/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
*/\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.io.*;\r
import java.util.*;\r
-import javax.swing.BorderFactory;\r
+\r
+import java.awt.*;\r
import java.awt.event.*;\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
import javax.swing.table.*;\r
-import java.io.*;\r
-import jalview.io.JalviewFileChooser;\r
\r
-public class FeatureSettings extends JPanel\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+\r
+public class FeatureSettings\r
+ extends JPanel\r
{\r
+ DasSourceBrowser dassourceBrowser;\r
+ jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher;\r
+ JPanel settingsPane = new JPanel();\r
+ JPanel dasSettingsPane = new JPanel();\r
\r
final FeatureRenderer fr;\r
- final AlignmentPanel ap;\r
- final AlignViewport av;\r
- Hashtable allFeatures;\r
- Object [][] originalData;\r
+ public 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
\r
- public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
+ public FeatureSettings(AlignFrame af)\r
{\r
- this.ap = ap;\r
- this.av = av;\r
- fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
- av.alignment.getSequences();\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300);\r
+ this.af = af;\r
+ fr = af.getFeatureRenderer();\r
\r
- setTableData();\r
+ transparency.setMaximum(100 - (int) (fr.transparency * 100));\r
\r
- final JSlider transparency = new JSlider(0, 70, 0);\r
- transparency.addChangeListener(new ChangeListener()\r
+ try\r
{\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);\r
- ap.repaint();\r
- }\r
- });\r
+ jbInit();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
\r
- JPanel transPanel = new JPanel(new FlowLayout());\r
- transPanel.add(new JLabel("Transparency"));\r
- transPanel.add(transparency);\r
+ table = new JTable();\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
- //////////////////////////////////////////////\r
- //We're going to need those OK cancel buttons\r
- JPanel buttonPanel = new JPanel(new FlowLayout());\r
- JButton button = new JButton("OK");\r
- button.addActionListener(new ActionListener()\r
+ table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
+\r
+ table.addMouseListener(new MouseAdapter()\r
{\r
- public void actionPerformed(ActionEvent evt)\r
+ public void mousePressed(MouseEvent evt)\r
{\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception exe)\r
- {}\r
+ selectedRow = table.rowAtPoint(evt.getPoint());\r
}\r
});\r
- buttonPanel.add(button);\r
- button = new JButton("Cancel");\r
- button.addActionListener(new ActionListener()\r
+\r
+ table.addMouseMotionListener(new MouseMotionAdapter()\r
{\r
- public void actionPerformed(ActionEvent evt)\r
+ public void mouseDragged(MouseEvent evt)\r
{\r
- try\r
+ int newRow = table.rowAtPoint(evt.getPoint());\r
+ if (newRow != selectedRow\r
+ && selectedRow != -1\r
+ && newRow != -1)\r
{\r
- updateFeatureRenderer(originalData);\r
- frame.setClosed(true);\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
- catch (Exception exe)\r
- {}\r
}\r
});\r
- buttonPanel.add(button);\r
\r
- button = new JButton("Load Colours");\r
- button.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- load();\r
- }\r
- });\r
- buttonPanel.add(button);\r
- button = new JButton("Save Colours");\r
- button.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- save();\r
- }\r
- });\r
- buttonPanel.add(button);\r
+ scrollPane.setViewportView(table);\r
+\r
+ dassourceBrowser = new DasSourceBrowser();\r
+ dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);\r
\r
- this.setLayout(new BorderLayout());\r
- JPanel bigPanel = new JPanel(new BorderLayout());\r
- bigPanel.add(transPanel, BorderLayout.SOUTH);\r
- bigPanel.add(scrollPane, BorderLayout.CENTER);\r
- if(groupPanel!=null)\r
+ if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null)\r
{\r
- groupPanel.setLayout(\r
- new GridLayout(groupPanel.getComponentCount()/3, 4));\r
- groupPanel.validate();\r
- bigPanel.add(groupPanel, BorderLayout.NORTH);\r
+ fr.findAllFeatures();\r
}\r
- add(bigPanel, BorderLayout.CENTER);\r
- add(buttonPanel, BorderLayout.SOUTH);\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
- void setTableData()\r
+ synchronized public void setTableData()\r
{\r
if (fr.featureGroups == null)\r
+ {\r
fr.featureGroups = new Hashtable();\r
- else\r
- fr.featureGroups.clear();\r
+ }\r
\r
- allFeatures = new Hashtable();\r
- SequenceFeature[] features;\r
+ Vector allFeatures = new Vector();\r
+ Vector allGroups = new Vector();\r
+ SequenceFeature[] tmpfeatures;\r
+ String group;\r
\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
- getSequenceFeatures();\r
+ for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)\r
+ {\r
+ if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().\r
+ getSequenceFeatures() == null)\r
+ {\r
+ continue;\r
+ }\r
\r
- if (features == null)\r
- continue;\r
+ tmpfeatures = af.getViewport().alignment.getSequenceAt(i).\r
+ getDatasetSequence().getSequenceFeatures();\r
\r
- int index = 0;\r
- while (index < features.length)\r
- {\r
- if(features[index].getFeatureGroup()!=null\r
- && !fr.featureGroups.containsKey(features[index].getFeatureGroup()))\r
- {\r
- fr.featureGroups.put(features[index].getFeatureGroup(), new Boolean(true));\r
- if(groupPanel==null)\r
- groupPanel = new JPanel();\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
+\r
+ if (groupPanel == null)\r
+ {\r
+ groupPanel = new JPanel();\r
+ }\r
+\r
+ boolean alreadyAdded = false;\r
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)\r
+ {\r
+ if ( ( (JCheckBox) groupPanel.getComponent(g))\r
+ .getText().equals(group))\r
+ {\r
+ alreadyAdded = true;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (alreadyAdded)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ fr.featureGroups.put(group, new Boolean(visible));\r
\r
- final JCheckBox check = new JCheckBox(features[index].getFeatureGroup(), true);\r
- check.setFont(new Font("Serif", Font.BOLD, 12));\r
- check.addItemListener(new ItemListener()\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
- public void itemStateChanged(ItemEvent evt)\r
+ fr.featureGroups.put(check.getText(),\r
+ new Boolean(check.isSelected()));\r
+ af.alignPanel.seqPanel.seqCanvas.repaint();\r
+ if (af.alignPanel.overviewPanel != null)\r
{\r
- if (fr.featureGroups.containsKey(check.getText()))\r
- {\r
- fr.featureGroups.put(check.getText(),\r
- new Boolean(check.isSelected()));\r
- ap.seqPanel.seqCanvas.repaint();\r
- if (ap.overviewPanel != null)\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- resetTable();\r
+ af.alignPanel.overviewPanel.updateOverviewImage();\r
}\r
- });\r
- groupPanel.add(check);\r
- }\r
- if (!allFeatures.contains(features[index].getType()))\r
- {\r
- if(features[index].featureGroup!=null)\r
- allFeatures.put(features[index].getType(), features[index].featureGroup);\r
- else\r
- allFeatures.put(features[index].getType(), "NOGROUP");\r
+\r
+ resetTable(true);\r
+ }\r
+ });\r
+ groupPanel.add(check);\r
+ }\r
+ }\r
+\r
+ if (!allFeatures.contains(tmpfeatures[index].getType()))\r
+ {\r
+ allFeatures.addElement(tmpfeatures[index].getType());\r
+ }\r
+ index++;\r
}\r
- index++;\r
}\r
- }\r
- if(allFeatures.size()<1)\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
- "No Sequence Features", JOptionPane.WARNING_MESSAGE);\r
\r
- return;\r
- }\r
+ resetTable(false);\r
\r
- resetTable();\r
+ validate();\r
}\r
\r
- void resetTable()\r
+ void resetTable(boolean groupsChanged)\r
{\r
- int fSize = allFeatures.size();\r
+ SequenceFeature[] tmpfeatures;\r
+ String group = null, type;\r
+ Vector visibleChecks = new Vector();\r
\r
- String type;\r
- boolean originalExists = false;\r
- if (originalData != null)\r
- originalExists = true;\r
- else\r
- originalData = new Object[fSize][3];\r
-\r
- Object[][] tmp = new Object[fSize][3];\r
- int tmpIndex = 0;\r
-\r
- Enumeration en = allFeatures.keys();\r
- int i=0;\r
- while(en.hasMoreElements())\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
- type = en.nextElement().toString();\r
- Color col = fr.getColour(type);\r
\r
-\r
- //This will ignore any features which are in groups not shown\r
- if(fr.featureGroups==null\r
- || ((Boolean)fr.featureGroups.get(allFeatures.get(type))).booleanValue())\r
+ tmpfeatures = af.getViewport().alignment.getSequenceAt(i).\r
+ getDatasetSequence().getSequenceFeatures();\r
+ if (tmpfeatures == null)\r
{\r
- tmp[tmpIndex][0] = type;\r
- tmp[tmpIndex][1] = col;\r
- if (av.featuresDisplayed != null)\r
- tmp[tmpIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));\r
- else\r
- tmp[tmpIndex][2] = new Boolean(true);\r
-\r
- tmpIndex++;\r
+ continue;\r
}\r
\r
-\r
- if (!originalExists)\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
{\r
- originalData[i][0] = type;\r
- originalData[i][1] = col;\r
- if (av.featuresDisplayed != null)\r
- originalData[i][2] = new Boolean(av.featuresDisplayed.contains(type));\r
- else\r
- originalData[i][2] = new Boolean(true);\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
- i++;\r
}\r
\r
- Object [][]data = new Object[tmpIndex][3];\r
- System.arraycopy(tmp, 0, data,0, tmpIndex);\r
+ int fSize = visibleChecks.size();\r
+ Object[][] data = new Object[fSize][3];\r
+ int dataIndex = 0;\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
+ 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
- table.setDefaultEditor(Color.class,\r
- new ColorEditor());\r
+ if (!visibleChecks.contains(type))\r
+ {\r
+ continue;\r
+ }\r
\r
- table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
+ data[dataIndex][0] = type;\r
+ data[dataIndex][1] = fr.getColour(type);\r
+ data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.\r
+ containsKey(type));\r
+ dataIndex++;\r
+ visibleChecks.removeElement(type);\r
+ }\r
+ }\r
\r
- table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\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
- table.addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- selectedRow = table.rowAtPoint(evt.getPoint());\r
- }\r
- });\r
+ data[dataIndex][1] = fr.getColour(type);\r
+ if (data[dataIndex][1] == null)\r
+ {\r
+ //"Colour has been updated in another view!!"\r
+ fr.renderOrder = null;\r
+ return;\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
+ data[dataIndex][2] = new Boolean(true);\r
+ dataIndex++;\r
+ }\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
+ if (originalData == null)\r
+ {\r
+ originalData = new Object[data.length][3];\r
+ System.arraycopy(data, 0, originalData, 0, data.length);\r
+ }\r
\r
- table.setValueAt(temp[0], newRow, 0);\r
- table.setValueAt(temp[1], newRow, 1);\r
- table.setValueAt(temp[2], newRow, 2);\r
+ table.setModel(new FeatureTableModel(data));\r
+ table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
\r
- selectedRow = newRow;\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
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
- ap.repaint();\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error loading User ColourFile\n" + ex);\r
- }\r
- }\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"fc"},\r
+ new String[]\r
+ {"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
+ 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(),\r
+ 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
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"fc"},\r
+ new String[]\r
+ {"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
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
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.binding.JalviewUserColours ucs = new jalview.binding.\r
+ 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
- PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
- new FileOutputStream(choice), "UTF-8"));\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
- Enumeration e = fr.featureColours.keys();\r
- while(e.hasMoreElements())\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
- 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
+ table.setValueAt(\r
+ new Boolean(!value.booleanValue()),\r
+ i, 2);\r
+ }\r
+ }\r
\r
- ucs.marshal(out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\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
+ public void updateFeatureRenderer(Object[][] data)\r
{\r
- fr.setFeaturePriority( data );\r
- ap.repaint();\r
+ fr.setFeaturePriority(data);\r
+ af.alignPanel.repaint();\r
\r
- if(ap.overviewPanel!=null)\r
- ap.overviewPanel.updateOverviewImage();\r
+ if (af.alignPanel.overviewPanel != null)\r
+ {\r
+ af.alignPanel.overviewPanel.updateOverviewImage();\r
+ }\r
}\r
\r
- int selectedRow =-1;\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
+ JButton cancelDAS = 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
+ 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
+ cancelDAS.setEnabled(false);\r
+ cancelDAS.setText("Cancel Fetch");\r
+ cancelDAS.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cancelDAS_actionPerformed(e);\r
+ }\r
+ });\r
+ this.add(tabbedPane, java.awt.BorderLayout.CENTER);\r
+ tabbedPane.addTab("Feature 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(cancelDAS);\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
+ fetchDAS.setEnabled(false);\r
+ cancelDAS.setEnabled(true);\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() > 0)\r
+ {\r
+ iSize = af.getViewport().getSelectionGroup().getSize();\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
+ dasFeatureFetcher =\r
+ new jalview.io.DasSequenceFeatureFetcher(\r
+ dataset,\r
+ this,\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
+ public void complete()\r
+ {\r
+ fetchDAS.setEnabled(true);\r
+ cancelDAS.setEnabled(false);\r
+ }\r
+\r
+ public void cancelDAS_actionPerformed(ActionEvent e)\r
+ {\r
+ dasFeatureFetcher.cancel();\r
+ fetchDAS.setEnabled(true);\r
+ cancelDAS.setEnabled(false);\r
+ }\r
\r
/////////////////////////////////////////////////////////////////////////\r
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html\r
this.data = data;\r
}\r
\r
- private String[] columnNames = {"Feature Type", "Colour","Display"};\r
- private Object[][] data;\r
+ private String[] columnNames =\r
+ {\r
+ "Feature Type", "Colour", "Display"};\r
+ private Object[][] data;\r
\r
- public Object[][] getData()\r
- {\r
- return data;\r
- }\r
+ public Object[][] getData()\r
+ {\r
+ return data;\r
+ }\r
\r
- public int getColumnCount() {\r
- return columnNames.length;\r
- }\r
+ public void setData(Object[][] data)\r
+ {\r
+ this.data = data;\r
+ }\r
\r
- public Object[] getRow(int row)\r
- {\r
- return data[row];\r
- }\r
+ public int getColumnCount()\r
+ {\r
+ return columnNames.length;\r
+ }\r
\r
- public int getRowCount() {\r
- return data.length;\r
- }\r
+ public Object[] getRow(int row)\r
+ {\r
+ return data[row];\r
+ }\r
\r
- public String getColumnName(int col) {\r
- return columnNames[col];\r
- }\r
+ public int getRowCount()\r
+ {\r
+ return data.length;\r
+ }\r
\r
- public Object getValueAt(int row, int col) {\r
- return data[row][col];\r
- }\r
+ public String getColumnName(int col)\r
+ {\r
+ return columnNames[col];\r
+ }\r
\r
- public Class getColumnClass(int c) {\r
- return getValueAt(0, c).getClass();\r
- }\r
+ public Object getValueAt(int row, int col)\r
+ {\r
+ return data[row][col];\r
+ }\r
\r
- public boolean isCellEditable(int row, int col) {\r
- return col==0 ? false:true;\r
- }\r
+ public Class getColumnClass(int c)\r
+ {\r
+ return getValueAt(0, c).getClass();\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
+ public boolean isCellEditable(int row, int col)\r
+ {\r
+ return col == 0 ? false : true;\r
+ }\r
+\r
+ public void setValueAt(Object value, int row, int col)\r
+ {\r
+ data[row][col] = value;\r
+ fireTableCellUpdated(row, col);\r
+ updateFeatureRenderer(data);\r
+ }\r
+\r
+ }\r
+\r
+ class ColorRenderer\r
+ extends JLabel implements TableCellRenderer\r
+ {\r
+ javax.swing.border.Border unselectedBorder = null;\r
+ javax.swing.border.Border selectedBorder = null;\r
+\r
+ public ColorRenderer()\r
+ {\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
+ {\r
+ Color newColor = (Color) color;\r
+ setBackground(newColor);\r
+ if (isSelected)\r
+ {\r
+ if (selectedBorder == null)\r
+ {\r
+ selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,\r
+ table.getSelectionBackground());\r
+ }\r
+ setBorder(selectedBorder);\r
+ }\r
+ else\r
+ {\r
+ if (unselectedBorder == null)\r
+ {\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
- 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
\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
+class ColorEditor\r
+ extends AbstractCellEditor implements TableCellEditor,\r
+ ActionListener\r
+{\r
+ Color currentColor;\r
+ JButton button;\r
+ JColorChooser colorChooser;\r
+ JDialog dialog;\r
+ protected static final String EDIT = "edit";\r
+\r
+ public ColorEditor()\r
+ {\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
+\r
+ if (EDIT.equals(e.getActionCommand()))\r
+ {\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
+ }\r
+ else\r
+ { //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
+ {\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
+ {\r
+ currentColor = (Color) value;\r
+ return button;\r
+ }\r
}\r