X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=419cb341f0a0b1a076cb0482b6b0067ea1697ab3;hb=e4fe46502d641a228ee4877d2a5a8443eb75f189;hp=40635c04d05435b1daf19adc69a3459e4a7beef9;hpb=6d1f6d9f50eb9beca568907bd90bda54a133986a;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 40635c0..419cb34 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,21 +20,27 @@ */ package jalview.gui; +import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; import jalview.bin.Cache; -import jalview.datamodel.SequenceFeature; +import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +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; @@ -55,6 +61,7 @@ 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; @@ -75,7 +82,6 @@ import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JLayeredPane; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JScrollPane; @@ -122,6 +128,10 @@ public class FeatureSettings extends JPanel implements JPanel transPanel = new JPanel(new GridLayout(1, 2)); + private static final int MIN_WIDTH = 400; + + private static final int MIN_HEIGHT = 400; + public FeatureSettings(AlignFrame af) { this.af = af; @@ -160,8 +170,8 @@ public class FeatureSettings extends JPanel implements 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() @@ -178,14 +188,16 @@ public class FeatureSettings extends JPanel implements } else if (evt.getClickCount() == 2) { + boolean invertSelection = evt.isAltDown(); + boolean toggleSelection = Platform.isControlDown(evt); + boolean extendSelection = evt.isShiftDown(); fr.ap.alignFrame.avc.markColumnsContainingFeatures( - evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(), - evt.isMetaDown(), + invertSelection, extendSelection, toggleSelection, (String) table.getValueAt(selectedRow, 0)); } } - // isPopupTrigger fires on mouseReleased on Mac + // isPopupTrigger fires on mouseReleased on Windows @Override public void mouseReleased(MouseEvent evt) { @@ -207,11 +219,20 @@ public class FeatureSettings extends JPanel implements int newRow = table.rowAtPoint(evt.getPoint()); if (newRow != selectedRow && selectedRow != -1 && newRow != -1) { + /* + * 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(); - Object[] temp = data[selectedRow]; - data[selectedRow] = data[newRow]; - data[newRow] = temp; + 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; @@ -251,7 +272,7 @@ public class FeatureSettings extends JPanel implements frame = new JInternalFrame(); frame.setContentPane(this); - if (new jalview.util.Platform().isAMac()) + if (Platform.isAMac()) { Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), @@ -263,6 +284,7 @@ public class FeatureSettings extends JPanel implements MessageManager.getString("label.sequence_feature_settings"), 400, 450); } + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { @@ -281,6 +303,8 @@ public class FeatureSettings extends JPanel implements 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 })); JMenuItem scr = new JMenuItem( @@ -336,7 +360,7 @@ public class FeatureSettings extends JPanel implements // 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() { @@ -347,7 +371,7 @@ public class FeatureSettings extends JPanel implements { if (e.getSource() == mxcol) { - if (typeCol instanceof Color) + if (featureColour.isSimpleColour()) { FeatureColourChooser fc = new FeatureColourChooser(me.fr, type); @@ -361,8 +385,7 @@ public class FeatureSettings extends JPanel implements "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); } } @@ -378,7 +401,9 @@ public class FeatureSettings extends JPanel implements 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(), @@ -445,50 +470,26 @@ public class FeatureSettings extends JPanel implements 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; @Override synchronized public void discoverAllFeatureData() { - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); - SequenceFeature[] tmpfeatures; - String group; - for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) - { - tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) - .getSequenceFeatures(); - if (tmpfeatures == null) - { - continue; - } + Set allGroups = new HashSet(); + AlignmentI alignment = af.getViewport().getAlignment(); - int index = 0; - while (index < tmpfeatures.length) + for (int i = 0; i < alignment.getHeight(); i++) + { + SequenceI seq = alignment.getSequenceAt(i); + for (String group : seq.getFeatures().getFeatureGroups(true)) { - if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) - { - index++; - continue; - } - - if (tmpfeatures[index].getFeatureGroup() != null) - { - group = tmpfeatures[index].featureGroup; - if (!allGroups.contains(group)) - { - allGroups.addElement(group); - checkGroupState(group); - } - } - - if (!allFeatures.contains(tmpfeatures[index].getType())) + if (group != null && !allGroups.contains(group)) { - allFeatures.addElement(tmpfeatures[index].getType()); + allGroups.add(group); + checkGroupState(group); } - index++; } } @@ -554,77 +555,65 @@ public class FeatureSettings extends JPanel implements synchronized void resetTable(String[] groupChanged) { - if (resettingTable == true) + if (resettingTable) { return; } resettingTable = true; - typeWidth = new Hashtable(); + typeWidth = new Hashtable(); // TODO: change avWidth calculation to 'per-sequence' average and use long // rather than float - float[] avWidth = null; - SequenceFeature[] tmpfeatures; - String group = null, type; - Vector visibleChecks = new Vector(); - - // Find out which features should be visible depending on which groups - // are selected / deselected - // and recompute average width ordering + + Set displayableTypes = new HashSet(); + + /* + * determine which feature types may be visible depending on + * which groups are selected, and recompute average width data + */ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) { - tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) - .getSequenceFeatures(); - if (tmpfeatures == null) - { - continue; - } + SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i); - int index = 0; - while (index < tmpfeatures.length) + /* + * get the sequence's groups for positional features + * and keep track of which groups are visible + */ + Set groups = seq.getFeatures().getFeatureGroups(true); + Set visibleGroups = new HashSet(); + for (String group : groups) { - group = tmpfeatures[index].featureGroup; - - if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) - { - index++; - continue; - } - if (group == null || checkGroupState(group)) { - type = tmpfeatures[index].getType(); - if (!visibleChecks.contains(type)) - { - visibleChecks.addElement(type); - } - } - if (!typeWidth.containsKey(tmpfeatures[index].getType())) - { - typeWidth.put(tmpfeatures[index].getType(), - avWidth = new float[3]); - } - else - { - avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType()); + visibleGroups.add(group); } - avWidth[0]++; - if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd()) - { - avWidth[1] += 1 + tmpfeatures[index].getBegin() - - tmpfeatures[index].getEnd(); - } - else + } + + /* + * get distinct feature types for visible groups + * record distinct visible types, and their count and total length + */ + Set types = seq.getFeatures().getFeatureTypesForGroups(true, + visibleGroups.toArray(new String[visibleGroups.size()])); + for (String type : types) + { + displayableTypes.add(type); + float[] avWidth = typeWidth.get(type); + if (avWidth == null) { - avWidth[1] += 1 + tmpfeatures[index].getEnd() - - tmpfeatures[index].getBegin(); + avWidth = new float[2]; + typeWidth.put(type, avWidth); } - index++; + // todo this could include features with a non-visible group + // - do we greatly care? + // todo should we include non-displayable features here, and only + // update when features are added? + avWidth[0] += seq.getFeatures().getFeatureCount(true, type); + avWidth[1] += seq.getFeatures().getTotalFeatureLength(type); } } - int fSize = visibleChecks.size(); - Object[][] data = new Object[fSize][3]; + Object[][] data = new Object[displayableTypes.size()][3]; int dataIndex = 0; if (fr.hasRenderOrder()) @@ -640,9 +629,9 @@ public class FeatureSettings extends JPanel implements List frl = fr.getRenderOrder(); for (int ro = frl.size() - 1; ro > -1; ro--) { - type = frl.get(ro); + String type = frl.get(ro); - if (!visibleChecks.contains(type)) + if (!displayableTypes.contains(type)) { continue; } @@ -652,16 +641,17 @@ public class FeatureSettings extends JPanel implements data[dataIndex][2] = new Boolean(af.getViewport() .getFeaturesDisplayed().isVisible(type)); dataIndex++; - visibleChecks.removeElement(type); + displayableTypes.remove(type); } } - fSize = visibleChecks.size(); - for (int i = 0; i < fSize; i++) + /* + * process any extra features belonging only to + * a group which was just selected + */ + while (!displayableTypes.isEmpty()) { - // These must be extra features belonging to the group - // which was just selected - type = visibleChecks.elementAt(i).toString(); + String type = displayableTypes.iterator().next(); data[dataIndex][0] = type; data[dataIndex][1] = fr.getFeatureStyle(type); @@ -674,6 +664,7 @@ public class FeatureSettings extends JPanel implements data[dataIndex][2] = new Boolean(true); dataIndex++; + displayableTypes.remove(type); } if (originalData == null) @@ -730,12 +721,9 @@ public class FeatureSettings extends JPanel implements void load() { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - new String[] { "fc" }, - new String[] { "Sequence Feature Colours" }, + JalviewFileChooser chooser = new JalviewFileChooser("fc", "Sequence Feature Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager .getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); @@ -751,8 +739,7 @@ public class FeatureSettings extends JPanel implements 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--) { @@ -771,7 +758,7 @@ public class FeatureSettings extends JPanel implements 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()) { @@ -783,31 +770,28 @@ public class FeatureSettings extends JPanel implements } 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()); } @@ -829,12 +813,9 @@ public class FeatureSettings extends JPanel implements void save() { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - new String[] { "fc" }, - new String[] { "Sequence Feature Colours" }, + JalviewFileChooser chooser = new JalviewFileChooser("fc", "Sequence Feature Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager .getString("label.save_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.save")); @@ -851,50 +832,40 @@ public class FeatureSettings extends JPanel implements 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); } @@ -930,7 +901,7 @@ public class FeatureSettings extends JPanel implements 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 @@ -1253,7 +1224,8 @@ public class FeatureSettings extends JPanel implements fetchDAS.setEnabled(false); cancelDAS.setEnabled(true); dassourceBrowser.setGuiEnabled(false); - Vector selectedSources = dassourceBrowser.getSelectedSources(); + Vector selectedSources = dassourceBrowser + .getSelectedSources(); doDasFeatureFetch(selectedSources, true, true); } @@ -1312,7 +1284,7 @@ public class FeatureSettings extends JPanel implements * 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); } @@ -1323,7 +1295,7 @@ public class FeatureSettings extends JPanel implements * * @return vector of selected das source nicknames */ - public Vector getSelectedSources() + public Vector getSelectedSources() { return dassourceBrowser.getSelectedSources(); } @@ -1337,7 +1309,7 @@ public class FeatureSettings extends JPanel implements * 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 @@ -1398,15 +1370,15 @@ public class FeatureSettings extends JPanel implements public void noDasSourceActive() { complete(); - JOptionPane + JvOptionPane .showInternalConfirmDialog( Desktop.desktop, MessageManager .getString("label.no_das_sources_selected_warn"), MessageManager .getString("label.no_das_sources_selected_title"), - JOptionPane.DEFAULT_OPTION, - JOptionPane.INFORMATION_MESSAGE); + JvOptionPane.DEFAULT_OPTION, + JvOptionPane.INFORMATION_MESSAGE); } // /////////////////////////////////////////////////////////////////////// @@ -1503,10 +1475,11 @@ public class FeatureSettings extends JPanel implements } @Override - public Component getTableCellRendererComponent(JTable table, + 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); @@ -1514,11 +1487,11 @@ public class FeatureSettings extends JPanel implements // 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()); } @@ -1526,20 +1499,16 @@ public class FeatureSettings extends JPanel implements { 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 @@ -1547,9 +1516,8 @@ public class FeatureSettings extends JPanel implements if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getBackground()); + tbl.getBackground()); } - // comp. setBorder(unselectedBorder); } @@ -1563,7 +1531,7 @@ public class FeatureSettings extends JPanel implements * @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) @@ -1579,23 +1547,23 @@ public class FeatureSettings extends JPanel implements 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()) { @@ -1609,7 +1577,7 @@ public class FeatureSettings extends JPanel implements } 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); @@ -1637,7 +1605,7 @@ public class FeatureSettings extends JPanel implements class FeatureIcon implements Icon { - GraduatedColor gcol; + FeatureColourI gcol; Color backg; @@ -1649,7 +1617,7 @@ 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; @@ -1689,7 +1657,7 @@ 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)); @@ -1703,7 +1671,7 @@ class FeatureIcon implements Icon } else { - Color minCol = gcol.getMinColor(); + Color minCol = gcol.getMinColour(); g.setColor(minCol); g.fillRect(0, 0, s1, height); if (midspace) @@ -1711,7 +1679,7 @@ 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); } } @@ -1722,14 +1690,12 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { FeatureSettings me; - GraduatedColor currentGColor; + FeatureColourI currentColor; FeatureColourChooser chooser; String type; - Color currentColor; - JButton button; JColorChooser colorChooser; @@ -1769,11 +1735,11 @@ 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 @@ -1790,15 +1756,13 @@ 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(); @@ -1810,10 +1774,6 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, @Override public Object getCellEditorValue() { - if (currentColor == null) - { - return currentGColor; - } return currentColor; } @@ -1822,18 +1782,16 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, 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()); @@ -1842,8 +1800,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { button.setText(""); button.setIcon(null); - currentColor = (Color) value; - button.setBackground(currentColor); + button.setBackground(currentColor.getColour()); } return button; }