chb.getState()); - if (chb.getState()) - { - minmax.put(type, null); - } - else + JColorChooser colorChooser; + + @Override + public void actionPerformed(ActionEvent e) { - minmax.put(type, typeMinMax); + if (e.getSource() == mxcol) + { + if (featureColour.isSimpleColour()) + { + FeatureColourChooser fc = new FeatureColourChooser(me.fr, + type); + fc.addActionListener(this); + } + else + { + // bring up simple color chooser + colorChooser = new JColorChooser(); + JDialog dialog = JColorChooser.createDialog(me, + "Select new Colour", true, // modal + colorChooser, this, // OK button handler + null); // no CANCEL button handler + colorChooser.setColor(featureColour.getMaxColour()); + dialog.setVisible(true); + } + } + else + { + if (e.getSource() instanceof FeatureColourChooser) + { + FeatureColourChooser fc = (FeatureColourChooser) e + .getSource(); + table.setValueAt(fc.getLastColour(), selectedRow, 1); + table.validate(); + } + else + { + // probably the color chooser! + table.setValueAt(new FeatureColour(colorChooser.getColor()), + selectedRow, 1); + table.validate(); + me.updateFeatureRenderer( + ((FeatureTableModel) table.getModel()).getData(), + false); + } + } } - } - }); - men.add(chb); + }); + } } + 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); } @@ -231,58 +484,26 @@ public class FeatureSettings extends JPanel private boolean handlingUpdate = false; /** - * contains a float[3] for each feature type string. created by setTableData + * holds {featureCount, totalExtent} for each feature type */ - Hashtable typeWidth = null; + Map typeWidth = null; - synchronized public void setTableData() + @Override + synchronized public void discoverAllFeatureData() { - if (fr.featureGroups == null) - { - fr.featureGroups = new Hashtable(); - } - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); - SequenceFeature[] tmpfeatures; - String group; - for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) - { - if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence() - .getSequenceFeatures() == null) - { - continue; - } - - tmpfeatures = af.getViewport().alignment.getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures(); + Set allGroups = new HashSet<>(); + AlignmentI alignment = af.getViewport().getAlignment(); - int index = 0; - while (index < tmpfeatures.length) + for (int i = 0; i < alignment.getHeight(); i++) + { + SequenceI seq = alignment.getSequenceAt(i); + for (String group : seq.getFeatures().getFeatureGroups(true)) { - if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) - { - index++; - continue; - } - - if (tmpfeatures[index].getFeatureGroup() != null) - { - group = tmpfeatures[index].featureGroup; - if (!allGroups.contains(group)) - { - allGroups.addElement(group); - if (group != null) - { - checkGroupState(group); - } - } - } - - if (!allFeatures.contains(tmpfeatures[index].getType())) + if (group != null && !allGroups.contains(group)) { - allFeatures.addElement(tmpfeatures[index].getType()); + allGroups.add(group); + checkGroupState(group); } - index++; } } @@ -292,217 +513,272 @@ 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(); + fr.setGroupVisibility(check.getText(), check.isSelected()); + af.alignPanel.getSeqPanel().seqCanvas.repaint(); if (af.alignPanel.overviewPanel != null) { af.alignPanel.overviewPanel.updateOverviewImage(); } - resetTable(new String[] - { grp }); + resetTable(new String[] { grp }); } }); 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) + if (group == null || checkGroupState(group)) { - index++; - continue; + visibleGroups.add(group); } - - if (group == null || fr.featureGroups.get(group) == null - || ((Boolean) fr.featureGroups.get(group)).booleanValue()) - { - if (group != null) - checkGroupState(group); - type = tmpfeatures[index].getType(); - if (!visibleChecks.contains(type)) - { - visibleChecks.addElement(type); - } - } - if (!typeWidth.containsKey(tmpfeatures[index].getType())) - { - typeWidth.put(tmpfeatures[index].getType(), - avWidth = new float[3]); - } - else - { - avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType()); - } - avWidth[0]++; - if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd()) - { - avWidth[1] += 1 + tmpfeatures[index].getBegin() - - tmpfeatures[index].getEnd(); - } - else + } + foundGroups.addAll(groups); + + /* + * get distinct feature types for visible groups + * record distinct visible types, and their count and total length + */ + Set types = seq.getFeatures().getFeatureTypesForGroups(true, + visibleGroups.toArray(new String[visibleGroups.size()])); + for (String type : types) + { + displayableTypes.add(type); + float[] avWidth = typeWidth.get(type); + if (avWidth == null) { - avWidth[1] += 1 + tmpfeatures[index].getEnd() - - tmpfeatures[index].getBegin(); + avWidth = new float[2]; + typeWidth.put(type, avWidth); } - index++; + // todo this could include features with a non-visible group + // - do we greatly care? + // todo should we include non-displayable features here, and only + // update when features are added? + avWidth[0] += seq.getFeatures().getFeatureCount(true, type); + avWidth[1] += seq.getFeatures().getTotalFeatureLength(type); } } - int fSize = visibleChecks.size(); - Object[][] data = new Object[fSize][3]; + Object[][] data = new Object[displayableTypes.size()][3]; int dataIndex = 0; - if (fr.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][1] = fr.getFeatureStyle(type); + data[dataIndex][2] = new Boolean( + af.getViewport().getFeaturesDisplayed().isVisible(type)); dataIndex++; - visibleChecks.removeElement(type); + displayableTypes.remove(type); } } - fSize = visibleChecks.size(); - for (int i = 0; i < fSize; i++) + /* + * process any extra features belonging only to + * a group which was just selected + */ + while (!displayableTypes.isEmpty()) { - // These must be extra features belonging to the group - // which was just selected - type = visibleChecks.elementAt(i).toString(); + String type = displayableTypes.iterator().next(); data[dataIndex][0] = type; - data[dataIndex][1] = fr.getColour(type); + data[dataIndex][1] = fr.getFeatureStyle(type); if (data[dataIndex][1] == null) { // "Colour has been updated in another view!!" - fr.renderOrder = null; + fr.clearRenderOrder(); return; } data[dataIndex][2] = new Boolean(true); dataIndex++; + displayableTypes.remove(type); } if (originalData == null) { originalData = new Object[data.length][3]; - System.arraycopy(data, 0, originalData, 0, data.length); + for (int i = 0; i < data.length; i++) + { + System.arraycopy(data[i], 0, originalData[i], 0, 3); + } + } + else + { + updateOriginalData(data); } table.setModel(new FeatureTableModel(data)); table.getColumnModel().getColumn(0).setPreferredWidth(200); - if (groupPanel != null) - { - groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1, - 4)); - - groupPanel.validate(); - bigPanel.add(groupPanel, BorderLayout.NORTH); - } + groupPanel.setLayout( + new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4)); + pruneGroups(foundGroups); + groupPanel.validate(); updateFeatureRenderer(data, groupChanged != null); resettingTable = false; } /** + * Updates 'originalData' (used for restore on Cancel) if we detect that + * changes have been made outwith this dialog + *
    + *
  • a new feature type added (and made visible)
    • + *
  • a feature colour changed (in the Amend Features dialog)
    • + *
+ * + * @param foundData + */ + protected void updateOriginalData(Object[][] foundData) + { + // todo LinkedHashMap instead of Object[][] would be nice + + Object[][] currentData = ((FeatureTableModel) table.getModel()) + .getData(); + for (Object[] row : foundData) + { + String type = (String) row[0]; + boolean found = false; + for (Object[] current : currentData) + { + if (type.equals(current[0])) + { + found = true; + /* + * currently dependent on object equality here; + * really need an equals method on FeatureColour + */ + if (!row[1].equals(current[1])) + { + /* + * feature colour has changed externally - update originalData + */ + for (Object[] original : originalData) + { + if (type.equals(original[0])) + { + original[1] = row[1]; + break; + } + } + } + break; + } + } + if (!found) + { + /* + * new feature detected - add to original data (on top) + */ + Object[][] newData = new Object[originalData.length + 1][3]; + for (int i = 0; i < originalData.length; i++) + { + System.arraycopy(originalData[i], 0, newData[i + 1], 0, 3); + } + newData[0] = row; + originalData = newData; + } + } + } + + /** + * Remove from the groups panel any checkboxes for groups that are not in the + * foundGroups set. This enables removing a group from the display when the + * last feature in that group is deleted. + * + * @param foundGroups + */ + protected void pruneGroups(Set foundGroups) + { + for (int g = 0; g < groupPanel.getComponentCount(); g++) + { + JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g); + if (!foundGroups.contains(checkbox.getText())) + { + groupPanel.remove(checkbox); + } + } + } + + /** * reorder data based on the featureRenderers global priority list. * * @param data @@ -515,23 +791,28 @@ 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); + } } 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); @@ -541,17 +822,63 @@ public class FeatureSettings extends JPanel try { - InputStreamReader in = new InputStreamReader(new FileInputStream( - file), "UTF-8"); + InputStreamReader in = new InputStreamReader( + new FileInputStream(file), "UTF-8"); - jalview.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))); + jalview.schemabinding.version2.Colour newcol = jucs.getColour(i); + if (newcol.hasMax()) + { + Color mincol = null, maxcol = null; + try + { + mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16)); + maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16)); + + } catch (Exception e) + { + Cache.log.warn("Couldn't parse out graduated feature color.", + e); + } + FeatureColourI gcol = new FeatureColour(mincol, maxcol, + newcol.getMin(), newcol.getMax()); + if (newcol.hasAutoScale()) + { + gcol.setAutoScaled(newcol.getAutoScale()); + } + if (newcol.hasColourByLabel()) + { + gcol.setColourByLabel(newcol.getColourByLabel()); + } + if (newcol.hasThreshold()) + { + gcol.setThreshold(newcol.getThreshold()); + } + if (newcol.getThreshType().length() > 0) + { + String ttyp = newcol.getThreshType(); + if (ttyp.equalsIgnoreCase("ABOVE")) + { + gcol.setAboveThreshold(true); + } + if (ttyp.equalsIgnoreCase("BELOW")) + { + gcol.setBelowThreshold(true); + } + } + fr.setColour(name = newcol.getName(), gcol); + } + else + { + Color color = new Color( + Integer.parseInt(jucs.getColour(i).getRGB(), 16)); + fr.setColour(name = jucs.getColour(i).getName(), + new FeatureColour(color)); + } fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount()); } if (table != null) @@ -572,44 +899,60 @@ public class FeatureSettings extends JPanel void save() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), new String[] - { "fc" }, new String[] - { "Sequence Feature Colours" }, "Sequence Feature Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("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(); + jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours(); ucs.setSchemeName("Sequence Features"); try { PrintWriter out = new PrintWriter(new OutputStreamWriter( new FileOutputStream(choice), "UTF-8")); - Enumeration e = fr.featureColours.keys(); - float[] sortOrder = new float[fr.featureColours.size()]; - String[] sortTypes = new String[fr.featureColours.size()]; + Set fr_colours = fr.getAllFeatureColours(); + Iterator e = fr_colours.iterator(); + float[] sortOrder = new float[fr_colours.size()]; + String[] sortTypes = new String[fr_colours.size()]; int i = 0; - while (e.hasMoreElements()) + while (e.hasNext()) { - sortTypes[i] = e.nextElement().toString(); + sortTypes[i] = e.next(); sortOrder[i] = fr.getOrder(sortTypes[i]); i++; } - jalview.util.QuickSort.sort(sortOrder, sortTypes); + QuickSort.sort(sortOrder, sortTypes); sortOrder = null; for (i = 0; i < sortTypes.length; i++) { - jalview.binding.Colour col = new jalview.binding.Colour(); + jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setName(sortTypes[i]); - col.setRGB(jalview.util.Format.getHexString(fr.getColour(col - .getName()))); + FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]); + if (fcol.isSimpleColour()) + { + col.setRGB(Format.getHexString(fcol.getColour())); + } + else + { + col.setRGB(Format.getHexString(fcol.getMaxColour())); + col.setMin(fcol.getMin()); + col.setMax(fcol.getMax()); + col.setMinRGB( + jalview.util.Format.getHexString(fcol.getMinColour())); + col.setAutoScale(fcol.isAutoScaled()); + col.setThreshold(fcol.getThreshold()); + col.setColourByLabel(fcol.isColourByLabel()); + col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" + : (fcol.isBelowThreshold() ? "BELOW" : "NONE")); + } ucs.addColour(col); } ucs.marshal(out); @@ -634,7 +977,9 @@ public class FeatureSettings extends JPanel public void orderByAvWidth() { if (table == null || table.getModel() == null) + { return; + } Object[][] data = ((FeatureTableModel) table.getModel()).getData(); float[] width = new float[data.length]; float[] awidth; @@ -642,7 +987,7 @@ public class FeatureSettings extends JPanel int num = 0; for (int i = 0; i < data.length; i++) { - awidth = (float[]) typeWidth.get(data[i][0]); + awidth = typeWidth.get(data[i][0]); if (awidth[0] > 0) { width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better @@ -656,7 +1001,9 @@ public class FeatureSettings extends JPanel width[i] = 0; } if (max < width[i]) + { max = width[i]; + } } boolean sort = false; for (int i = 0; i < width.length; i++) @@ -676,11 +1023,15 @@ public class FeatureSettings extends JPanel fr.setOrder(data[i][0].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(); @@ -702,10 +1053,19 @@ public class FeatureSettings extends JPanel updateFeatureRenderer(data, true); } + /** + * Update the priority order of features; only repaint if this changed the + * order of visible features + * + * @param data + * @param visibleNew + */ private void updateFeatureRenderer(Object[][] data, boolean visibleNew) { - fr.setFeaturePriority(data, visibleNew); - af.alignPanel.paintAlignment(true); + if (fr.setFeaturePriority(data, visibleNew)) + { + af.alignPanel.paintAlignment(true); + } } int selectedRow = -1; @@ -748,7 +1108,9 @@ public class FeatureSettings extends JPanel JButton sortByDens = new JButton(); - JPanel transbuttons = new JPanel(new BorderLayout()); + JButton help = new JButton(); + + JPanel transbuttons = new JPanel(new GridLayout(5, 1)); private void jbInit() throws Exception { @@ -756,74 +1118,121 @@ public class FeatureSettings extends JPanel settingsPane.setLayout(borderLayout2); dasSettingsPane.setLayout(borderLayout3); bigPanel.setLayout(borderLayout4); - invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - invert.setText("Invert Selection"); + + groupPanel = new JPanel(); + bigPanel.add(groupPanel, BorderLayout.NORTH); + + invert.setFont(JvSwingUtils.getLabelFont()); + invert.setText(MessageManager.getString("label.invert_selection")); 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"); + optimizeOrder.setFont(JvSwingUtils.getLabelFont()); + optimizeOrder.setText(MessageManager.getString("label.optimise_order")); optimizeOrder.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { orderByAvWidth(); } }); - sortByScore.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - sortByScore.setText("Seq sort by Score"); + sortByScore.setFont(JvSwingUtils.getLabelFont()); + sortByScore + .setText(MessageManager.getString("label.seq_sort_by_score")); sortByScore.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - sortByScore(null); + af.avc.sortAlignmentByFeatureScore(null); } }); - sortByDens.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - sortByDens.setText("Seq Sort by density"); + sortByDens.setFont(JvSwingUtils.getLabelFont()); + sortByDens.setText( + MessageManager.getString("label.sequence_sort_by_density")); sortByDens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - sortByDens(null); + af.avc.sortAlignmentByFeatureDensity(null); } }); - cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - cancel.setText("Cancel"); + 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(); + } + } + }); + 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(JvSwingUtils.getLabelFont()); + cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { + fr.setTransparency(originalTransparency); updateFeatureRenderer(originalData); close(); } }); - ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - ok.setText("OK"); + ok.setFont(JvSwingUtils.getLabelFont()); + ok.setText(MessageManager.getString("action.ok")); 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"); + loadColours.setFont(JvSwingUtils.getLabelFont()); + loadColours.setText(MessageManager.getString("label.load_colours")); 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"); + saveColours.setFont(JvSwingUtils.getLabelFont()); + saveColours.setText(MessageManager.getString("label.save_colours")); saveColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { save(); @@ -831,25 +1240,33 @@ public class FeatureSettings extends JPanel }); 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); + } } }); 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); @@ -858,28 +1275,34 @@ public class FeatureSettings extends 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); + tabbedPane.addTab(MessageManager.getString("label.feature_settings"), + settingsPane); + tabbedPane.addTab(MessageManager.getString("label.das_settings"), + dasSettingsPane); bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); + transbuttons.add(optimizeOrder); + transbuttons.add(invert); + transbuttons.add(sortByScore); + transbuttons.add(sortByDens); + transbuttons.add(help); + JPanel sliderPanel = new JPanel(); + sliderPanel.add(transparency); transPanel.add(transparency); - 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); - buttonPanel.add(sortByScore); - buttonPanel.add(sortByDens); bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER); dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH); dasButtonPanel.add(fetchDAS); @@ -889,123 +1312,13 @@ public class FeatureSettings extends JPanel settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH); } - protected void sortByDens(String[] typ) - { - sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); - } - - protected void sortBy(String[] typ, String methodText, final String method) - { - if (typ == null) - { - typ = getDisplayedFeatureTypes(); - } - String gps[] = null; - gps = getDisplayedFeatureGroups(); - if (typ != null) - { - for (int i = 0; i < typ.length; i++) - { - System.err.println("Sorting on Types:" + typ[i]); - } - } - if (gps != null) - { - - for (int i = 0; i < gps.length; i++) - { - System.err.println("Sorting on groups:" + gps[i]); - } - } - AlignmentPanel alignPanel = af.alignPanel; - AlignmentI al = alignPanel.av.getAlignment(); - - int start, stop; - SequenceGroup sg = alignPanel.av.getSelectionGroup(); - if (sg != null) - { - start = sg.getStartRes(); - stop = sg.getEndRes(); - } - else - { - start = 0; - stop = al.getWidth(); - } - SequenceI[] oldOrder = al.getSequencesArray(); - AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); - af.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av - .getAlignment())); - alignPanel.paintAlignment(true); - - } - - protected void sortByScore(String[] typ) - { - sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); - } - - private String[] getDisplayedFeatureTypes() - { - String[] typ = null; - if (fr != null) - { - synchronized (fr.renderOrder) - { - typ = new String[fr.renderOrder.length]; - System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length); - for (int i = 0; i < typ.length; i++) - { - if (af.viewport.featuresDisplayed.get(typ[i]) == null) - { - typ[i] = null; - } - } - } - } - return typ; - } - - private String[] getDisplayedFeatureGroups() - { - String[] gps = null; - if (fr != null) - { - - if (fr.featureGroups != null) - { - Enumeration en = fr.featureGroups.keys(); - gps = new String[fr.featureColours.size()]; - int g = 0; - boolean valid = false; - while (en.hasMoreElements()) - { - String gp = (String) en.nextElement(); - Boolean on = (Boolean) fr.featureGroups.get(gp); - if (on != null && on.booleanValue()) - { - valid = true; - gps[g++] = gp; - } - } - while (g < gps.length) - { - gps[g++] = null; - } - if (!valid) - { - return null; - } - } - } - return gps; - } - 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); } @@ -1016,12 +1329,12 @@ public class FeatureSettings extends JPanel * @param checkDbRefs * @param promptFetchDbRefs */ - private void doDasFeatureFetch(Vector selectedSources, + private void doDasFeatureFetch(List selectedSources, boolean checkDbRefs, boolean promptFetchDbRefs) { SequenceI[] dataset, seqs; int iSize; - AlignViewport vp = af.getViewport(); + AlignmentViewport vp = af.getViewport(); if (vp.getSelectionGroup() != null && vp.getSelectionGroup().getSize() > 0) { @@ -1061,12 +1374,12 @@ public class FeatureSettings extends JPanel * nicknames in sources * * @param sources - * Vector of Strings to resolve to DAS source nicknames. + * Vector of Strings to resolve to DAS source nicknames. * @return sources that are present in source list. */ - public Vector resolveSourceNicknames(Vector sources) + public List resolveSourceNicknames(Vector sources) { - return dassourceBrowser.resolveSourceNicknames(sources); + return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); } /** @@ -1075,7 +1388,7 @@ public class FeatureSettings extends JPanel * * @return vector of selected das source nicknames */ - public Vector getSelectedSources() + public Vector getSelectedSources() { return dassourceBrowser.getSelectedSources(); } @@ -1085,29 +1398,42 @@ public class FeatureSettings extends JPanel * 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) + public void fetchDasFeatures(Vector sources, boolean block) { initDasSources(); - Vector resolved = resolveSourceNicknames(sources); + List resolved = dassourceBrowser.sourceRegistry + .resolveSourceNicknames(sources); if (resolved.size() == 0) { resolved = dassourceBrowser.getSelectedSources(); } if (resolved.size() > 0) { - final Vector dassources = resolved; - SwingUtilities.invokeLater(new Runnable() + final List dassources = resolved; + fetchDAS.setEnabled(false); + // cancelDAS.setEnabled(true); doDasFetch does this. + Runnable fetcher = new Runnable() { + @Override public void run() { - fetchDAS.setEnabled(false); - cancelDAS.setEnabled(true); doDasFeatureFetch(dassources, true, false); } - }); + }; + if (block) + { + fetcher.run(); + } + else + { + SwingUtilities.invokeLater(fetcher); + } } } @@ -1121,6 +1447,8 @@ public class FeatureSettings extends JPanel { fetchDAS.setEnabled(true); cancelDAS.setEnabled(false); + dassourceBrowser.setGuiEnabled(true); + } public void cancelDAS_actionPerformed(ActionEvent e) @@ -1129,18 +1457,16 @@ public class FeatureSettings extends JPanel { dasFeatureFetcher.cancel(); } - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); + complete(); } 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); + 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); } // /////////////////////////////////////////////////////////////////////// @@ -1153,8 +1479,10 @@ public class FeatureSettings extends JPanel this.data = data; } - private String[] columnNames = - { "Feature Type", "Colour", "Display" }; + private String[] columnNames = { + MessageManager.getString("label.feature_type"), + MessageManager.getString("action.colour"), + MessageManager.getString("label.display") }; private Object[][] data; @@ -1168,6 +1496,7 @@ public class FeatureSettings extends JPanel this.data = data; } + @Override public int getColumnCount() { return columnNames.length; @@ -1178,31 +1507,37 @@ public class FeatureSettings extends JPanel return data[row]; } + @Override public int getRowCount() { return data.length; } + @Override public String getColumnName(int col) { return columnNames[col]; } + @Override public Object getValueAt(int row, int col) { return data[row][col]; } + @Override public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } + @Override public boolean isCellEditable(int row, int col) { return col == 0 ? false : true; } + @Override public void setValueAt(Object value, int row, int col) { data[row][col] = value; @@ -1218,23 +1553,48 @@ 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) - { - Color newColor = (Color) color; - setBackground(newColor); + @Override + public Component getTableCellRendererComponent(JTable tbl, Object color, + boolean isSelected, boolean hasFocus, int row, int column) + { + FeatureColourI cellColour = (FeatureColourI) color; + // JLabel comp = new JLabel(); + // comp. + setOpaque(true); + // comp. + // setBounds(getBounds()); + Color newColor; + setToolTipText(baseTT); + setBackground(tbl.getBackground()); + if (!cellColour.isSimpleColour()) + { + Rectangle cr = tbl.getCellRect(row, column, false); + FeatureSettings.renderGraduatedColor(this, cellColour, + (int) cr.getWidth(), (int) cr.getHeight()); + + } + else + { + this.setText(""); + this.setIcon(null); + newColor = cellColour.getColour(); + setBackground(newColor); + } if (isSelected) { if (selectedBorder == null) { selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getSelectionBackground()); + tbl.getSelectionBackground()); } setBorder(selectedBorder); } @@ -1243,22 +1603,185 @@ 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; } } + + /** + * 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; + String tt = ""; + String tx = ""; + if (gcol.isAboveThreshold()) + { + thr = true; + tx += ">"; + tt += "Thresholded (Above " + gcol.getThreshold() + ") "; + } + if (gcol.isBelowThreshold()) + { + thr = true; + tx += "<"; + tt += "Thresholded (Below " + gcol.getThreshold() + ") "; + } + if (gcol.isColourByLabel()) + { + tt = "Coloured by label text. " + tt; + if (thr) + { + tx += " "; + } + tx += "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); + if (tt.length() > 0) + { + if (comp.getToolTipText() == null) + { + comp.setToolTipText(tt); + } + else + { + comp.setToolTipText(tt + " " + comp.getToolTipText()); + } + } + } } -class ColorEditor extends AbstractCellEditor implements TableCellEditor, - ActionListener +class FeatureIcon implements Icon { - Color currentColor; + 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 + { + s1 = width / 2; + e1 = s1; + } + } + + @Override + public int getIconWidth() + { + return width; + } + + @Override + public int getIconHeight() + { + 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); + } + } +} + +class ColorEditor extends AbstractCellEditor + implements TableCellEditor, ActionListener +{ + FeatureSettings me; + + FeatureColourI currentColor; + + FeatureColourChooser chooser; + + String type; JButton button; @@ -1268,8 +1791,11 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, protected static final String EDIT = "edit"; - public ColorEditor() + int selectedRow = 0; + + public ColorEditor(FeatureSettings me) { + this.me = me; // Set up the editor (from the table's point of view), // which is a button. // This button brings up the color chooser dialog, @@ -1288,6 +1814,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, /** * Handles events from the editor button and from the dialog's OK button. */ + @Override public void actionPerformed(ActionEvent e) { @@ -1295,31 +1822,73 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { // The user has clicked the cell, so // bring up the dialog. - button.setBackground(currentColor); - colorChooser.setColor(currentColor); - dialog.setVisible(true); - + if (currentColor.isSimpleColour()) + { + // bring up simple color chooser + button.setBackground(currentColor.getColour()); + colorChooser.setColor(currentColor.getColour()); + dialog.setVisible(true); + } + else + { + // bring up graduated chooser. + chooser = new FeatureColourChooser(me.fr, type); + chooser.setRequestFocusEnabled(true); + chooser.requestFocus(); + chooser.addActionListener(this); + } // Make the renderer reappear. fireEditingStopped(); } else { // User pressed dialog's "OK" button. - currentColor = colorChooser.getColor(); + if (currentColor.isSimpleColour()) + { + currentColor = new FeatureColour(colorChooser.getColor()); + } + else + { + currentColor = chooser.getLastColour(); + } + me.table.setValueAt(getCellEditorValue(), selectedRow, 1); + fireEditingStopped(); + me.table.validate(); } } // Implement the one CellEditor method that AbstractCellEditor doesn't. + @Override public Object getCellEditorValue() { return currentColor; } // Implement the one method defined by TableCellEditor. + @Override public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row, int column) { - currentColor = (Color) value; + currentColor = (FeatureColourI) value; + this.selectedRow = row; + type = me.table.getValueAt(row, 0).toString(); + button.setOpaque(true); + button.setBackground(me.getBackground()); + if (!currentColor.isSimpleColour()) + { + JLabel btn = new JLabel(); + btn.setSize(button.getSize()); + FeatureSettings.renderGraduatedColor(btn, currentColor); + button.setBackground(btn.getBackground()); + button.setIcon(btn.getIcon()); + button.setText(btn.getText()); + } + else + { + button.setText(""); + button.setIcon(null); + button.setBackground(currentColor.getColour()); + } return button; } }