+ 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