/*\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
-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
+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 AlignFrame af;\r
- Object [][] originalData;\r
+ public final AlignFrame af;\r
+ Object[][] originalData;\r
final JInternalFrame frame;\r
JScrollPane scrollPane = new JScrollPane();\r
JTable table;\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
+ transparency.setMaximum(100 - (int) (fr.transparency * 100));\r
\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\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
+ 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
- if (af.getViewport().featuresDisplayed == null || fr.renderOrder==null)\r
- fr.findAllFeatures();\r
+ scrollPane.setViewportView(table);\r
\r
+ dassourceBrowser = new DasSourceBrowser();\r
+ dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);\r
+\r
+ if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null)\r
+ {\r
+ fr.findAllFeatures();\r
+ }\r
\r
setTableData();\r
\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
}\r
\r
- public void setTableData()\r
+ synchronized public void setTableData()\r
{\r
- alignmentHasFeatures = false;\r
-\r
if (fr.featureGroups == null)\r
+ {\r
fr.featureGroups = new Hashtable();\r
+ }\r
\r
Vector allFeatures = new Vector();\r
Vector allGroups = new Vector();\r
\r
for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)\r
{\r
- if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
+ if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().\r
+ getSequenceFeatures() == null)\r
+ {\r
continue;\r
+ }\r
\r
- alignmentHasFeatures = true;\r
-\r
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ tmpfeatures = af.getViewport().alignment.getSequenceAt(i).\r
+ getDatasetSequence().getSequenceFeatures();\r
\r
int index = 0;\r
while (index < tmpfeatures.length)\r
{\r
- if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0)\r
+ if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)\r
{\r
index++;\r
continue;\r
}\r
\r
- if(tmpfeatures[index].getFeatureGroup()!=null)\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
+ 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(!alignmentHasFeatures)\r
- {\r
- // try\r
- // { frame.setClosed(true); }\r
- // catch (Exception ex){}\r
+ if (alreadyAdded)\r
+ {\r
+ continue;\r
+ }\r
\r
- // JOptionPane.showInternalMessageDialog(\r
- /// Desktop.desktop, "No features have been added to this alignment!",\r
- //\r
- // return;\r
- }\r
+ fr.featureGroups.put(group, new Boolean(visible));\r
\r
- resetTable(false);\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
+ {\r
+ af.alignPanel.overviewPanel.updateOverviewImage();\r
+ }\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 resetTable(boolean groupsChanged)\r
{\r
- SequenceFeature [] tmpfeatures;\r
- String group=null, type;\r
- Vector visibleChecks = new Vector();\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
+ //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
+ tmpfeatures = af.getViewport().alignment.getSequenceAt(i).\r
+ getDatasetSequence().getSequenceFeatures();\r
+ if (tmpfeatures == null)\r
+ {\r
+ continue;\r
+ }\r
\r
- int index = 0;\r
- while (index < tmpfeatures.length)\r
- {\r
- group = tmpfeatures[index].featureGroup;\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
+ 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
+ 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
- type = tmpfeatures[index].getType();\r
- if(!visibleChecks.contains(type) )\r
- {\r
- visibleChecks.addElement(type);\r
- }\r
+ visibleChecks.addElement(type);\r
}\r
- index++;\r
}\r
+ index++;\r
+ }\r
}\r
\r
int fSize = visibleChecks.size();\r
- Object [][] data = new Object[fSize][3];\r
+ Object[][] data = new Object[fSize][3];\r
int dataIndex = 0;\r
\r
- if(fr.renderOrder!=null)\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
+ for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)\r
{\r
- type = fr.renderOrder[ro];\r
+ type = fr.renderOrder[ro];\r
\r
- if(!visibleChecks.contains(type))\r
- continue;\r
+ if (!visibleChecks.contains(type))\r
+ {\r
+ continue;\r
+ }\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
+ 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
fSize = visibleChecks.size();\r
- for(int i=0; i<fSize; i++)\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
data[dataIndex][0] = 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
\r
- if(originalData==null)\r
+ if (originalData == null)\r
{\r
originalData = new Object[data.length][3];\r
- System.arraycopy(data,0,originalData,0,data.length);\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
-\r
- selectedRow = newRow;\r
- }\r
- }\r
- });\r
-\r
if (groupPanel != null)\r
{\r
groupPanel.setLayout(\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
+ 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
- {\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
+ 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
- ucs.marshal(out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
+ Enumeration e = fr.featureColours.keys();\r
+ while (e.hasMoreElements())\r
{\r
- ex.printStackTrace();\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
+ for (int i = 0; i < table.getRowCount(); i++)\r
{\r
- Boolean value = (Boolean)table.getValueAt(i,2);\r
+ Boolean value = (Boolean) table.getValueAt(i, 2);\r
\r
table.setValueAt(\r
new Boolean(!value.booleanValue()),\r
- i,2);\r
+ i, 2);\r
}\r
}\r
\r
\r
}\r
\r
- public void updateFeatureRenderer(Object [][] data)\r
+ public void updateFeatureRenderer(Object[][] data)\r
{\r
- fr.setFeaturePriority( data );\r
+ fr.setFeaturePriority(data);\r
af.alignPanel.repaint();\r
\r
- if(af.alignPanel.overviewPanel!=null)\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
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
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- updateFeatureRenderer(originalData);\r
- close();\r
+ updateFeatureRenderer(originalData);\r
+ close();\r
}\r
});\r
ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
}\r
});\r
\r
-\r
transparency.setMaximum(70);\r
fetchDAS.setText("Fetch DAS Features");\r
fetchDAS.addActionListener(new ActionListener()\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("Display Settings", settingsPane );\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
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
public void fetchDAS_actionPerformed(ActionEvent e)\r
{\r
+ fetchDAS.setEnabled(false);\r
+ cancelDAS.setEnabled(true);\r
Vector selectedSources = dassourceBrowser.getSelectedSources();\r
\r
- int uniprotCount = 0;\r
- for(int i=0; i<selectedSources.size(); i++)\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
- DasSource source = (DasSource)selectedSources.elementAt(i);\r
- DasCoordinateSystem [] coords = source.getCoordinateSystem();\r
- for(int c=0; c<coords.length; c++)\r
- {\r
- if (coords[c].getName().equalsIgnoreCase("UniProt"))\r
- {\r
- uniprotCount++;\r
- break;\r
- }\r
- }\r
+ iSize = af.getViewport().getAlignment().getHeight();\r
+ seqs = af.getViewport().getAlignment().getSequencesArray();\r
}\r
\r
- System.out.println("User selection is "\r
- + (((float)uniprotCount/(float)selectedSources.size())*100)\r
- +" % Uniprot");\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(af.getViewport().getAlignment(),\r
- af,\r
- selectedSources);\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
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
/////////////////////////////////////////////////////////////////////////\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 void setData(Object[][] data)\r
- {\r
- this.data = data;\r
- }\r
+ public void setData(Object[][] data)\r
+ {\r
+ this.data = data;\r
+ }\r
\r
- public int getColumnCount() {\r
- return columnNames.length;\r
- }\r
+ public int getColumnCount()\r
+ {\r
+ return columnNames.length;\r
+ }\r
\r
- public Object[] getRow(int row)\r
- {\r
- return data[row];\r
- }\r
+ public Object[] getRow(int row)\r
+ {\r
+ return data[row];\r
+ }\r
\r
- public int getRowCount() {\r
- return data.length;\r
- }\r
+ public int getRowCount()\r
+ {\r
+ return data.length;\r
+ }\r
\r
- public String getColumnName(int col) {\r
- return columnNames[col];\r
- }\r
+ public String getColumnName(int col)\r
+ {\r
+ return columnNames[col];\r
+ }\r
\r
- public Object getValueAt(int row, int col) {\r
- return data[row][col];\r
- }\r
+ public Object getValueAt(int row, int col)\r
+ {\r
+ return data[row][col];\r
+ }\r
\r
- public Class getColumnClass(int c) {\r
- return getValueAt(0, c).getClass();\r
- }\r
+ public Class getColumnClass(int c)\r
+ {\r
+ return getValueAt(0, c).getClass();\r
+ }\r
\r
- public boolean isCellEditable(int row, int col) {\r
- return col==0 ? false:true;\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
- data[row][col] = value;\r
- fireTableCellUpdated(row, col);\r
- updateFeatureRenderer(data);\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
- 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
+ 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
+ }\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
git://source.jalview.org / jalview.git / blobdiff