X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=15f3e5bce42950084bf4dd97fdb66dc7e6ed5eb1;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=918fc02770efbec0d41753e3a211036d90c67d9f;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 918fc02..15f3e5b 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,14 +20,19 @@ */ package jalview.gui; +import jalview.api.FeatureColourI; +import jalview.api.FeatureSettingsControllerI; import jalview.bin.Cache; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +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; @@ -53,9 +58,11 @@ import java.io.FileOutputStream; import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; +import java.util.Arrays; import java.util.Hashtable; import java.util.Iterator; import java.util.List; +import java.util.Map; import java.util.Set; import java.util.Vector; @@ -88,7 +95,8 @@ import javax.swing.table.AbstractTableModel; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; -public class FeatureSettings extends JPanel +public class FeatureSettings extends JPanel implements + FeatureSettingsControllerI { DasSourceBrowser dassourceBrowser; @@ -123,7 +131,8 @@ public class FeatureSettings extends JPanel this.af = af; fr = af.getFeatureRenderer(); // allow transparency to be recovered - transparency.setMaximum(100 - (int) ((originalTransparency=fr.getTransparency()) * 100)); + transparency.setMaximum(100 - (int) ((originalTransparency = fr + .getTransparency()) * 100)); try { @@ -133,15 +142,18 @@ 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) { + 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 JvSwingUtils.wrapTooltip(true, MessageManager + .getString("label.feature_settings_click_drag")); } return null; } @@ -152,16 +164,17 @@ public class FeatureSettings extends JPanel table.setDefaultEditor(Color.class, new ColorEditor(this)); - table.setDefaultEditor(GraduatedColor.class, new ColorEditor(this)); - table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer()); + 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 (SwingUtilities.isRightMouseButton(evt)) + if (evt.isPopupTrigger()) { popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), table.getValueAt(selectedRow, 1), fr.getMinMax(), @@ -169,14 +182,16 @@ public class FeatureSettings extends JPanel } else if (evt.getClickCount() == 2) { + boolean invertSelection = evt.isAltDown(); + boolean toggleSelection = Platform.isControlDown(evt); + boolean extendSelection = evt.isShiftDown(); fr.ap.alignFrame.avc.markColumnsContainingFeatures( - evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(), - evt.isMetaDown(), + invertSelection, extendSelection, toggleSelection, (String) table.getValueAt(selectedRow, 0)); } } - // isPopupTrigger fires on mouseReleased on Mac + // isPopupTrigger fires on mouseReleased on Windows @Override public void mouseReleased(MouseEvent evt) { @@ -185,38 +200,41 @@ public class FeatureSettings extends JPanel { popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), table.getValueAt(selectedRow, 1), fr.getMinMax(), - evt.getX(), - evt.getY()); + evt.getX(), evt.getY()); } } }); table.addMouseMotionListener(new MouseMotionAdapter() { + @Override public void mouseDragged(MouseEvent evt) { int newRow = table.rowAtPoint(evt.getPoint()); if (newRow != selectedRow && selectedRow != -1 && newRow != -1) { - Object[] temp = new Object[3]; - temp[0] = table.getValueAt(selectedRow, 0); - temp[1] = table.getValueAt(selectedRow, 1); - temp[2] = table.getValueAt(selectedRow, 2); - - table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0); - table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1); - table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2); - - table.setValueAt(temp[0], newRow, 0); - table.setValueAt(temp[1], newRow, 1); - table.setValueAt(temp[2], newRow, 2); - + /* + * reposition 'selectedRow' to 'newRow' (the dragged to location) + * this could be more than one row away for a very fast drag action + * so just swap it with adjacent rows until we get it there + */ + Object[][] data = ((FeatureTableModel) table.getModel()) + .getData(); + int direction = newRow < selectedRow ? -1 : 1; + for (int i = selectedRow; i != newRow; i += direction) + { + Object[] temp = data[i]; + data[i] = data[i + direction]; + data[i + direction] = temp; + } + updateFeatureRenderer(data); + table.repaint(); selectedRow = newRow; } } }); -// table.setToolTipText(JvSwingUtils.wrapTooltip(true, -// MessageManager.getString("label.feature_settings_click_drag"))); + // table.setToolTipText(JvSwingUtils.wrapTooltip(true, + // MessageManager.getString("label.feature_settings_click_drag"))); scrollPane.setViewportView(table); dassourceBrowser = new DasSourceBrowser(this); @@ -227,11 +245,12 @@ public class FeatureSettings extends JPanel 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) @@ -247,7 +266,7 @@ public class FeatureSettings extends JPanel frame = new JInternalFrame(); frame.setContentPane(this); - if (new jalview.util.Platform().isAMac()) + if (Platform.isAMac()) { Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), @@ -262,6 +281,7 @@ public class FeatureSettings extends JPanel frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -273,11 +293,13 @@ public class FeatureSettings extends JPanel } protected void popupSort(final int selectedRow, final String type, - final Object typeCol, final Hashtable minmax, int x, int y) + final Object typeCol, final Map minmax, int x, + int y) { + final FeatureColourI featureColour = (FeatureColourI) typeCol; + JPopupMenu men = new JPopupMenu(MessageManager.formatMessage( - "label.settings_for_param", new String[] - { type })); + "label.settings_for_param", new String[] { type })); JMenuItem scr = new JMenuItem( MessageManager.getString("label.sort_by_score")); men.add(scr); @@ -285,10 +307,11 @@ public class FeatureSettings extends JPanel scr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.af.avc.sortAlignmentByFeatureScore(new String[] - { type }); + me.af.avc.sortAlignmentByFeatureScore(Arrays + .asList(new String[] { type })); } }); @@ -297,17 +320,18 @@ public class FeatureSettings extends JPanel dens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.af.avc.sortAlignmentByFeatureDensity(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 float[][] typeMinMax = minmax.get(type); /* * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); // * this is broken at the moment and isn't that useful anyway! @@ -322,24 +346,25 @@ public class FeatureSettings extends JPanel * * men.add(chb); */ - if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null) + if (typeMinMax != null && typeMinMax[0] != null) { // if (table.getValueAt(row, column)); // graduated colourschemes for those where minmax exists for the // positional features final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( "Graduated Colour"); - mxcol.setSelected(!(typeCol instanceof Color)); + mxcol.setSelected(!featureColour.isSimpleColour()); men.add(mxcol); mxcol.addActionListener(new ActionListener() { JColorChooser colorChooser; + @Override public void actionPerformed(ActionEvent e) { if (e.getSource() == mxcol) { - if (typeCol instanceof Color) + if (featureColour.isSimpleColour()) { FeatureColourChooser fc = new FeatureColourChooser(me.fr, type); @@ -353,8 +378,7 @@ public class FeatureSettings extends JPanel "Select new Colour", true, // modal colorChooser, this, // OK button handler null); // no CANCEL button handler - colorChooser.setColor(((GraduatedColor) typeCol) - .getMaxColor()); + colorChooser.setColor(featureColour.getMaxColour()); dialog.setVisible(true); } } @@ -370,7 +394,9 @@ public class FeatureSettings extends JPanel else { // probably the color chooser! - table.setValueAt(colorChooser.getColor(), selectedRow, 1); + table.setValueAt( + new FeatureColour(colorChooser.getColor()), + selectedRow, 1); table.validate(); me.updateFeatureRenderer( ((FeatureTableModel) table.getModel()).getData(), @@ -386,7 +412,6 @@ public class FeatureSettings extends JPanel MessageManager.getString("label.select_columns_containing")); selCols.addActionListener(new ActionListener() { - @Override public void actionPerformed(ActionEvent arg0) { @@ -398,7 +423,6 @@ public class FeatureSettings extends JPanel MessageManager.getString("label.select_columns_not_containing")); clearCols.addActionListener(new ActionListener() { - @Override public void actionPerformed(ActionEvent arg0) { @@ -406,8 +430,30 @@ public class FeatureSettings extends JPanel 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); } @@ -419,12 +465,13 @@ public class FeatureSettings extends JPanel /** * contains a float[3] for each feature type string. created by setTableData */ - Hashtable typeWidth = null; + Map typeWidth = null; - synchronized public void setTableData() + @Override + synchronized public void discoverAllFeatureData() { - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); + Vector allFeatures = new Vector(); + Vector allGroups = new Vector(); SequenceFeature[] tmpfeatures; String group; for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) @@ -504,6 +551,7 @@ public class FeatureSettings extends JPanel check.setFont(new Font("Serif", Font.BOLD, 12)); check.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent evt) { fr.setGroupVisibility(check.getText(), check.isSelected()); @@ -513,8 +561,7 @@ public class FeatureSettings extends JPanel af.alignPanel.overviewPanel.updateOverviewImage(); } - resetTable(new String[] - { grp }); + resetTable(new String[] { grp }); } }); groupPanel.add(check); @@ -530,13 +577,13 @@ public class FeatureSettings extends JPanel return; } resettingTable = true; - typeWidth = new Hashtable(); + typeWidth = new Hashtable(); // TODO: change avWidth calculation to 'per-sequence' average and use long // rather than float float[] avWidth = null; SequenceFeature[] tmpfeatures; String group = null, type; - Vector visibleChecks = new Vector(); + Vector visibleChecks = new Vector(); // Find out which features should be visible depending on which groups // are selected / deselected @@ -577,7 +624,7 @@ public class FeatureSettings extends JPanel } else { - avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType()); + avWidth = typeWidth.get(tmpfeatures[index].getType()); } avWidth[0]++; if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd()) @@ -702,11 +749,13 @@ public class FeatureSettings extends JPanel void load() { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "fc" }, new String[] - { "Sequence Feature Colours" }, "Sequence Feature Colours"); + 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(MessageManager.getString("label.load_feature_colours")); + chooser.setDialogTitle(MessageManager + .getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); int value = chooser.showOpenDialog(this); @@ -720,9 +769,7 @@ public class FeatureSettings extends JPanel InputStreamReader in = new InputStreamReader(new FileInputStream( file), "UTF-8"); - jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours(); - jucs = jucs - .unmarshal(in); + JalviewUserColours jucs = JalviewUserColours.unmarshal(in); for (int i = jucs.getColourCount() - 1; i >= 0; i--) { @@ -741,7 +788,7 @@ public class FeatureSettings extends JPanel Cache.log.warn("Couldn't parse out graduated feature color.", e); } - GraduatedColor gcol = new GraduatedColor(mincol, maxcol, + FeatureColourI gcol = new FeatureColour(mincol, maxcol, newcol.getMin(), newcol.getMax()); if (newcol.hasAutoScale()) { @@ -753,31 +800,28 @@ public class FeatureSettings extends JPanel } if (newcol.hasThreshold()) { - gcol.setThresh(newcol.getThreshold()); - gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default + gcol.setThreshold(newcol.getThreshold()); } if (newcol.getThreshType().length() > 0) { String ttyp = newcol.getThreshType(); - if (ttyp.equalsIgnoreCase("NONE")) - { - gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); - } if (ttyp.equalsIgnoreCase("ABOVE")) { - gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); + gcol.setAboveThreshold(true); } if (ttyp.equalsIgnoreCase("BELOW")) { - gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); + gcol.setBelowThreshold(true); } } fr.setColour(name = newcol.getName(), gcol); } else { - fr.setColour(name = jucs.getColour(i).getName(), new Color( - Integer.parseInt(jucs.getColour(i).getRGB(), 16))); + 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()); } @@ -800,11 +844,12 @@ 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"); + Cache.getProperty("LAST_DIRECTORY"), new String[] { "fc" }, + new String[] { "Sequence Feature Colours" }, + "Sequence Feature Colours"); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_feature_colours")); + chooser.setDialogTitle(MessageManager + .getString("label.save_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -819,50 +864,40 @@ public class FeatureSettings extends JPanel PrintWriter out = new PrintWriter(new OutputStreamWriter( new FileOutputStream(choice), "UTF-8")); - Set fr_colours = fr.getAllFeatureColours(); - Iterator e = fr_colours.iterator(); + 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.hasNext()) { - sortTypes[i] = e.next().toString(); + sortTypes[i] = e.next(); sortOrder[i] = fr.getOrder(sortTypes[i]); i++; } - jalview.util.QuickSort.sort(sortOrder, sortTypes); + QuickSort.sort(sortOrder, sortTypes); sortOrder = null; - Object fcol; - GraduatedColor gcol; for (i = 0; i < sortTypes.length; i++) { jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setName(sortTypes[i]); - col.setRGB(jalview.util.Format.getHexString(fr.getColour(col - .getName()))); - fcol = fr.getFeatureStyle(sortTypes[i]); - if (fcol instanceof GraduatedColor) + FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]); + if (fcol.isSimpleColour()) { - gcol = (GraduatedColor) fcol; - col.setMin(gcol.getMin()); - col.setMax(gcol.getMax()); - col.setMinRGB(jalview.util.Format.getHexString(gcol - .getMinColor())); - col.setAutoScale(gcol.isAutoScale()); - col.setThreshold(gcol.getThresh()); - col.setColourByLabel(gcol.isColourByLabel()); - switch (gcol.getThreshType()) - { - case AnnotationColourGradient.NO_THRESHOLD: - col.setThreshType("NONE"); - break; - case AnnotationColourGradient.ABOVE_THRESHOLD: - col.setThreshType("ABOVE"); - break; - case AnnotationColourGradient.BELOW_THRESHOLD: - col.setThreshType("BELOW"); - break; - } + 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); } @@ -898,7 +933,7 @@ 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 @@ -939,9 +974,9 @@ public class FeatureSettings extends JPanel } } if (sort) - { + { jalview.util.QuickSort.sort(width, data); - // update global priority order + // update global priority order } updateFeatureRenderer(data, false); @@ -964,10 +999,19 @@ 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; @@ -1024,6 +1068,7 @@ public class FeatureSettings extends JPanel invert.setText(MessageManager.getString("label.invert_selection")); invert.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { invertSelection(); @@ -1033,6 +1078,7 @@ public class FeatureSettings extends JPanel optimizeOrder.setText(MessageManager.getString("label.optimise_order")); optimizeOrder.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { orderByAvWidth(); @@ -1043,6 +1089,7 @@ public class FeatureSettings extends JPanel .setText(MessageManager.getString("label.seq_sort_by_score")); sortByScore.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { af.avc.sortAlignmentByFeatureScore(null); @@ -1053,6 +1100,7 @@ public class FeatureSettings extends JPanel .getString("label.sequence_sort_by_density")); sortByDens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { af.avc.sortAlignmentByFeatureDensity(null); @@ -1062,6 +1110,7 @@ public class FeatureSettings extends JPanel help.setText(MessageManager.getString("action.help")); help.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { try @@ -1077,6 +1126,7 @@ public class FeatureSettings extends JPanel help.setText(MessageManager.getString("action.help")); help.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { try @@ -1092,6 +1142,7 @@ public class FeatureSettings extends JPanel cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { fr.setTransparency(originalTransparency); @@ -1103,6 +1154,7 @@ public class FeatureSettings extends JPanel ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { close(); @@ -1112,6 +1164,7 @@ public class FeatureSettings extends JPanel loadColours.setText(MessageManager.getString("label.load_colours")); loadColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { load(); @@ -1121,6 +1174,7 @@ public class FeatureSettings extends JPanel saveColours.setText(MessageManager.getString("label.save_colours")); saveColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { save(); @@ -1128,6 +1182,7 @@ public class FeatureSettings extends JPanel }); transparency.addChangeListener(new ChangeListener() { + @Override public void stateChanged(ChangeEvent evt) { fr.setTransparency((100 - transparency.getValue()) / 100f); @@ -1141,6 +1196,7 @@ public class FeatureSettings extends JPanel fetchDAS.setText(MessageManager.getString("label.fetch_das_features")); fetchDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { fetchDAS_actionPerformed(e); @@ -1149,6 +1205,7 @@ public class FeatureSettings extends JPanel saveDAS.setText(MessageManager.getString("action.save_as_default")); saveDAS.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { saveDAS_actionPerformed(e); @@ -1160,14 +1217,17 @@ public class FeatureSettings extends JPanel 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(MessageManager.getString("label.feature_settings"), settingsPane); - tabbedPane.addTab(MessageManager.getString("label.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); @@ -1196,7 +1256,8 @@ public class FeatureSettings extends JPanel fetchDAS.setEnabled(false); cancelDAS.setEnabled(true); dassourceBrowser.setGuiEnabled(false); - Vector selectedSources = dassourceBrowser.getSelectedSources(); + Vector selectedSources = dassourceBrowser + .getSelectedSources(); doDasFeatureFetch(selectedSources, true, true); } @@ -1255,7 +1316,7 @@ public class FeatureSettings extends JPanel * Vector of Strings to resolve to DAS source nicknames. * @return sources that are present in source list. */ - public List resolveSourceNicknames(Vector sources) + public List resolveSourceNicknames(Vector sources) { return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); } @@ -1266,7 +1327,7 @@ public class FeatureSettings extends JPanel * * @return vector of selected das source nicknames */ - public Vector getSelectedSources() + public Vector getSelectedSources() { return dassourceBrowser.getSelectedSources(); } @@ -1280,7 +1341,7 @@ public class FeatureSettings extends JPanel * if true then runs in same thread, otherwise passes to the Swing * executor */ - public void fetchDasFeatures(Vector sources, boolean block) + public void fetchDasFeatures(Vector sources, boolean block) { initDasSources(); List resolved = dassourceBrowser.sourceRegistry @@ -1297,6 +1358,7 @@ public class FeatureSettings extends JPanel Runnable fetcher = new Runnable() { + @Override public void run() { doDasFeatureFetch(dassources, true, false); @@ -1361,8 +1423,10 @@ public class FeatureSettings extends JPanel this.data = data; } - private String[] columnNames = - { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") }; + private String[] columnNames = { + MessageManager.getString("label.feature_type"), + MessageManager.getString("action.colour"), + MessageManager.getString("label.display") }; private Object[][] data; @@ -1376,6 +1440,7 @@ public class FeatureSettings extends JPanel this.data = data; } + @Override public int getColumnCount() { return columnNames.length; @@ -1386,31 +1451,37 @@ 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; @@ -1435,10 +1506,12 @@ public class FeatureSettings extends JPanel setVerticalTextPosition(SwingConstants.CENTER); } - public Component getTableCellRendererComponent(JTable table, + @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); @@ -1446,11 +1519,11 @@ public class FeatureSettings extends JPanel // setBounds(getBounds()); Color newColor; setToolTipText(baseTT); - setBackground(table.getBackground()); - if (color instanceof GraduatedColor) + setBackground(tbl.getBackground()); + if (!cellColour.isSimpleColour()) { - Rectangle cr = table.getCellRect(row, column, false); - FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color, + Rectangle cr = tbl.getCellRect(row, column, false); + FeatureSettings.renderGraduatedColor(this, cellColour, (int) cr.getWidth(), (int) cr.getHeight()); } @@ -1458,20 +1531,16 @@ public class FeatureSettings extends JPanel { this.setText(""); this.setIcon(null); - newColor = (Color) color; - // comp. + newColor = cellColour.getColour(); setBackground(newColor); - // comp.setToolTipText("RGB value: " + newColor.getRed() + ", " - // + newColor.getGreen() + ", " + newColor.getBlue()); } if (isSelected) { if (selectedBorder == null) { selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getSelectionBackground()); + tbl.getSelectionBackground()); } - // comp. setBorder(selectedBorder); } else @@ -1479,9 +1548,8 @@ public class FeatureSettings extends JPanel if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getBackground()); + tbl.getBackground()); } - // comp. setBorder(unselectedBorder); } @@ -1495,7 +1563,7 @@ public class FeatureSettings extends JPanel * @param comp * @param gcol */ - public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol) + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol) { int w = comp.getWidth(), h = comp.getHeight(); if (w < 20) @@ -1511,23 +1579,23 @@ public class FeatureSettings extends JPanel renderGraduatedColor(comp, gcol, w, h); } - public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol, + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol, int w, int h) { boolean thr = false; String tt = ""; String tx = ""; - if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) + if (gcol.isAboveThreshold()) { thr = true; tx += ">"; - tt += "Thresholded (Above " + gcol.getThresh() + ") "; + tt += "Thresholded (Above " + gcol.getThreshold() + ") "; } - if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD) + if (gcol.isBelowThreshold()) { thr = true; tx += "<"; - tt += "Thresholded (Below " + gcol.getThresh() + ") "; + tt += "Thresholded (Below " + gcol.getThreshold() + ") "; } if (gcol.isColourByLabel()) { @@ -1541,7 +1609,7 @@ public class FeatureSettings extends JPanel } else { - Color newColor = gcol.getMaxColor(); + Color newColor = gcol.getMaxColour(); comp.setBackground(newColor); // System.err.println("Width is " + w / 2); Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr); @@ -1569,7 +1637,7 @@ public class FeatureSettings extends JPanel class FeatureIcon implements Icon { - GraduatedColor gcol; + FeatureColourI gcol; Color backg; @@ -1581,7 +1649,7 @@ class FeatureIcon implements Icon Color mpcolour = Color.white; - FeatureIcon(GraduatedColor gfc, Color bg, int w, int h, boolean mspace) + FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace) { gcol = gfc; backg = bg; @@ -1600,16 +1668,19 @@ class FeatureIcon implements Icon } } + @Override public int getIconWidth() { return width; } + @Override public int getIconHeight() { return height; } + @Override public void paintIcon(Component c, Graphics g, int x, int y) { @@ -1618,7 +1689,7 @@ class FeatureIcon implements Icon g.setColor(backg); g.fillRect(0, 0, width, height); // need an icon here. - g.setColor(gcol.getMaxColor()); + g.setColor(gcol.getMaxColour()); g.setFont(new Font("Verdana", Font.PLAIN, 9)); @@ -1632,7 +1703,7 @@ class FeatureIcon implements Icon } else { - Color minCol = gcol.getMinColor(); + Color minCol = gcol.getMinColour(); g.setColor(minCol); g.fillRect(0, 0, s1, height); if (midspace) @@ -1640,7 +1711,7 @@ class FeatureIcon implements Icon g.setColor(Color.white); g.fillRect(s1, 0, e1 - s1, height); } - g.setColor(gcol.getMaxColor()); + g.setColor(gcol.getMaxColour()); g.fillRect(0, e1, width - e1, height); } } @@ -1651,14 +1722,12 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { FeatureSettings me; - GraduatedColor currentGColor; + FeatureColourI currentColor; FeatureColourChooser chooser; String type; - Color currentColor; - JButton button; JColorChooser colorChooser; @@ -1690,6 +1759,7 @@ 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) { @@ -1697,11 +1767,11 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { // The user has clicked the cell, so // bring up the dialog. - if (currentColor != null) + if (currentColor.isSimpleColour()) { // bring up simple color chooser - button.setBackground(currentColor); - colorChooser.setColor(currentColor); + button.setBackground(currentColor.getColour()); + colorChooser.setColor(currentColor.getColour()); dialog.setVisible(true); } else @@ -1718,15 +1788,13 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, } else { // User pressed dialog's "OK" button. - if (currentColor != null) + if (currentColor.isSimpleColour()) { - currentColor = colorChooser.getColor(); + currentColor = new FeatureColour(colorChooser.getColor()); } else { - // class cast exceptions may be raised if the chooser created on a - // non-graduated color - currentGColor = (GraduatedColor) chooser.getLastColour(); + currentColor = chooser.getLastColour(); } me.table.setValueAt(getCellEditorValue(), selectedRow, 1); fireEditingStopped(); @@ -1735,31 +1803,27 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, } // Implement the one CellEditor method that AbstractCellEditor doesn't. + @Override public Object getCellEditorValue() { - if (currentColor == null) - { - return currentGColor; - } return currentColor; } // Implement the one method defined by TableCellEditor. + @Override public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row, int column) { - currentGColor = null; - currentColor = null; + currentColor = (FeatureColourI) value; this.selectedRow = row; type = me.table.getValueAt(row, 0).toString(); button.setOpaque(true); button.setBackground(me.getBackground()); - if (value instanceof GraduatedColor) + if (!currentColor.isSimpleColour()) { - currentGColor = (GraduatedColor) value; JLabel btn = new JLabel(); btn.setSize(button.getSize()); - FeatureSettings.renderGraduatedColor(btn, currentGColor); + FeatureSettings.renderGraduatedColor(btn, currentColor); button.setBackground(btn.getBackground()); button.setIcon(btn.getIcon()); button.setText(btn.getText()); @@ -1768,8 +1832,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { button.setText(""); button.setIcon(null); - currentColor = (Color) value; - button.setBackground(currentColor); + button.setBackground(currentColor.getColour()); } return button; }