X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=632ad00cc611b36cccfb7c3ea766083050552d06;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=24058089d7f1b16c5255f90b2a77d1c059d9816f;hpb=38a10817438b42f7cba2ee95d4d65cb9672926ab;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 2405808..632ad00 100755 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,783 +1,1126 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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 - * 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. - * - * 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 - */ -package jalview.gui; - -import jalview.datamodel.*; -import javax.swing.*; -import javax.swing.event.*; -import java.awt.*; -import java.util.*; -import javax.swing.BorderFactory; -import java.awt.event.*; -import javax.swing.table.*; -import java.io.*; -import jalview.io.JalviewFileChooser; -import java.awt.BorderLayout; -import java.awt.Font; -import java.awt.Color; - -public class FeatureSettings extends JPanel -{ - DasSourceBrowser dassourceBrowser; - jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher; - JPanel settingsPane = new JPanel(); - JPanel dasSettingsPane = new JPanel(); - - final FeatureRenderer fr; - public final AlignFrame af; - Object [][] originalData; - final JInternalFrame frame; - JScrollPane scrollPane = new JScrollPane(); - JTable table; - JPanel groupPanel; - JSlider transparency = new JSlider(); - - JPanel transPanel = new JPanel(new FlowLayout()); - - public FeatureSettings(AlignFrame af) - { - this.af = af; - fr = af.getFeatureRenderer(); - - transparency.setMaximum( 100 - (int)(fr.transparency*100) ) ; - - try - { - jbInit(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - - table = new JTable(); - table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setDefaultRenderer(Color.class, - new ColorRenderer()); - - table.setDefaultEditor(Color.class, - new ColorEditor()); - - table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); - - table.addMouseListener(new MouseAdapter() - { - public void mousePressed(MouseEvent evt) - { - selectedRow = table.rowAtPoint(evt.getPoint()); - } - }); - - table.addMouseMotionListener(new MouseMotionAdapter() - { - 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); - - selectedRow = newRow; - } - } - }); - - scrollPane.setViewportView(table); - - dassourceBrowser = new DasSourceBrowser(); - dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - - - - if (af.getViewport().featuresDisplayed == null || fr.renderOrder==null) - fr.findAllFeatures(); - - setTableData(); - - frame = new JInternalFrame(); - frame.setContentPane(this); - Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450); - frame.setLayer(JLayeredPane.PALETTE_LAYER); - } - - synchronized public void setTableData() - { - if (fr.featureGroups == null) - fr.featureGroups = new Hashtable(); - - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); - SequenceFeature[] tmpfeatures; - String group; - - for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) - { - if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null) - continue; - - tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures(); - - int index = 0; - while (index < tmpfeatures.length) - { - 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); - - boolean visible = true; - if (fr.featureGroups.containsKey(group)) - { - visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue(); - } - - if (groupPanel == null) - { - groupPanel = new JPanel(); - } - - boolean alreadyAdded = false; - for(int g=0; g-1; ro--) - { - type = fr.renderOrder[ro]; - - if(!visibleChecks.contains(type)) - continue; - - data[dataIndex][0] = type; - data[dataIndex][1] = fr.getColour(type); - data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type)); - dataIndex++; - visibleChecks.removeElement(type); - } - } - - fSize = visibleChecks.size(); - for(int i=0; i0) - { - iSize = af.getViewport().getSelectionGroup().getSize(false); - dataset = new SequenceI[iSize]; - seqs = af.getViewport().getSelectionGroup(). - getSequencesInOrder( - af.getViewport().getAlignment()); - } - else - { - iSize = af.getViewport().getAlignment().getHeight(); - seqs = af.getViewport().getAlignment().getSequencesArray(); - } - - dataset = new SequenceI[iSize]; - for (int i = 0; i < iSize; i++) - { - dataset[i] = seqs[i].getDatasetSequence(); - } - - dasFeatureFetcher = - new jalview.io.DasSequenceFeatureFetcher( - dataset, - this, - selectedSources); - - af.getViewport().setShowSequenceFeatures(true); - af.showSeqFeatures.setSelected(true); - } - - public void saveDAS_actionPerformed(ActionEvent e) - { - dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties); - } - - public void complete() - { - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); - } - - public void cancelDAS_actionPerformed(ActionEvent e) - { - dasFeatureFetcher.cancel(); - fetchDAS.setEnabled(true); - cancelDAS.setEnabled(false); - } - - ///////////////////////////////////////////////////////////////////////// - // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html - ///////////////////////////////////////////////////////////////////////// - class FeatureTableModel - extends AbstractTableModel - { - FeatureTableModel(Object[][] data) - { - this.data = data; - } - - private String[] columnNames = {"Feature Type", "Colour","Display"}; - private Object[][] data; - - public Object[][] getData() - { - return data; - } - - public void setData(Object[][] data) - { - this.data = data; - } - - public int getColumnCount() { - return columnNames.length; - } - - public Object[] getRow(int row) - { - return data[row]; - } - - public int getRowCount() { - return data.length; - } - - public String getColumnName(int col) { - return columnNames[col]; - } - - public Object getValueAt(int row, int col) { - return data[row][col]; - } - - public Class getColumnClass(int c) { - return getValueAt(0, c).getClass(); - } - - public boolean isCellEditable(int row, int col) { - return col==0 ? false:true; - } - - public void setValueAt(Object value, int row, int col) { - data[row][col] = value; - fireTableCellUpdated(row, col); - updateFeatureRenderer(data); - } - - } - class ColorRenderer extends JLabel - implements TableCellRenderer { - javax.swing.border.Border unselectedBorder = null; - javax.swing.border.Border selectedBorder = null; - - public ColorRenderer() { - setOpaque(true); //MUST do this for background to show up. - } - - public Component getTableCellRendererComponent( - JTable table, Object color, - boolean isSelected, boolean hasFocus, - int row, int column) { - Color newColor = (Color)color; - setBackground(newColor); - if (isSelected) { - if (selectedBorder == null) { - selectedBorder = BorderFactory.createMatteBorder(2,5,2,5, - table.getSelectionBackground()); - } - setBorder(selectedBorder); - } else { - if (unselectedBorder == null) { - unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5, - table.getBackground()); - } - setBorder(unselectedBorder); - } - - setToolTipText("RGB value: " + newColor.getRed() + ", " - + newColor.getGreen() + ", " - + newColor.getBlue()); - return this; - } - } -} - - class ColorEditor extends AbstractCellEditor - implements TableCellEditor, - ActionListener { - Color currentColor; - JButton button; - JColorChooser colorChooser; - JDialog dialog; - protected static final String EDIT = "edit"; - - public ColorEditor() { - //Set up the editor (from the table's point of view), - //which is a button. - //This button brings up the color chooser dialog, - //which is the editor from the user's point of view. - button = new JButton(); - button.setActionCommand(EDIT); - button.addActionListener(this); - button.setBorderPainted(false); - //Set up the dialog that the button brings up. - colorChooser = new JColorChooser(); - dialog = JColorChooser.createDialog(button, - "Select new Colour", - true, //modal - colorChooser, - this, //OK button handler - null); //no CANCEL button handler - } - - /** - * 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. - fireEditingStopped(); - - } else { //User pressed dialog's "OK" button. - currentColor = colorChooser.getColor(); - } - } - - //Implement the one CellEditor method that AbstractCellEditor doesn't. - public Object getCellEditorValue() { - return currentColor; - } - - //Implement the one method defined by TableCellEditor. - public Component getTableCellEditorComponent(JTable table, - Object value, - boolean isSelected, - int row, - int column) { - currentColor = (Color)value; - return button; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 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 + * 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. + * + * 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 + */ +package jalview.gui; + +import java.io.*; +import java.util.*; + +import java.awt.*; +import java.awt.event.*; +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 +{ + DasSourceBrowser dassourceBrowser; + + jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher; + + JPanel settingsPane = new JPanel(); + + JPanel dasSettingsPane = new JPanel(); + + final FeatureRenderer fr; + + public final AlignFrame af; + + Object[][] originalData; + + final JInternalFrame frame; + + JScrollPane scrollPane = new JScrollPane(); + + JTable table; + + JPanel groupPanel; + + JSlider transparency = new JSlider(); + + JPanel transPanel = new JPanel(new FlowLayout()); + + public FeatureSettings(AlignFrame af) + { + this.af = af; + fr = af.getFeatureRenderer(); + + transparency.setMaximum(100 - (int) (fr.transparency * 100)); + + try + { + jbInit(); + } catch (Exception ex) + { + ex.printStackTrace(); + } + + table = new JTable(); + table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); + table.setFont(new Font("Verdana", Font.PLAIN, 12)); + table.setDefaultRenderer(Color.class, new ColorRenderer()); + + table.setDefaultEditor(Color.class, new ColorEditor()); + + table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); + + table.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent evt) + { + selectedRow = table.rowAtPoint(evt.getPoint()); + } + }); + + table.addMouseMotionListener(new MouseMotionAdapter() + { + 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); + + selectedRow = newRow; + } + } + }); + + scrollPane.setViewportView(table); + + dassourceBrowser = new DasSourceBrowser(); + dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); + + if (af.getViewport().featuresDisplayed == null + || fr.renderOrder == null) + { + fr.findAllFeatures(true); // display everything! + } + + setTableData(); + final PropertyChangeListener change; + 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; + } + } + + }); + + frame = new JInternalFrame(); + frame.setContentPane(this); + Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450); + frame + .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + fr.removePropertyChangeListener(change); + }; + }); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + } + + /** + * true when Feature Settings are updating from feature renderer + */ + private boolean handlingUpdate = false; + + /** + * contains a float[3] for each feature type string. created by setTableData + */ + Hashtable typeWidth = null; + + synchronized public void setTableData() + { + if (fr.featureGroups == null) + { + fr.featureGroups = new Hashtable(); + } + Vector allFeatures = new Vector(); + Vector allGroups = new Vector(); + SequenceFeature[] tmpfeatures; + String group; + for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) + { + if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence() + .getSequenceFeatures() == null) + { + continue; + } + + tmpfeatures = af.getViewport().alignment.getSequenceAt(i) + .getDatasetSequence().getSequenceFeatures(); + + int index = 0; + while (index < tmpfeatures.length) + { + if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) + { + index++; + continue; + } + + if (tmpfeatures[index].getFeatureGroup() != null) + { + group = tmpfeatures[index].featureGroup; + if (!allGroups.contains(group)) + { + allGroups.addElement(group); + if (group != null) + { + checkGroupState(group); + } + } + } + + if (!allFeatures.contains(tmpfeatures[index].getType())) + { + allFeatures.addElement(tmpfeatures[index].getType()); + } + index++; + } + } + + resetTable(null); + + validate(); + } + + /** + * + * @param group + * @return true if group has been seen before and is already added to set. + */ + private boolean checkGroupState(String group) + { + boolean visible; + if (fr.featureGroups.containsKey(group)) + { + visible = ((Boolean) fr.featureGroups.get(group)).booleanValue(); + } + else + { + visible = true; // new group is always made visible + } + + if (groupPanel == null) + { + groupPanel = new JPanel(); + } + + boolean alreadyAdded = false; + for (int g = 0; g < groupPanel.getComponentCount(); g++) + { + if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group)) + { + alreadyAdded = true; + ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible); + break; + } + } + + if (alreadyAdded) + { + + return true; + } + + fr.featureGroups.put(group, new Boolean(visible)); + final String grp = group; + final JCheckBox check = new JCheckBox(group, visible); + check.setFont(new Font("Serif", Font.BOLD, 12)); + check.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent evt) + { + fr.featureGroups.put(check.getText(), new Boolean(check + .isSelected())); + af.alignPanel.seqPanel.seqCanvas.repaint(); + if (af.alignPanel.overviewPanel != null) + { + af.alignPanel.overviewPanel.updateOverviewImage(); + } + + resetTable(new String[] + { grp }); + } + }); + groupPanel.add(check); + return false; + } + + boolean resettingTable = false; + + synchronized void resetTable(String[] groupChanged) + { + 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++) + { + + tmpfeatures = af.getViewport().alignment.getSequenceAt(i) + .getDatasetSequence().getSequenceFeatures(); + if (tmpfeatures == null) + { + continue; + } + + int index = 0; + while (index < tmpfeatures.length) + { + group = tmpfeatures[index].featureGroup; + + if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) + { + index++; + continue; + } + + if (group == null || fr.featureGroups.get(group) == null + || ((Boolean) fr.featureGroups.get(group)).booleanValue()) + { + if (group != null) + checkGroupState(group); + type = tmpfeatures[index].getType(); + if (!visibleChecks.contains(type)) + { + visibleChecks.addElement(type); + } + } + if (!typeWidth.containsKey(tmpfeatures[index].getType())) + { + typeWidth.put(tmpfeatures[index].getType(), + avWidth = new float[3]); + } + else + { + avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType()); + } + avWidth[0]++; + if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd()) + { + avWidth[1] += 1 + tmpfeatures[index].getBegin() + - tmpfeatures[index].getEnd(); + } + else + { + avWidth[1] += 1 + tmpfeatures[index].getEnd() + - tmpfeatures[index].getBegin(); + } + index++; + } + } + + int fSize = visibleChecks.size(); + Object[][] data = new Object[fSize][3]; + int dataIndex = 0; + + if (fr.renderOrder != null) + { + 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]; + + if (!visibleChecks.contains(type)) + { + continue; + } + + data[dataIndex][0] = type; + data[dataIndex][1] = fr.getColour(type); + data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed + .containsKey(type)); + dataIndex++; + visibleChecks.removeElement(type); + } + } + + fSize = visibleChecks.size(); + for (int i = 0; i < fSize; i++) + { + // 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); + if (data[dataIndex][1] == null) + { + // "Colour has been updated in another view!!" + fr.renderOrder = null; + return; + } + + data[dataIndex][2] = new Boolean(true); + dataIndex++; + } + + if (originalData == null) + { + originalData = new Object[data.length][3]; + System.arraycopy(data, 0, originalData, 0, data.length); + } + + table.setModel(new FeatureTableModel(data)); + table.getColumnModel().getColumn(0).setPreferredWidth(200); + + if (groupPanel != null) + { + groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1, + 4)); + + groupPanel.validate(); + bigPanel.add(groupPanel, BorderLayout.NORTH); + } + + 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; + float[] order = new float[data.length]; + for (int i = 0; i < order.length; i++) + { + order[i] = fr.getOrder(data[i][0].toString()); + if (order[i] < 0) + order[i] = fr.setOrder(data[i][0].toString(), i / order.length); + if (i > 1) + sort = sort || order[i - 1] > order[i]; + } + if (sort) + jalview.util.QuickSort.sort(order, data); + } + + void load() + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache + .getProperty("LAST_DIRECTORY"), new String[] + { "fc" }, new String[] + { "Sequence Feature Colours" }, "Sequence Feature Colours"); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Load Feature Colours"); + chooser.setToolTipText("Load"); + + int value = chooser.showOpenDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + File file = chooser.getSelectedFile(); + + try + { + InputStreamReader in = new InputStreamReader(new FileInputStream( + file), "UTF-8"); + + jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours(); + jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in); + + for (int i = jucs.getColourCount() - 1; i >= 0; i--) + { + String name; + fr.setColour(name = jucs.getColour(i).getName(), new Color( + Integer.parseInt(jucs.getColour(i).getRGB(), 16))); + fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount()); + } + if (table != null) + { + resetTable(null); + Object[][] data = ((FeatureTableModel) table.getModel()) + .getData(); + ensureOrder(data); + updateFeatureRenderer(data, false); + table.repaint(); + } + } catch (Exception ex) + { + System.out.println("Error loading User Colour File\n" + ex); + } + } + } + + void save() + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache + .getProperty("LAST_DIRECTORY"), new String[] + { "fc" }, new String[] + { "Sequence Feature Colours" }, "Sequence Feature Colours"); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Save Feature Colour Scheme"); + chooser.setToolTipText("Save"); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours(); + ucs.setSchemeName("Sequence Features"); + try + { + PrintWriter out = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(choice), "UTF-8")); + + 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()) + { + sortTypes[i] = e.nextElement().toString(); + sortOrder[i] = fr.getOrder(sortTypes[i]); + i++; + } + jalview.util.QuickSort.sort(sortOrder, sortTypes); + sortOrder = null; + for (i = 0; i < sortTypes.length; i++) + { + jalview.binding.Colour col = new jalview.binding.Colour(); + col.setName(sortTypes[i]); + col.setRGB(jalview.util.Format.getHexString(fr.getColour(col + .getName()))); + ucs.addColour(col); + } + ucs.marshal(out); + out.close(); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + public void invertSelection() + { + for (int i = 0; i < table.getRowCount(); i++) + { + Boolean value = (Boolean) table.getValueAt(i, 2); + + table.setValueAt(new Boolean(!value.booleanValue()), i, 2); + } + } + + public void orderByAvWidth() + { + if (table == null || table.getModel() == null) + return; + Object[][] data = ((FeatureTableModel) table.getModel()).getData(); + float[] width = new float[data.length]; + float[] awidth; + float max = 0; + int num = 0; + for (int i = 0; i < data.length; i++) + { + awidth = (float[]) typeWidth.get(data[i][0]); + if (awidth[0] > 0) + { + width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better + // weight - but have to make per + // sequence, too (awidth[2]) + // if (width[i]==1) // hack to distinguish single width sequences. + 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) + { + 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]; + } + if (sort) + jalview.util.QuickSort.sort(width, data); + // update global priority order + + updateFeatureRenderer(data, false); + table.repaint(); + } + + public void close() + { + try + { + frame.setClosed(true); + } catch (Exception exe) + { + } + + } + + public void updateFeatureRenderer(Object[][] data) + { + updateFeatureRenderer(data, true); + } + + private void updateFeatureRenderer(Object[][] data, boolean visibleNew) + { + fr.setFeaturePriority(data, visibleNew); + af.alignPanel.paintAlignment(true); + } + + int selectedRow = -1; + + JTabbedPane tabbedPane = new JTabbedPane(); + + BorderLayout borderLayout1 = new BorderLayout(); + + BorderLayout borderLayout2 = new BorderLayout(); + + BorderLayout borderLayout3 = new BorderLayout(); + + JPanel bigPanel = new JPanel(); + + BorderLayout borderLayout4 = new BorderLayout(); + + JButton invert = new JButton(); + + JPanel buttonPanel = new JPanel(); + + JButton cancel = new JButton(); + + JButton ok = new JButton(); + + JButton loadColours = new JButton(); + + JButton saveColours = new JButton(); + + JPanel dasButtonPanel = new JPanel(); + + JButton fetchDAS = new JButton(); + + JButton saveDAS = new JButton(); + + JButton cancelDAS = new JButton(); + + JButton optimizeOrder = new JButton(); + + JPanel transbuttons = new JPanel(new BorderLayout()); + + private void jbInit() throws Exception + { + this.setLayout(borderLayout1); + settingsPane.setLayout(borderLayout2); + dasSettingsPane.setLayout(borderLayout3); + bigPanel.setLayout(borderLayout4); + invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + invert.setText("Invert Selection"); + invert.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + invertSelection(); + } + }); + optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + optimizeOrder.setText("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"); + cancel.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + updateFeatureRenderer(originalData); + close(); + } + }); + ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + ok.setText("OK"); + ok.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + close(); + } + }); + loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + loadColours.setText("Load Colours"); + loadColours.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + load(); + } + }); + saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + saveColours.setText("Save Colours"); + saveColours.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + save(); + } + }); + transparency.addChangeListener(new ChangeListener() + { + public void stateChanged(ChangeEvent evt) + { + fr.setTransparency((float) (100 - transparency.getValue()) / 100f); + af.alignPanel.paintAlignment(true); + } + }); + + transparency.setMaximum(70); + fetchDAS.setText("Fetch DAS Features"); + fetchDAS.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + fetchDAS_actionPerformed(e); + } + }); + saveDAS.setText("Save as default"); + saveDAS.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + saveDAS_actionPerformed(e); + } + }); + dasButtonPanel.setBorder(BorderFactory.createEtchedBorder()); + dasSettingsPane.setBorder(null); + cancelDAS.setEnabled(false); + cancelDAS.setText("Cancel Fetch"); + cancelDAS.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + cancelDAS_actionPerformed(e); + } + }); + this.add(tabbedPane, java.awt.BorderLayout.CENTER); + tabbedPane.addTab("Feature Settings", settingsPane); + tabbedPane.addTab("DAS Settings", dasSettingsPane); + bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); + transPanel.add(transparency); + transbuttons.add(invert, java.awt.BorderLayout.NORTH); + transbuttons.add(optimizeOrder, java.awt.BorderLayout.SOUTH); + transPanel.add(transbuttons); + buttonPanel.add(ok); + buttonPanel.add(cancel); + buttonPanel.add(loadColours); + buttonPanel.add(saveColours); + bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER); + dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH); + dasButtonPanel.add(fetchDAS); + dasButtonPanel.add(cancelDAS); + dasButtonPanel.add(saveDAS); + settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER); + settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH); + } + + public void fetchDAS_actionPerformed(ActionEvent e) + { + fetchDAS.setEnabled(false); + cancelDAS.setEnabled(true); + 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(Vector selectedSources, + boolean checkDbRefs, boolean promptFetchDbRefs) + { + SequenceI[] dataset, seqs; + int iSize; + AlignViewport vp = af.getViewport(); + if (vp.getSelectionGroup() != null + && vp.getSelectionGroup().getSize() > 0) + { + iSize = vp.getSelectionGroup().getSize(); + dataset = new SequenceI[iSize]; + seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment()); + } + else + { + iSize = vp.getAlignment().getHeight(); + seqs = vp.getAlignment().getSequencesArray(); + } + + dataset = new SequenceI[iSize]; + for (int i = 0; i < iSize; i++) + { + dataset[i] = seqs[i].getDatasetSequence(); + } + + cancelDAS.setEnabled(true); + dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset, + this, selectedSources, checkDbRefs, promptFetchDbRefs); + af.getViewport().setShowSequenceFeatures(true); + af.showSeqFeatures.setSelected(true); + } + + /** + * 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 + */ + public void fetchDasFeatures(Vector sources) + { + Thread thr = new Thread(new Runnable() + { + public void run() + { + // this actually initialises the das source list + dassourceBrowser.paintComponent(null); // yuk + } + }); + thr.start(); + while (dassourceBrowser.loadingDasSources + || dassourceBrowser.dasSources == null) + { + try + { + Thread.sleep(10); + } catch (Exception e) + { + } + ; + } + Vector resolved = new Vector(); + if (sources != null) + { + for (int i = 0; i < dassourceBrowser.dasSources.length; i++) + { + if (sources.contains(dassourceBrowser.dasSources[i].getNickname())) + { + if (!resolved.contains(dassourceBrowser.dasSources[i])) + { + resolved.addElement(dassourceBrowser.dasSources[i]); + } + } + } + } + if (resolved.size() == 0) + { + resolved = dassourceBrowser.getSelectedSources(); + } + if (resolved.size() > 0) + { + final Vector dassources = resolved; + SwingUtilities.invokeLater(new Runnable() + { + + public void run() + { + fetchDAS.setEnabled(false); + cancelDAS.setEnabled(true); + doDasFeatureFetch(dassources, true, false); + + } + }); + } + } + + public void saveDAS_actionPerformed(ActionEvent e) + { + dassourceBrowser + .saveProperties(jalview.bin.Cache.applicationProperties); + } + + public void complete() + { + fetchDAS.setEnabled(true); + cancelDAS.setEnabled(false); + } + + public void cancelDAS_actionPerformed(ActionEvent e) + { + if (dasFeatureFetcher != null) + { + dasFeatureFetcher.cancel(); + } + fetchDAS.setEnabled(true); + cancelDAS.setEnabled(false); + } + + public void noDasSourceActive() + { + complete(); + JOptionPane.showInternalConfirmDialog(Desktop.desktop, + "No das sources were selected.\n" + + "Please select some sources and\n" + " try again.", + "No Sources Selected", JOptionPane.DEFAULT_OPTION, + JOptionPane.INFORMATION_MESSAGE); + } + + // /////////////////////////////////////////////////////////////////////// + // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html + // /////////////////////////////////////////////////////////////////////// + class FeatureTableModel extends AbstractTableModel + { + FeatureTableModel(Object[][] data) + { + this.data = data; + } + + private String[] columnNames = + { "Feature Type", "Colour", "Display" }; + + private Object[][] data; + + public Object[][] getData() + { + return data; + } + + public void setData(Object[][] data) + { + this.data = data; + } + + public int getColumnCount() + { + return columnNames.length; + } + + public Object[] getRow(int row) + { + return data[row]; + } + + public int getRowCount() + { + return data.length; + } + + public String getColumnName(int col) + { + return columnNames[col]; + } + + public Object getValueAt(int row, int col) + { + return data[row][col]; + } + + public Class getColumnClass(int c) + { + return getValueAt(0, c).getClass(); + } + + public boolean isCellEditable(int row, int col) + { + return col == 0 ? false : true; + } + + public void setValueAt(Object value, int row, int col) + { + data[row][col] = value; + fireTableCellUpdated(row, col); + updateFeatureRenderer(data); + } + + } + + class ColorRenderer extends JLabel implements TableCellRenderer + { + javax.swing.border.Border unselectedBorder = null; + + javax.swing.border.Border selectedBorder = null; + + public ColorRenderer() + { + setOpaque(true); // MUST do this for background to show up. + } + + public Component getTableCellRendererComponent(JTable table, + Object color, boolean isSelected, boolean hasFocus, int row, + int column) + { + Color newColor = (Color) color; + setBackground(newColor); + if (isSelected) + { + if (selectedBorder == null) + { + selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + table.getSelectionBackground()); + } + setBorder(selectedBorder); + } + else + { + if (unselectedBorder == null) + { + unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + table.getBackground()); + } + setBorder(unselectedBorder); + } + + setToolTipText("RGB value: " + newColor.getRed() + ", " + + newColor.getGreen() + ", " + newColor.getBlue()); + return this; + } + } +} + +class ColorEditor extends AbstractCellEditor implements TableCellEditor, + ActionListener +{ + Color currentColor; + + JButton button; + + JColorChooser colorChooser; + + JDialog dialog; + + protected static final String EDIT = "edit"; + + public ColorEditor() + { + // Set up the editor (from the table's point of view), + // which is a button. + // This button brings up the color chooser dialog, + // which is the editor from the user's point of view. + button = new JButton(); + button.setActionCommand(EDIT); + button.addActionListener(this); + button.setBorderPainted(false); + // Set up the dialog that the button brings up. + colorChooser = new JColorChooser(); + dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal + colorChooser, this, // OK button handler + null); // no CANCEL button handler + } + + /** + * 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. + fireEditingStopped(); + + } + else + { // User pressed dialog's "OK" button. + currentColor = colorChooser.getColor(); + } + } + + // Implement the one CellEditor method that AbstractCellEditor doesn't. + public Object getCellEditorValue() + { + return currentColor; + } + + // Implement the one method defined by TableCellEditor. + public Component getTableCellEditorComponent(JTable table, Object value, + boolean isSelected, int row, int column) + { + currentColor = (Color) value; + return button; + } +}