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
+ JPanel settingsPane = new JPanel();\r
+ JPanel dasSettingsPane = new JPanel();\r
\r
final FeatureRenderer fr;\r
- final AlignmentPanel ap;\r
- final AlignViewport av;\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
- public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
+ JPanel transPanel = new JPanel(new FlowLayout());\r
+\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
+ 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
+ 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
+ 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
+ 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, 300);\r
+ Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
\r
- setTableData();\r
+ synchronized public void setTableData()\r
+ {\r
+ if (fr.featureGroups == null)\r
+ fr.featureGroups = new Hashtable();\r
\r
- final JSlider transparency = new JSlider(0, 70, 0);\r
- transparency.addChangeListener(new ChangeListener()\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
- public void stateChanged(ChangeEvent evt)\r
- {\r
- fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);\r
- ap.repaint();\r
- }\r
- });\r
+ if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
+ continue;\r
\r
- JPanel transPanel = new JPanel(new FlowLayout());\r
- transPanel.add(new JLabel("Transparency"));\r
- transPanel.add(transparency);\r
+ tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\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
- {\r
- public void actionPerformed(ActionEvent evt)\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
{\r
- try\r
+ if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0)\r
{\r
- frame.setClosed(true);\r
+ index++;\r
+ continue;\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
+ if(tmpfeatures[index].getFeatureGroup()!=null)\r
{\r
- updateFeatureRenderer(originalData);\r
- frame.setClosed(true);\r
- }\r
- catch (Exception exe)\r
- {}\r
- }\r
- });\r
- buttonPanel.add(button);\r
+ group = tmpfeatures[index].featureGroup;\r
+ if(!allGroups.contains(group))\r
+ {\r
+ allGroups.addElement(group);\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
+ boolean visible = true;\r
+ if (fr.featureGroups.containsKey(group))\r
+ {\r
+ visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();\r
+ }\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 = new JPanel();\r
+ }\r
\r
- add(bigPanel, BorderLayout.CENTER);\r
- add(buttonPanel, BorderLayout.SOUTH);\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
+ 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
+ allFeatures.addElement(tmpfeatures[index].getType());\r
+ }\r
+ index ++;\r
+ }\r
+ }\r
\r
+ resetTable(false);\r
\r
+ validate();\r
}\r
\r
- void setTableData()\r
+\r
+ void resetTable(boolean groupsChanged)\r
{\r
- Vector allFeatures = new Vector();\r
- Vector features;\r
- Enumeration e;\r
- SequenceFeature sf;\r
+ SequenceFeature [] tmpfeatures;\r
+ String group=null, type;\r
+ Vector visibleChecks = new Vector();\r
\r
- for(int i=0; i< av.alignment.getHeight(); i++)\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
- features = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
- if(features==null)\r
- continue;\r
\r
- e = features.elements();\r
- while(e.hasMoreElements())\r
- {\r
- sf = (SequenceFeature)e.nextElement();\r
- if(!allFeatures.contains(sf.getType()))\r
- {\r
- allFeatures.addElement(sf.getType());\r
- }\r
- }\r
- }\r
- if(allFeatures.size()<1)\r
- {\r
- try{\r
- frame.setClosed(true);\r
- }catch(Exception ex){}\r
- return;\r
- }\r
+ tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ if (tmpfeatures == null)\r
+ continue;\r
\r
- int fSize = allFeatures.size();\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
+ {\r
+ group = tmpfeatures[index].featureGroup;\r
\r
- String type;\r
- boolean originalExists = false;\r
- if(originalData!=null)\r
- originalExists = true;\r
- else\r
- originalData = new Object[fSize][3];\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
- for(int i=0; i<fSize; i++)\r
+ int dataIndex = 0;\r
+\r
+ if(fr.renderOrder!=null)\r
{\r
- type = allFeatures.elementAt(i).toString();\r
- Color col = fr.getColour(type);\r
- data[i][0]=type;\r
- data[i][1]=col;\r
- if(fr.featuresDisplayed!=null)\r
- data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
- else\r
- data[i][2] = new Boolean(true);\r
-\r
- if(!originalExists)\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
- originalData[i][0] = type;\r
- originalData[i][1] = col;\r
- if (fr.featuresDisplayed != null)\r
- originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
- else\r
- originalData[i][2] = new Boolean(true);\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
- //Now build the table\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
+ 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.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
+ table.setModel(new FeatureTableModel(data));\r
+ table.getColumnModel().getColumn(0).setPreferredWidth(200);\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
+ 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
}\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
Enumeration e = fr.featureColours.keys();\r
while(e.hasMoreElements())\r
{\r
-\r
-\r
jalview.binding.Colour col = new jalview.binding.Colour();\r
col.setName(e.nextElement().toString());\r
col.setRGB(jalview.util.Format.getHexString(\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
- ap.repaint();\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
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
git://source.jalview.org / jalview.git / blobdiff