-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-import javax.swing.BorderFactory;\r
-import java.awt.event.*;\r
-import javax.swing.table.*;\r
-import java.io.*;\r
-import jalview.io.JalviewFileChooser;\r
-import java.awt.BorderLayout;\r
-import java.awt.Font;\r
-import java.awt.Color;\r
-import org.biojava.dasobert.dasregistry.DasSource;\r
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
-\r
-public class FeatureSettings extends JPanel\r
-{\r
- DasSourceBrowser dassourceBrowser;\r
- JPanel settingsPane = new JPanel();\r
- JPanel dasSettingsPane = new JPanel();\r
-\r
- final FeatureRenderer fr;\r
- final AlignFrame af;\r
- Object [][] originalData;\r
- final JInternalFrame frame;\r
- JScrollPane scrollPane = new JScrollPane();\r
- JTable table;\r
- JPanel groupPanel;\r
- JSlider transparency = new JSlider();\r
-\r
- JPanel transPanel = new JPanel(new FlowLayout());\r
- boolean alignmentHasFeatures = false;\r
-\r
- public FeatureSettings(AlignFrame af)\r
- {\r
- this.af = af;\r
- fr = af.getFeatureRenderer();\r
-\r
- transparency.setMaximum( 100 - (int)(fr.transparency*100) ) ;\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- dassourceBrowser = new DasSourceBrowser();\r
- dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);\r
-\r
-\r
-\r
- if (af.getViewport().featuresDisplayed == null || fr.renderOrder==null)\r
- fr.findAllFeatures();\r
-\r
-\r
- setTableData();\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
-\r
- public void setTableData()\r
- {\r
- alignmentHasFeatures = false;\r
-\r
- if (fr.featureGroups == null)\r
- fr.featureGroups = new Hashtable();\r
-\r
- Vector allFeatures = new Vector();\r
- Vector allGroups = new Vector();\r
- SequenceFeature[] tmpfeatures;\r
- String group;\r
-\r
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)\r
- {\r
- if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
- continue;\r
-\r
- alignmentHasFeatures = true;\r
-\r
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
-\r
- int index = 0;\r
- while (index < tmpfeatures.length)\r
- {\r
- if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0)\r
- {\r
- index++;\r
- continue;\r
- }\r
-\r
- if(tmpfeatures[index].getFeatureGroup()!=null)\r
- {\r
- group = tmpfeatures[index].featureGroup;\r
- if(!allGroups.contains(group))\r
- {\r
- allGroups.addElement(group);\r
-\r
- boolean visible = true;\r
- if (fr.featureGroups.containsKey(group))\r
- {\r
- visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();\r
- }\r
- else\r
- {\r
- fr.featureGroups.put(group, new Boolean(visible));\r
- if (groupPanel == null)\r
- {\r
- groupPanel = new JPanel();\r
- }\r
-\r
- final JCheckBox check = new JCheckBox(group, visible);\r
- check.setFont(new Font("Serif", Font.BOLD, 12));\r
- check.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- fr.featureGroups.put(check.getText(),\r
- new Boolean(check.isSelected()));\r
- af.alignPanel.seqPanel.seqCanvas.repaint();\r
- if (af.alignPanel.overviewPanel != null)\r
- af.alignPanel.overviewPanel.updateOverviewImage();\r
-\r
- resetTable(true);\r
- }\r
- });\r
- groupPanel.add(check);\r
- }\r
- }\r
-\r
- }\r
-\r
- if (!allFeatures.contains(tmpfeatures[index].getType()))\r
- {\r
- allFeatures.addElement(tmpfeatures[index].getType());\r
- }\r
- index ++;\r
- }\r
- }\r
-\r
-\r
- if(!alignmentHasFeatures)\r
- {\r
- // try\r
- // { frame.setClosed(true); }\r
- // catch (Exception ex){}\r
-\r
- // JOptionPane.showInternalMessageDialog(\r
- /// Desktop.desktop, "No features have been added to this alignment!",\r
- //\r
- // return;\r
- }\r
-\r
- resetTable(false);\r
- }\r
-\r
-\r
- void resetTable(boolean groupsChanged)\r
- {\r
- SequenceFeature [] tmpfeatures;\r
- String group=null, type;\r
- Vector visibleChecks = new Vector();\r
-\r
- //Find out which features should be visible depending on which groups\r
- //are selected / deselected\r
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)\r
- {\r
-\r
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
- if (tmpfeatures == null)\r
- continue;\r
-\r
- int index = 0;\r
- while (index < tmpfeatures.length)\r
- {\r
- group = tmpfeatures[index].featureGroup;\r
-\r
- if(tmpfeatures[index].begin==0 && tmpfeatures[index].end==0)\r
- {\r
- index ++;\r
- continue;\r
- }\r
-\r
- if (group==null || fr.featureGroups.get(group)==null ||\r
- ((Boolean) fr.featureGroups.get(group)).booleanValue())\r
- {\r
- type = tmpfeatures[index].getType();\r
- if(!visibleChecks.contains(type) )\r
- {\r
- visibleChecks.addElement(type);\r
- }\r
- }\r
- index++;\r
- }\r
- }\r
-\r
- int fSize = visibleChecks.size();\r
- Object [][] data = new Object[fSize][3];\r
- int dataIndex = 0;\r
-\r
- if(fr.renderOrder!=null)\r
- {\r
- //First add the checks in the previous render order,\r
- //in case the window has been closed and reopened\r
- for(int ro=fr.renderOrder.length-1; ro>-1; ro--)\r
- {\r
- type = fr.renderOrder[ro];\r
-\r
- if(!visibleChecks.contains(type))\r
- continue;\r
-\r
- data[dataIndex][0] = type;\r
- data[dataIndex][1] = fr.getColour(type);\r
- data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));\r
- dataIndex++;\r
- visibleChecks.removeElement(type);\r
- }\r
- }\r
-\r
- fSize = visibleChecks.size();\r
- for(int i=0; i<fSize; i++)\r
- {\r
- //These must be extra features belonging to the group\r
- //which was just selected\r
- type = visibleChecks.elementAt(i).toString();\r
- data[dataIndex][0] = type;\r
-\r
- data[dataIndex][1] = fr.getColour(type);\r
- data[dataIndex][2] = new Boolean(true);\r
- dataIndex++;\r
- }\r
-\r
- if(originalData==null)\r
- {\r
- originalData = new Object[data.length][3];\r
- System.arraycopy(data,0,originalData,0,data.length);\r
- }\r
-\r
- table = new JTable(new FeatureTableModel(data));\r
- scrollPane.setViewportView(table);\r
- table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
- table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
- table.setDefaultRenderer(Color.class,\r
- new ColorRenderer());\r
-\r
- table.setDefaultEditor(Color.class,\r
- new ColorEditor());\r
-\r
- table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
-\r
- table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
-\r
- table.addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- selectedRow = table.rowAtPoint(evt.getPoint());\r
- }\r
- });\r
-\r
- table.addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- int newRow = table.rowAtPoint(evt.getPoint());\r
- if(newRow!=selectedRow\r
- && selectedRow!=-1\r
- && newRow!=-1)\r
- {\r
- Object[] temp = new Object[3];\r
- temp[0] = table.getValueAt(selectedRow, 0);\r
- temp[1] = table.getValueAt(selectedRow, 1);\r
- temp[2] = table.getValueAt(selectedRow, 2);\r
-\r
- table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
- table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
- table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
-\r
- table.setValueAt(temp[0], newRow, 0);\r
- table.setValueAt(temp[1], newRow, 1);\r
- table.setValueAt(temp[2], newRow, 2);\r
-\r
- selectedRow = newRow;\r
- }\r
- }\r
- });\r
-\r
- if (groupPanel != null)\r
- {\r
- groupPanel.setLayout(\r
- new GridLayout(fr.featureGroups.size() / 4 + 1, 4));\r
-\r
- groupPanel.validate();\r
- bigPanel.add(groupPanel, BorderLayout.NORTH);\r
- }\r
-\r
- updateFeatureRenderer(data);\r
-\r
- }\r
-\r
- void load()\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "fc" },\r
- new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Load Feature Colours");\r
- chooser.setToolTipText("Load");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- File file = chooser.getSelectedFile();\r
-\r
- try\r
- {\r
- InputStreamReader in = new InputStreamReader(new FileInputStream(\r
- file), "UTF-8");\r
-\r
- jalview.binding.JalviewUserColours jucs = new jalview.binding.\r
- JalviewUserColours();\r
- jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
-\r
-\r
- for (int i = 0; i < jucs.getColourCount(); i++)\r
- {\r
- fr.setColour( jucs.getColour(i).getName(),\r
- new Color(Integer.parseInt( jucs.getColour(i).getRGB(), 16)));\r
- }\r
-\r
- setTableData();\r
- af.alignPanel.repaint();\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error loading User Colour File\n" + ex);\r
- }\r
- }\r
- }\r
-\r
- void save()\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "fc" },\r
- new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Save Feature Colour Scheme");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
- ucs.setSchemeName("Sequence Features");\r
- try\r
- {\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
- new FileOutputStream(choice), "UTF-8"));\r
-\r
- Enumeration e = fr.featureColours.keys();\r
- while(e.hasMoreElements())\r
- {\r
- jalview.binding.Colour col = new jalview.binding.Colour();\r
- col.setName(e.nextElement().toString());\r
- col.setRGB(jalview.util.Format.getHexString(\r
- fr.getColour(col.getName())));\r
- ucs.addColour(col);\r
- }\r
-\r
- ucs.marshal(out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- public void invertSelection()\r
- {\r
- for(int i=0; i<table.getRowCount(); i++)\r
- {\r
- Boolean value = (Boolean)table.getValueAt(i,2);\r
-\r
- table.setValueAt(\r
- new Boolean(!value.booleanValue()),\r
- i,2);\r
- }\r
- }\r
-\r
- public void close()\r
- {\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception exe)\r
- {}\r
-\r
- }\r
-\r
- public void updateFeatureRenderer(Object [][] data)\r
- {\r
- fr.setFeaturePriority( data );\r
- af.alignPanel.repaint();\r
-\r
- if(af.alignPanel.overviewPanel!=null)\r
- af.alignPanel.overviewPanel.updateOverviewImage();\r
- }\r
-\r
- int selectedRow =-1;\r
- JTabbedPane tabbedPane = new JTabbedPane();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- BorderLayout borderLayout3 = new BorderLayout();\r
- JPanel bigPanel = new JPanel();\r
- BorderLayout borderLayout4 = new BorderLayout();\r
- JButton invert = new JButton();\r
- JPanel buttonPanel = new JPanel();\r
- JButton cancel = new JButton();\r
- JButton ok = new JButton();\r
- JButton loadColours = new JButton();\r
- JButton saveColours = new JButton();\r
- JPanel dasButtonPanel = new JPanel();\r
- JButton fetchDAS = new JButton();\r
- JButton saveDAS = new JButton();\r
- private void jbInit()\r
- throws Exception\r
- {\r
- this.setLayout(borderLayout1);\r
- settingsPane.setLayout(borderLayout2);\r
- dasSettingsPane.setLayout(borderLayout3);\r
- bigPanel.setLayout(borderLayout4);\r
- invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- invert.setText("Invert Selection");\r
- invert.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- invertSelection();\r
- }\r
- });\r
- cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- cancel.setText("Cancel");\r
- cancel.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- updateFeatureRenderer(originalData);\r
- close();\r
- }\r
- });\r
- ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- ok.setText("OK");\r
- ok.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- close();\r
- }\r
- });\r
- loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- loadColours.setText("Load Colours");\r
- loadColours.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- load();\r
- }\r
- });\r
- saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- saveColours.setText("Save Colours");\r
- saveColours.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- save();\r
- }\r
- });\r
- transparency.addChangeListener(new ChangeListener()\r
- {\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);\r
- af.alignPanel.repaint();\r
- }\r
- });\r
-\r
-\r
- transparency.setMaximum(70);\r
- fetchDAS.setText("Fetch DAS Features");\r
- fetchDAS.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fetchDAS_actionPerformed(e);\r
- }\r
- });\r
- saveDAS.setText("Save as default");\r
- saveDAS.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- saveDAS_actionPerformed(e);\r
- }\r
- });\r
- dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());\r
- dasSettingsPane.setBorder(null);\r
- this.add(tabbedPane, java.awt.BorderLayout.CENTER);\r
- tabbedPane.addTab("Display Settings", settingsPane );\r
- tabbedPane.addTab("DAS Settings", dasSettingsPane);\r
- bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);\r
- transPanel.add(transparency);\r
- transPanel.add(invert);\r
- buttonPanel.add(ok);\r
- buttonPanel.add(cancel);\r
- buttonPanel.add(loadColours);\r
- buttonPanel.add(saveColours);\r
- bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);\r
- dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);\r
- dasButtonPanel.add(fetchDAS);\r
- dasButtonPanel.add(saveDAS);\r
- settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);\r
- settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);\r
- }\r
-\r
- public void fetchDAS_actionPerformed(ActionEvent e)\r
- {\r
- Vector selectedSources = dassourceBrowser.getSelectedSources();\r
-\r
- SequenceI [] dataset, seqs ;\r
- int iSize;\r
-\r
- if(af.getViewport().getSelectionGroup()!=null\r
- && af.getViewport().getSelectionGroup().getSize(false)>0)\r
- {\r
- iSize = af.getViewport().getSelectionGroup().getSize(false);\r
- dataset = new SequenceI[iSize];\r
- seqs = af.getViewport().getSelectionGroup().\r
- getSequencesInOrder(\r
- af.getViewport().getAlignment());\r
- }\r
- else\r
- {\r
- iSize = af.getViewport().getAlignment().getHeight();\r
- seqs = af.getViewport().getAlignment().getSequencesArray();\r
- }\r
-\r
- dataset = new SequenceI[iSize];\r
- for (int i = 0; i < iSize; i++)\r
- {\r
- dataset[i] = seqs[i].getDatasetSequence();\r
- }\r
-\r
- new jalview.io.DasSequenceFeatureFetcher(\r
- dataset,\r
- af,\r
- selectedSources);\r
-\r
- af.getViewport().setShowSequenceFeatures(true);\r
- af.showSeqFeatures.setSelected(true);\r
- }\r
-\r
- public void saveDAS_actionPerformed(ActionEvent e)\r
- {\r
- dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties);\r
- }\r
-\r
- /////////////////////////////////////////////////////////////////////////\r
- // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html\r
- /////////////////////////////////////////////////////////////////////////\r
- class FeatureTableModel\r
- extends AbstractTableModel\r
- {\r
- FeatureTableModel(Object[][] data)\r
- {\r
- this.data = data;\r
- }\r
-\r
- private String[] columnNames = {"Feature Type", "Colour","Display"};\r
- private Object[][] data;\r
-\r
- public Object[][] getData()\r
- {\r
- return data;\r
- }\r
-\r
- public void setData(Object[][] data)\r
- {\r
- this.data = data;\r
- }\r
-\r
- public int getColumnCount() {\r
- return columnNames.length;\r
- }\r
-\r
- public Object[] getRow(int row)\r
- {\r
- return data[row];\r
- }\r
-\r
- public int getRowCount() {\r
- return data.length;\r
- }\r
-\r
- public String getColumnName(int col) {\r
- return columnNames[col];\r
- }\r
-\r
- public Object getValueAt(int row, int col) {\r
- return data[row][col];\r
- }\r
-\r
- public Class getColumnClass(int c) {\r
- return getValueAt(0, c).getClass();\r
- }\r
-\r
- public boolean isCellEditable(int row, int col) {\r
- return col==0 ? false:true;\r
- }\r
-\r
- public void setValueAt(Object value, int row, int col) {\r
- data[row][col] = value;\r
- fireTableCellUpdated(row, col);\r
- updateFeatureRenderer(data);\r
- }\r
-\r
- }\r
- class ColorRenderer extends JLabel\r
- implements TableCellRenderer {\r
- javax.swing.border.Border unselectedBorder = null;\r
- javax.swing.border.Border selectedBorder = null;\r
-\r
- public ColorRenderer() {\r
- setOpaque(true); //MUST do this for background to show up.\r
- }\r
-\r
- public Component getTableCellRendererComponent(\r
- JTable table, Object color,\r
- boolean isSelected, boolean hasFocus,\r
- int row, int column) {\r
- Color newColor = (Color)color;\r
- setBackground(newColor);\r
- if (isSelected) {\r
- if (selectedBorder == null) {\r
- selectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
- table.getSelectionBackground());\r
- }\r
- setBorder(selectedBorder);\r
- } else {\r
- if (unselectedBorder == null) {\r
- unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
- table.getBackground());\r
- }\r
- setBorder(unselectedBorder);\r
- }\r
-\r
- setToolTipText("RGB value: " + newColor.getRed() + ", "\r
- + newColor.getGreen() + ", "\r
- + newColor.getBlue());\r
- return this;\r
- }\r
- }\r
-}\r
-\r
- class ColorEditor extends AbstractCellEditor\r
- implements TableCellEditor,\r
- ActionListener {\r
- Color currentColor;\r
- JButton button;\r
- JColorChooser colorChooser;\r
- JDialog dialog;\r
- protected static final String EDIT = "edit";\r
-\r
- public ColorEditor() {\r
- //Set up the editor (from the table's point of view),\r
- //which is a button.\r
- //This button brings up the color chooser dialog,\r
- //which is the editor from the user's point of view.\r
- button = new JButton();\r
- button.setActionCommand(EDIT);\r
- button.addActionListener(this);\r
- button.setBorderPainted(false);\r
- //Set up the dialog that the button brings up.\r
- colorChooser = new JColorChooser();\r
- dialog = JColorChooser.createDialog(button,\r
- "Select new Colour",\r
- true, //modal\r
- colorChooser,\r
- this, //OK button handler\r
- null); //no CANCEL button handler\r
- }\r
-\r
- /**\r
- * Handles events from the editor button and from\r
- * the dialog's OK button.\r
- */\r
- public void actionPerformed(ActionEvent e) {\r
-\r
- if (EDIT.equals(e.getActionCommand())) {\r
- //The user has clicked the cell, so\r
- //bring up the dialog.\r
- button.setBackground(currentColor);\r
- colorChooser.setColor(currentColor);\r
- dialog.setVisible(true);\r
-\r
- //Make the renderer reappear.\r
- fireEditingStopped();\r
-\r
- } else { //User pressed dialog's "OK" button.\r
- currentColor = colorChooser.getColor();\r
- }\r
- }\r
-\r
- //Implement the one CellEditor method that AbstractCellEditor doesn't.\r
- public Object getCellEditorValue() {\r
- return currentColor;\r
- }\r
-\r
- //Implement the one method defined by TableCellEditor.\r
- public Component getTableCellEditorComponent(JTable table,\r
- Object value,\r
- boolean isSelected,\r
- int row,\r
- int column) {\r
- currentColor = (Color)value;\r
- return button;\r
- }\r
-}\r
+/*
+ * 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
+ * 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();
+
+ SequenceI[] dataset, seqs;
+ int iSize;
+
+ if (af.getViewport().getSelectionGroup() != null
+ && af.getViewport().getSelectionGroup().getSize() > 0)
+ {
+ iSize = af.getViewport().getSelectionGroup().getSize();
+ 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.ws.DasSequenceFeatureFetcher(
+ dataset,
+ this,
+ selectedSources);
+ cancelDAS.setEnabled(true);
+ 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);
+ }
+ public void noDasSourceActive()
+ {
+ 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);
+ complete();
+ }
+
+ /////////////////////////////////////////////////////////////////////////
+ // 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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff