X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=a2d0559ad32291b7c97191f8b912d4ec1338d37d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=4c0450cca8128a1854277ae99df62c90a9d5a1d1;hpb=50fc0be07fc2672defdcca49c51bf28eb49ffba4;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java old mode 100755 new mode 100644 index 4c0450c..a2d0559 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,82 +1,165 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; +import jalview.api.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.util.MessageManager; +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.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.datamodel.*; -import jalview.io.*; - -public class FeatureSettings - extends JPanel +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.Hashtable; +import java.util.Iterator; +import java.util.List; +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.JOptionPane; +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; - jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher; + + jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher; + JPanel settingsPane = new JPanel(); + JPanel dasSettingsPane = new JPanel(); final FeatureRenderer fr; + public final AlignFrame af; + Object[][] originalData; + + private float originalTransparency; + final JInternalFrame frame; + JScrollPane scrollPane = new JScrollPane(); + JTable table; + JPanel groupPanel; + JSlider transparency = new JSlider(); - JPanel transPanel = new JPanel(new FlowLayout()); + JPanel transPanel = new JPanel(new GridLayout(1, 2)); 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 { jbInit(); - } - catch (Exception ex) + } catch (Exception ex) { 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.setDefaultRenderer(Color.class, new ColorRenderer()); - table.setDefaultEditor(Color.class, - new ColorEditor()); + table.setDefaultEditor(Color.class, new ColorEditor(this)); + table.setDefaultEditor(GraduatedColor.class, new ColorEditor(this)); + table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer()); table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table.addMouseListener(new MouseAdapter() @@ -84,6 +167,32 @@ public class FeatureSettings public void mousePressed(MouseEvent evt) { selectedRow = table.rowAtPoint(evt.getPoint()); + if (SwingUtilities.isRightMouseButton(evt)) + { + popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), + table.getValueAt(selectedRow, 1), fr.getMinMax(), + evt.getX(), evt.getY()); + } + else if (evt.getClickCount() == 2) + { + fr.ap.alignFrame.avc.markColumnsContainingFeatures( + evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(), + evt.isMetaDown(), + (String) table.getValueAt(selectedRow, 0)); + } + } + + // isPopupTrigger fires on mouseReleased on Mac + @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()); + } } }); @@ -92,9 +201,7 @@ public class FeatureSettings public void mouseDragged(MouseEvent evt) { int newRow = table.rowAtPoint(evt.getPoint()); - if (newRow != selectedRow - && selectedRow != -1 - && newRow != -1) + if (newRow != selectedRow && selectedRow != -1 && newRow != -1) { Object[] temp = new Object[3]; temp[0] = table.getValueAt(selectedRow, 0); @@ -113,76 +220,225 @@ public class FeatureSettings } } }); - + // 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() { + final FeatureSettings fs = this; + fr.addPropertyChangeListener(change = new PropertyChangeListener() + { public void propertyChange(PropertyChangeEvent evt) { - if (!fs.resettingTable && !fs.handlingUpdate) { - fs.handlingUpdate=true; - fs.resetTable(null); // new groups may be added with new seuqence feature types only - fs.handlingUpdate=false; + if (!fs.resettingTable && !fs.handlingUpdate) + { + fs.handlingUpdate = true; + fs.resetTable(null); // new groups may be added with new seuqence + // feature types only + fs.handlingUpdate = false; } } - + }); - + frame = new JInternalFrame(); frame.setContentPane(this); - Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450); + if (new jalview.util.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.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + javax.swing.event.InternalFrameEvent evt) { fr.removePropertyChangeListener(change); - } - ; + dassourceBrowser.fs = null; + }; }); frame.setLayer(JLayeredPane.PALETTE_LAYER); } + + protected void popupSort(final int selectedRow, final String type, + final Object typeCol, final Hashtable minmax, int x, int y) + { + 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() + { + + public void actionPerformed(ActionEvent e) + { + me.af.avc.sortAlignmentByFeatureScore(new String[] { type }); + } + + }); + JMenuItem dens = new JMenuItem( + MessageManager.getString("label.sort_by_density")); + dens.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + me.af.avc.sortAlignmentByFeatureDensity(new String[] { type }); + } + + }); + men.add(dens); + if (minmax != null) + { + final Object 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 && ((float[][]) 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)); + men.add(mxcol); + mxcol.addActionListener(new ActionListener() + { + JColorChooser colorChooser; + + public void actionPerformed(ActionEvent e) + { + if (e.getSource() == mxcol) + { + if (typeCol instanceof Color) + { + 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(((GraduatedColor) typeCol) + .getMaxColor()); + 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(colorChooser.getColor(), selectedRow, 1); + table.validate(); + me.updateFeatureRenderer( + ((FeatureTableModel) table.getModel()).getData(), + false); + } + } + } + + }); + } + } + 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); + } + }); + men.add(selCols); + men.add(clearCols); + men.show(table, x, y); + } + /** * true when Feature Settings are updating from feature renderer */ - private boolean handlingUpdate=false; - + private boolean handlingUpdate = false; + /** * contains a float[3] for each feature type string. created by setTableData */ - Hashtable typeWidth=null; - synchronized public void setTableData() + Hashtable typeWidth = null; + + @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++) + for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) { - if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence(). - getSequenceFeatures() == null) + tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) + .getSequenceFeatures(); + if (tmpfeatures == null) { continue; } - tmpfeatures = af.getViewport().alignment.getSequenceAt(i). - getDatasetSequence().getSequenceFeatures(); - int index = 0; while (index < tmpfeatures.length) { @@ -198,10 +454,7 @@ public class FeatureSettings if (!allGroups.contains(group)) { allGroups.addElement(group); - if (group!=null) - { - checkGroupState(group); - } + checkGroupState(group); } } @@ -212,89 +465,89 @@ public class FeatureSettings index++; } } - + resetTable(null); validate(); } + /** + * 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)) + private boolean checkGroupState(String group) + { + boolean visible = fr.checkGroupVisibility(group, true); + + if (groupPanel == null) { - visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue(); - } else { - visible=true; // new group is always made visible - } + groupPanel = new JPanel(); + } - if (groupPanel == null) + boolean alreadyAdded = false; + for (int g = 0; g < groupPanel.getComponentCount(); g++) + { + if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group)) { - groupPanel = new JPanel(); + alreadyAdded = true; + ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible); + break; } + } + + if (alreadyAdded) + { - boolean alreadyAdded = false; - for (int g = 0; g < groupPanel.getComponentCount(); g++) + return visible; + } + final String grp = group; + final JCheckBox check = new JCheckBox(group, visible); + check.setFont(new Font("Serif", Font.BOLD, 12)); + check.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent evt) { - if ( ( (JCheckBox) groupPanel.getComponent(g)) - .getText().equals(group)) + fr.setGroupVisibility(check.getText(), check.isSelected()); + af.alignPanel.getSeqPanel().seqCanvas.repaint(); + if (af.alignPanel.overviewPanel != null) { - alreadyAdded = true; - ((JCheckBox)groupPanel.getComponent(g)).setSelected(visible); - break; + af.alignPanel.overviewPanel.updateOverviewImage(); } - } - if (alreadyAdded) - { - - return true; + resetTable(new String[] { grp }); } + }); + groupPanel.add(check); + return visible; + } - fr.featureGroups.put(group, new Boolean(visible)); - final String grp = group; - final JCheckBox check = new JCheckBox(group, visible); - check.setFont(new Font("Serif", Font.BOLD, 12)); - check.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent evt) - { - fr.featureGroups.put(check.getText(), - new Boolean(check.isSelected())); - af.alignPanel.seqPanel.seqCanvas.repaint(); - if (af.alignPanel.overviewPanel != null) - { - af.alignPanel.overviewPanel.updateOverviewImage(); - } + boolean resettingTable = false; - resetTable(new String[] { grp } ); - } - }); - groupPanel.add(check); - return false; - } - boolean resettingTable=false; - void resetTable(String[] groupChanged) + synchronized void resetTable(String[] groupChanged) { - resettingTable=true; - typeWidth=new Hashtable(); - // TODO: change avWidth calculation to 'per-sequence' average and use long rather than float - float[] avWidth=null; + if (resettingTable == true) + { + return; + } + resettingTable = true; + 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++) + // 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().getAlignment().getHeight(); i++) { - tmpfeatures = af.getViewport().alignment.getSequenceAt(i). - getDatasetSequence().getSequenceFeatures(); + tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) + .getSequenceFeatures(); if (tmpfeatures == null) { continue; @@ -311,28 +564,33 @@ public class FeatureSettings continue; } - if (group == null || fr.featureGroups.get(group) == null || - ( (Boolean) fr.featureGroups.get(group)).booleanValue()) + if (group == null || checkGroupState(group)) { - 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 { + if (!typeWidth.containsKey(tmpfeatures[index].getType())) + { + typeWidth.put(tmpfeatures[index].getType(), + avWidth = new float[3]); + } + else + { avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType()); } avWidth[0]++; - if (tmpfeatures[index].getBegin()>tmpfeatures[index].getEnd()) + if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd()) + { + avWidth[1] += 1 + tmpfeatures[index].getBegin() + - tmpfeatures[index].getEnd(); + } + else { - avWidth[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd(); - } else { - avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin(); + avWidth[1] += 1 + tmpfeatures[index].getEnd() + - tmpfeatures[index].getBegin(); } index++; } @@ -342,15 +600,20 @@ public class FeatureSettings Object[][] data = new Object[fSize][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--) { - type = fr.renderOrder[ro]; + fr.findAllFeatures(groupChanged != null); // prod to update + // colourschemes. but don't + // affect display + // First add the checks in the previous render order, + // in case the window has been closed and reopened + } + List frl = fr.getRenderOrder(); + for (int ro = frl.size() - 1; ro > -1; ro--) + { + type = frl.get(ro); if (!visibleChecks.contains(type)) { @@ -358,8 +621,9 @@ public class FeatureSettings } 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); } @@ -368,16 +632,16 @@ public class FeatureSettings fSize = visibleChecks.size(); for (int i = 0; i < fSize; i++) { - //These must be extra features belonging to the group - //which was just selected + // These must be extra features belonging to the group + // which was just selected type = visibleChecks.elementAt(i).toString(); 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; + // "Colour has been updated in another view!!" + fr.clearRenderOrder(); return; } @@ -388,7 +652,10 @@ public class FeatureSettings 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); + } } table.setModel(new FeatureTableModel(data)); @@ -396,47 +663,55 @@ public class FeatureSettings if (groupPanel != null) { - groupPanel.setLayout( - new GridLayout(fr.featureGroups.size() / 4 + 1, 4)); + groupPanel.setLayout(new GridLayout( + fr.getFeatureGroupsSize() / 4 + 1, 4)); groupPanel.validate(); bigPanel.add(groupPanel, BorderLayout.NORTH); } - updateFeatureRenderer(data, groupChanged!=null); - resettingTable=false; + updateFeatureRenderer(data, groupChanged != null); + resettingTable = false; } + /** * reorder data based on the featureRenderers global priority list. + * * @param data */ private void ensureOrder(Object[][] data) { - boolean sort=false; + boolean sort = false; float[] order = new float[data.length]; - for (int i=0;i1) - sort = sort || order[i-1]>order[i]; + if (order[i] < 0) + { + order[i] = fr.setOrder(data[i][0].toString(), i / order.length); + } + if (i > 1) + { + sort = sort || order[i - 1] > order[i]; + } } if (sort) + { jalview.util.QuickSort.sort(order, data); + } } void load() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY"), new String[] - {"fc"}, - new String[] - {"Sequence Feature Colours"}, "Sequence Feature Colours"); + 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"); + chooser.setDialogTitle(MessageManager + .getString("label.load_feature_colours")); + chooser.setToolTipText(MessageManager.getString("action.load")); int value = chooser.showOpenDialog(this); @@ -447,29 +722,78 @@ public class FeatureSettings try { InputStreamReader in = new InputStreamReader(new FileInputStream( - file), "UTF-8"); + file), "UTF-8"); - jalview.binding.JalviewUserColours jucs = new jalview.binding. - JalviewUserColours(); - jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in); + jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours(); + jucs = jucs.unmarshal(in); - for (int i = jucs.getColourCount()-1; i >=0; i--) + for (int i = jucs.getColourCount() - 1; i >= 0; i--) { String name; - fr.setColour(name=jucs.getColour(i).getName(), - new Color(Integer.parseInt(jucs.getColour(i).getRGB(), - 16))); - fr.setOrder(name,(i==0) ? 0 : i/jucs.getColourCount()); + 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); + } + GraduatedColor gcol = new GraduatedColor(mincol, maxcol, + newcol.getMin(), newcol.getMax()); + if (newcol.hasAutoScale()) + { + gcol.setAutoScaled(newcol.getAutoScale()); + } + if (newcol.hasColourByLabel()) + { + gcol.setColourByLabel(newcol.getColourByLabel()); + } + if (newcol.hasThreshold()) + { + gcol.setThresh(newcol.getThreshold()); + gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default + } + 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); + } + if (ttyp.equalsIgnoreCase("BELOW")) + { + gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); + } + } + fr.setColour(name = newcol.getName(), gcol); + } + else + { + fr.setColour(name = jucs.getColour(i).getName(), new Color( + Integer.parseInt(jucs.getColour(i).getRGB(), 16))); + } + fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount()); } - if (table!=null) { + if (table != null) + { resetTable(null); - Object[][] data=((FeatureTableModel) table.getModel()).getData(); + Object[][] data = ((FeatureTableModel) table.getModel()) + .getData(); ensureOrder(data); - updateFeatureRenderer(data,false); + updateFeatureRenderer(data, false); table.repaint(); } - } - catch (Exception ex) + } catch (Exception ex) { System.out.println("Error loading User Colour File\n" + ex); } @@ -478,52 +802,78 @@ public class FeatureSettings void save() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( - "LAST_DIRECTORY"), new String[] - {"fc"}, - new String[] - {"Sequence Feature Colours"}, "Sequence Feature Colours"); + 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"); + 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()]; - int i=0; - while (e.hasMoreElements()) + new FileOutputStream(choice), "UTF-8")); + + 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.nextElement().toString(); - sortOrder[i] = fr.getOrder(sortTypes[i]); + sortTypes[i] = e.next().toString(); + sortOrder[i] = fr.getOrder(sortTypes[i]); i++; } jalview.util.QuickSort.sort(sortOrder, sortTypes); - sortOrder=null; - for (i=0; i0) { - width[i] = awidth[1]/awidth[0];// *awidth[0]*awidth[2]; - better weight - but have to make per sequence, too (awidth[2]) - //if (width[i]==1) // hack to distinguish single width sequences. - num++; - } else { - width[i]=0; - } - if (max 0) + { + width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better + // weight - but have to make per + // sequence, too (awidth[2]) + // if (width[i]==1) // hack to distinguish single width sequences. + num++; + } + else + { + width[i] = 0; + } + if (max < width[i]) + { + max = width[i]; + } + } + boolean sort = false; + for (int i = 0; i < width.length; i++) + { + // awidth = (float[]) typeWidth.get(data[i][0]); + if (width[i] == 0) { width[i] = fr.getOrder(data[i][0].toString()); - if (width[i]<0) + if (width[i] < 0) { - width[i] = fr.setOrder(data[i][0].toString(), i/data.length); + width[i] = fr.setOrder(data[i][0].toString(), i / data.length); } - } else { - width[i] /=max; // normalize - fr.setOrder(data[i][0].toString(), width[i]); // store for later } - if (i>0) - sort = sort || width[i-1]>width[i]; + else + { + width[i] /= max; // normalize + 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 - - updateFeatureRenderer(data,false); + // update global priority order + } + + updateFeatureRenderer(data, false); table.repaint(); } + public void close() { try { frame.setClosed(true); + } catch (Exception exe) + { } - catch (Exception exe) - {} } @@ -600,45 +968,65 @@ public class FeatureSettings { updateFeatureRenderer(data, true); } + private void updateFeatureRenderer(Object[][] data, boolean visibleNew) { fr.setFeaturePriority(data, visibleNew); af.alignPanel.paintAlignment(true); - - if (af.alignPanel.overviewPanel != null) - { - af.alignPanel.overviewPanel.updateOverviewImage(); - } } int selectedRow = -1; + JTabbedPane tabbedPane = new JTabbedPane(); + BorderLayout borderLayout1 = new BorderLayout(); + BorderLayout borderLayout2 = new BorderLayout(); + BorderLayout borderLayout3 = new BorderLayout(); + JPanel bigPanel = new JPanel(); + BorderLayout borderLayout4 = new BorderLayout(); + JButton invert = new JButton(); + JPanel buttonPanel = new JPanel(); + JButton cancel = new JButton(); + JButton ok = new JButton(); + JButton loadColours = new JButton(); + JButton saveColours = new JButton(); + JPanel dasButtonPanel = new JPanel(); + JButton fetchDAS = new JButton(); + JButton saveDAS = new JButton(); + JButton cancelDAS = new JButton(); + JButton optimizeOrder = new JButton(); - JPanel transbuttons = new JPanel(new BorderLayout()); - private void jbInit() - throws Exception + + JButton sortByScore = new JButton(); + + JButton sortByDens = new JButton(); + + JButton help = new JButton(); + + JPanel transbuttons = new JPanel(new GridLayout(5, 1)); + + private void jbInit() throws Exception { this.setLayout(borderLayout1); settingsPane.setLayout(borderLayout2); dasSettingsPane.setLayout(borderLayout3); bigPanel.setLayout(borderLayout4); - invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - invert.setText("Invert Selection"); + invert.setFont(JvSwingUtils.getLabelFont()); + invert.setText(MessageManager.getString("label.invert_selection")); invert.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -646,25 +1034,78 @@ public class FeatureSettings invertSelection(); } }); - optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - optimizeOrder.setText("Optimise Order"); - optimizeOrder.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { + optimizeOrder.setFont(JvSwingUtils.getLabelFont()); + optimizeOrder.setText(MessageManager.getString("label.optimise_order")); + optimizeOrder.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { orderByAvWidth(); } }); - cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - cancel.setText("Cancel"); + sortByScore.setFont(JvSwingUtils.getLabelFont()); + sortByScore + .setText(MessageManager.getString("label.seq_sort_by_score")); + sortByScore.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + af.avc.sortAlignmentByFeatureScore(null); + } + }); + sortByDens.setFont(JvSwingUtils.getLabelFont()); + sortByDens.setText(MessageManager + .getString("label.sequence_sort_by_density")); + sortByDens.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + af.avc.sortAlignmentByFeatureDensity(null); + } + }); + help.setFont(JvSwingUtils.getLabelFont()); + help.setText(MessageManager.getString("action.help")); + help.addActionListener(new ActionListener() + { + 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() + { + 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() { 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() { public void actionPerformed(ActionEvent e) @@ -672,8 +1113,8 @@ public class FeatureSettings 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() { public void actionPerformed(ActionEvent e) @@ -681,8 +1122,8 @@ public class FeatureSettings 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() { public void actionPerformed(ActionEvent e) @@ -694,13 +1135,15 @@ public class FeatureSettings { public void stateChanged(ChangeEvent evt) { - fr.setTransparency( (float) (100 - transparency.getValue()) / 100f); + 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() { public void actionPerformed(ActionEvent e) @@ -708,7 +1151,7 @@ public class FeatureSettings fetchDAS_actionPerformed(e); } }); - saveDAS.setText("Save as default"); + saveDAS.setText(MessageManager.getString("action.save_as_default")); saveDAS.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -719,7 +1162,7 @@ public class FeatureSettings 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() { public void actionPerformed(ActionEvent e) @@ -728,12 +1171,19 @@ public class FeatureSettings } }); 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); @@ -752,24 +1202,35 @@ public class FeatureSettings { fetchDAS.setEnabled(false); cancelDAS.setEnabled(true); + dassourceBrowser.setGuiEnabled(false); Vector selectedSources = dassourceBrowser.getSelectedSources(); + doDasFeatureFetch(selectedSources, true, true); + } + /** + * get the features from selectedSources for all or the current selection + * + * @param selectedSources + * @param checkDbRefs + * @param promptFetchDbRefs + */ + private void doDasFeatureFetch(List selectedSources, + boolean checkDbRefs, boolean promptFetchDbRefs) + { SequenceI[] dataset, seqs; int iSize; - - if (af.getViewport().getSelectionGroup() != null - && af.getViewport().getSelectionGroup().getSize() > 0) + AlignmentViewport vp = af.getViewport(); + if (vp.getSelectionGroup() != null + && vp.getSelectionGroup().getSize() > 0) { - iSize = af.getViewport().getSelectionGroup().getSize(); + iSize = vp.getSelectionGroup().getSize(); dataset = new SequenceI[iSize]; - seqs = af.getViewport().getSelectionGroup(). - getSequencesInOrder( - af.getViewport().getAlignment()); + seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment()); } else { - iSize = af.getViewport().getAlignment().getHeight(); - seqs = af.getViewport().getAlignment().getSequencesArray(); + iSize = vp.getAlignment().getHeight(); + seqs = vp.getAlignment().getSequencesArray(); } dataset = new SequenceI[iSize]; @@ -778,48 +1239,140 @@ public class FeatureSettings dataset[i] = seqs[i].getDatasetSequence(); } - dasFeatureFetcher = - new jalview.io.DasSequenceFeatureFetcher( - dataset, - this, - selectedSources); cancelDAS.setEnabled(true); + dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset, + this, selectedSources, checkDbRefs, promptFetchDbRefs); af.getViewport().setShowSequenceFeatures(true); af.showSeqFeatures.setSelected(true); } + /** + * blocking call to initialise the das source browser + */ + public void initDasSources() + { + dassourceBrowser.initDasSources(); + } + + /** + * examine the current list of das sources and return any matching the given + * nicknames in sources + * + * @param sources + * Vector of Strings to resolve to DAS source nicknames. + * @return sources that are present in source list. + */ + public List resolveSourceNicknames(Vector sources) + { + return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); + } + + /** + * get currently selected das sources. ensure you have called initDasSources + * before calling this. + * + * @return vector of selected das source nicknames + */ + public Vector getSelectedSources() + { + return dassourceBrowser.getSelectedSources(); + } + + /** + * properly initialise DAS fetcher and then initiate a new thread to fetch + * features from the named sources (rather than any turned on by default) + * + * @param sources + * @param block + * if true then runs in same thread, otherwise passes to the Swing + * executor + */ + public void fetchDasFeatures(Vector sources, boolean block) + { + initDasSources(); + List resolved = dassourceBrowser.sourceRegistry + .resolveSourceNicknames(sources); + if (resolved.size() == 0) + { + resolved = dassourceBrowser.getSelectedSources(); + } + if (resolved.size() > 0) + { + final List dassources = resolved; + fetchDAS.setEnabled(false); + // cancelDAS.setEnabled(true); doDasFetch does this. + Runnable fetcher = new Runnable() + { + + public void run() + { + doDasFeatureFetch(dassources, true, false); + + } + }; + if (block) + { + fetcher.run(); + } + else + { + SwingUtilities.invokeLater(fetcher); + } + } + } + public void saveDAS_actionPerformed(ActionEvent e) { - dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties); + dassourceBrowser + .saveProperties(jalview.bin.Cache.applicationProperties); } public void complete() { fetchDAS.setEnabled(true); cancelDAS.setEnabled(false); + dassourceBrowser.setGuiEnabled(true); + } public void cancelDAS_actionPerformed(ActionEvent e) { - dasFeatureFetcher.cancel(); - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); + if (dasFeatureFetcher != null) + { + dasFeatureFetcher.cancel(); + } + complete(); + } + + public void noDasSourceActive() + { + complete(); + JOptionPane + .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); } - ///////////////////////////////////////////////////////////////////////// + // /////////////////////////////////////////////////////////////////////// // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html - ///////////////////////////////////////////////////////////////////////// - class FeatureTableModel - extends AbstractTableModel + // /////////////////////////////////////////////////////////////////////// + class FeatureTableModel extends AbstractTableModel { FeatureTableModel(Object[][] data) { 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; public Object[][] getData() @@ -876,31 +1429,58 @@ public class FeatureSettings } - class ColorRenderer - extends JLabel implements TableCellRenderer + class ColorRenderer extends JLabel implements TableCellRenderer { javax.swing.border.Border unselectedBorder = null; + javax.swing.border.Border selectedBorder = null; + final String baseTT = "Click to edit, right/apple click for menu."; + public ColorRenderer() { - setOpaque(true); //MUST do this for background to show up. + setOpaque(true); // MUST do this for background to show up. + setHorizontalTextPosition(SwingConstants.CENTER); + setVerticalTextPosition(SwingConstants.CENTER); } - public Component getTableCellRendererComponent( - JTable table, Object color, - boolean isSelected, boolean hasFocus, - int row, int column) + public Component getTableCellRendererComponent(JTable table, + Object color, boolean isSelected, boolean hasFocus, int row, + int column) { - Color newColor = (Color) color; - setBackground(newColor); + // JLabel comp = new JLabel(); + // comp. + setOpaque(true); + // comp. + // setBounds(getBounds()); + Color newColor; + setToolTipText(baseTT); + setBackground(table.getBackground()); + if (color instanceof GraduatedColor) + { + Rectangle cr = table.getCellRect(row, column, false); + FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color, + (int) cr.getWidth(), (int) cr.getHeight()); + + } + else + { + this.setText(""); + this.setIcon(null); + newColor = (Color) color; + // comp. + 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()); + table.getSelectionBackground()); } + // comp. setBorder(selectedBorder); } else @@ -908,88 +1488,298 @@ public class FeatureSettings if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getBackground()); + table.getBackground()); } + // comp. 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, GraduatedColor 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, GraduatedColor gcol, + int w, int h) + { + boolean thr = false; + String tt = ""; + String tx = ""; + if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) + { + thr = true; + tx += ">"; + tt += "Thresholded (Above " + gcol.getThresh() + ") "; + } + if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD) + { + thr = true; + tx += "<"; + tt += "Thresholded (Below " + gcol.getThresh() + ") "; + } + if (gcol.isColourByLabel()) + { + tt = "Coloured by label text. " + tt; + if (thr) + { + tx += " "; + } + tx += "Label"; + comp.setIcon(null); + } + else + { + Color newColor = gcol.getMaxColor(); + 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 FeatureIcon implements Icon +{ + GraduatedColor 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(GraduatedColor 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; + } + } + + public int getIconWidth() + { + return width; + } + + public int getIconHeight() + { + return height; + } + + 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.getMaxColor()); + + 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.getMinColor(); + 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.getMaxColor()); + g.fillRect(0, e1, width - e1, height); + } + } } -class ColorEditor - extends AbstractCellEditor implements TableCellEditor, - ActionListener +class ColorEditor extends AbstractCellEditor implements TableCellEditor, + ActionListener { + FeatureSettings me; + + GraduatedColor currentGColor; + + FeatureColourChooser chooser; + + String type; + Color currentColor; + JButton button; + JColorChooser colorChooser; + JDialog dialog; + protected static final String EDIT = "edit"; - public ColorEditor() + int selectedRow = 0; + + public ColorEditor(FeatureSettings me) { - //Set up the editor (from the table's point of view), - //which is a button. - //This button brings up the color chooser dialog, - //which is the editor from the user's point of view. + this.me = me; + // Set up the editor (from the table's point of view), + // which is a button. + // This button brings up the color chooser dialog, + // which is the editor from the user's point of view. button = new JButton(); button.setActionCommand(EDIT); button.addActionListener(this); button.setBorderPainted(false); - //Set up the dialog that the button brings up. + // Set up the dialog that the button brings up. colorChooser = new JColorChooser(); - dialog = JColorChooser.createDialog(button, - "Select new Colour", - true, //modal - colorChooser, - this, //OK button handler - null); //no CANCEL button handler + dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal + colorChooser, this, // OK button handler + null); // no CANCEL button handler } /** - * Handles events from the editor button and from - * the dialog's OK button. + * Handles events from the editor button and from the dialog's OK button. */ public void actionPerformed(ActionEvent e) { if (EDIT.equals(e.getActionCommand())) { - //The user has clicked the cell, so - //bring up the dialog. - button.setBackground(currentColor); - colorChooser.setColor(currentColor); - dialog.setVisible(true); - - //Make the renderer reappear. + // The user has clicked the cell, so + // bring up the dialog. + if (currentColor != null) + { + // bring up simple color chooser + button.setBackground(currentColor); + colorChooser.setColor(currentColor); + 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(); + { // User pressed dialog's "OK" button. + if (currentColor != null) + { + currentColor = colorChooser.getColor(); + } + else + { + // class cast exceptions may be raised if the chooser created on a + // non-graduated color + currentGColor = (GraduatedColor) chooser.getLastColour(); + } + me.table.setValueAt(getCellEditorValue(), selectedRow, 1); + fireEditingStopped(); + me.table.validate(); } } - //Implement the one CellEditor method that AbstractCellEditor doesn't. + // Implement the one CellEditor method that AbstractCellEditor doesn't. public Object getCellEditorValue() { + if (currentColor == null) + { + return currentGColor; + } return currentColor; } - //Implement the one method defined by TableCellEditor. - public Component getTableCellEditorComponent(JTable table, - Object value, - boolean isSelected, - int row, - int column) + // Implement the one method defined by TableCellEditor. + public Component getTableCellEditorComponent(JTable table, Object value, + boolean isSelected, int row, int column) { - currentColor = (Color) value; + currentGColor = null; + currentColor = null; + this.selectedRow = row; + type = me.table.getValueAt(row, 0).toString(); + button.setOpaque(true); + button.setBackground(me.getBackground()); + if (value instanceof GraduatedColor) + { + currentGColor = (GraduatedColor) value; + JLabel btn = new JLabel(); + btn.setSize(button.getSize()); + FeatureSettings.renderGraduatedColor(btn, currentGColor); + button.setBackground(btn.getBackground()); + button.setIcon(btn.getIcon()); + button.setText(btn.getText()); + } + else + { + button.setText(""); + button.setIcon(null); + currentColor = (Color) value; + button.setBackground(currentColor); + } return button; } }