/*\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) 2006 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
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
\r
public class FeatureSettings 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
+ 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
- boolean alignmentHasFeatures = false;\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
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\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, 100 - (int)(fr.transparency*100) );\r
- transparency.addChangeListener(new ChangeListener()\r
- {\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);\r
- ap.repaint();\r
- }\r
- });\r
+ try\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
- JButton button = new JButton("Invert Selection");\r
- transPanel.add(button);\r
- button.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- invertSelection();\r
- }\r
- });\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
- //////////////////////////////////////////////\r
- //We're going to need those OK cancel buttons\r
- JPanel buttonPanel = new JPanel(new FlowLayout());\r
- button = new JButton("OK");\r
- button.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception exe)\r
- {}\r
- }\r
- });\r
- buttonPanel.add(button);\r
- button = new JButton("Cancel");\r
- button.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- try\r
- {\r
- updateFeatureRenderer(originalData);\r
- frame.setClosed(true);\r
- }\r
- catch (Exception exe)\r
- {}\r
- }\r
- });\r
- buttonPanel.add(button);\r
+ table.setDefaultEditor(Color.class,\r
+ new ColorEditor());\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
+ table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\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
- {\r
- groupPanel.setLayout(\r
- new GridLayout(fr.featureGroups.size() / 4 + 1, 4));\r
+ table.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ selectedRow = table.rowAtPoint(evt.getPoint());\r
+ }\r
+ });\r
\r
- groupPanel.validate();\r
- bigPanel.add(groupPanel, BorderLayout.NORTH);\r
- }\r
- add(bigPanel, BorderLayout.CENTER);\r
- add(buttonPanel, BorderLayout.SOUTH);\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
+ scrollPane.setViewportView(table);\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
+ 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
- alignmentHasFeatures = false;\r
-\r
if (fr.featureGroups == null)\r
fr.featureGroups = new Hashtable();\r
\r
SequenceFeature[] tmpfeatures;\r
String group;\r
\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)\r
{\r
- if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
+ if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
continue;\r
\r
- alignmentHasFeatures = true;\r
-\r
- tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
\r
int index = 0;\r
while (index < tmpfeatures.length)\r
visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();\r
}\r
\r
- fr.featureGroups.put(group, new Boolean(visible));\r
-\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
+ if (groupPanel == null)\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
+ groupPanel = new JPanel();\r
+ }\r
\r
- resetTable(true);\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
- groupPanel.add(check);\r
\r
- }\r
+ if(alreadyAdded)\r
+ continue;\r
+\r
+ fr.featureGroups.put(group, new Boolean(visible));\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
if (!allFeatures.contains(tmpfeatures[index].getType()))\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
- "No Sequence Features", JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
-\r
resetTable(false);\r
+\r
+ validate();\r
}\r
\r
+\r
void resetTable(boolean groupsChanged)\r
{\r
SequenceFeature [] tmpfeatures;\r
\r
//Find out which features should be visible depending on which groups\r
//are selected / deselected\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)\r
{\r
- if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
+\r
+ tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ if (tmpfeatures == null)\r
continue;\r
\r
- tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
int index = 0;\r
while (index < tmpfeatures.length)\r
{\r
\r
data[dataIndex][0] = type;\r
data[dataIndex][1] = fr.getColour(type);\r
- data[dataIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));\r
+ data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));\r
dataIndex++;\r
visibleChecks.removeElement(type);\r
}\r
type = visibleChecks.elementAt(i).toString();\r
data[dataIndex][0] = type;\r
\r
- if(fr.getColour(type)==null)\r
- fr.createRandomColour(type);\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
data[dataIndex][2] = new Boolean(true);\r
dataIndex++;\r
}\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.setModel(new FeatureTableModel(data));\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
+ if (groupPanel != null)\r
+ {\r
+ groupPanel.setLayout(\r
+ new GridLayout(fr.featureGroups.size() / 4 + 1, 4));\r
\r
- selectedRow = newRow;\r
- }\r
- }\r
- });\r
+ groupPanel.validate();\r
+ bigPanel.add(groupPanel, BorderLayout.NORTH);\r
+ }\r
\r
updateFeatureRenderer(data);\r
\r
}\r
\r
setTableData();\r
- ap.repaint();\r
+ af.alignPanel.repaint();\r
}\r
catch (Exception ex)\r
{\r
- System.out.println("Error loading User ColourFile\n" + ex);\r
+ System.out.println("Error loading User Colour File\n" + ex);\r
}\r
}\r
}\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
- ap.repaint();\r
+ af.alignPanel.repaint();\r
\r
- if(ap.overviewPanel!=null)\r
- ap.overviewPanel.updateOverviewImage();\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
+ 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
+\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