+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void ok_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
+ Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
+\r
+ Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
+ Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
+ Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
+\r
+ Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
+ Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
+\r
+ if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
+ Cache.applicationProperties.remove("EPS_RENDERING");\r
+ else\r
+ Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
+\r
+ if(defaultBrowser.getText().trim().length()<1)\r
+ Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
+ else\r
+ Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
+ defaultBrowser.getText());\r
+\r
+ jalview.util.BrowserLauncher.resetBrowser();\r
+\r
+ if(nameLinks.size()>0)\r
+ {\r
+ StringBuffer links = new StringBuffer();\r
+ sequenceURLLinks = new Vector();\r
+ for (int i = 0; i < nameLinks.size(); i++)\r
+ {\r
+ sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
+ links.append(sequenceURLLinks.elementAt(i).toString());\r
+ links.append("|");\r
+ }\r
+ // remove last "|"\r
+ links.setLength( links.length()-1 );\r
+ Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
+ }\r
+ else\r
+ Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
+\r
+\r
+ Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
+\r
+ if (proxyServerTB.getText().trim().length() < 1)\r
+ Cache.applicationProperties.remove("PROXY_SERVER");\r
+ else\r
+ Cache.applicationProperties.setProperty("PROXY_SERVER",\r
+ proxyServerTB.getText());\r
+\r
+ if (proxyPortTB.getText().trim().length() < 1)\r
+ Cache.applicationProperties.remove("PROXY_PORT");\r
+ else\r
+ Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
+\r
+ if(useProxy.isSelected())\r
+ {\r
+ System.setProperty("http.proxyHost", proxyServerTB.getText());\r
+ System.setProperty("http.proxyPort", proxyPortTB.getText());\r
+ }\r
+ else\r
+ {\r
+ System.setProperty("http.proxyHost","");\r
+ System.setProperty("http.proxyPort","");\r
+ }\r
+\r
+\r
+ Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
+\r
+ Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
+ Boolean.toString(autoCalculateConsCheck.isSelected()));\r
+ Cache.applicationProperties.setProperty("PAD_GAPS",\r
+ Boolean.toString(padGaps.isSelected()));\r
+ Cache.saveProperties();\r
+ try\r
+ {\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void startupFileTextfield_mouseClicked()\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"),\r
+ new String[]\r
+ {\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\r
+ {\r
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Select startup file");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
+ chooser.getSelectedFormat());\r
+ startupFileTextfield.setText(chooser.getSelectedFile()\r
+ .getAbsolutePath());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void cancel_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void annotations_actionPerformed(ActionEvent e)\r
+ {\r
+ conservation.setEnabled(annotations.isSelected());\r
+ quality.setEnabled(annotations.isSelected());\r
+ identity.setEnabled(annotations.isSelected());\r
+ }\r
+\r
+\r
+ public void newLink_actionPerformed(ActionEvent e) {\r
+\r
+ GSequenceLink link = new GSequenceLink();\r
+ boolean valid = false;\r
+ while( !valid )\r
+ {\r
+ if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
+ "New sequence URL link",\r
+ JOptionPane.OK_CANCEL_OPTION\r
+ ,-1, null)\r
+ == JOptionPane.OK_OPTION)\r
+ {\r
+ if (link.checkValid())\r
+ {\r
+ nameLinks.addElement(link.getName());\r
+ urlLinks.addElement(link.getURL());\r
+ updateLinkData();\r
+ valid = true;\r
+ }\r
+ }\r
+ else\r
+ break;\r
+ }\r
+ }\r
+\r
+ public void editLink_actionPerformed(ActionEvent e) {\r
+ GSequenceLink link = new GSequenceLink();\r
+\r
+ int index = linkNameList.getSelectedIndex();\r
+ if(index==-1)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
+ ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+\r
+ link.setName( nameLinks.elementAt(index).toString() );\r
+ link.setURL( urlLinks.elementAt(index).toString() );\r
+\r
+ boolean valid = false;\r
+ while (!valid)\r
+ {\r
+\r
+ if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
+ "New sequence URL link",\r
+ JOptionPane.OK_CANCEL_OPTION\r
+ ,-1, null)\r
+ == JOptionPane.OK_OPTION)\r
+ {\r
+ if (link.checkValid())\r
+ {\r
+ nameLinks.setElementAt(link.getName(), index);\r
+ urlLinks.setElementAt(link.getURL(), index);\r
+ updateLinkData();\r
+ valid = true;\r
+ }\r
+ }\r
+\r
+ else\r
+ break;\r
+ }\r
+ }\r
+\r
+ public void deleteLink_actionPerformed(ActionEvent e) {\r
+ int index = linkNameList.getSelectedIndex();\r
+ if(index==-1)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
+ ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+ nameLinks.removeElementAt(index);\r
+ urlLinks.removeElementAt(index);\r
+ updateLinkData();\r
+ }\r
+\r
+ void updateLinkData()\r
+ {\r
+ linkNameList.setListData(nameLinks);\r
+ linkURLList.setListData(urlLinks);\r
+ }\r
+\r
+ public void defaultBrowser_mouseClicked(MouseEvent e)\r
+ {\r
+ JFileChooser chooser = new JFileChooser(".");\r
+ chooser.setDialogTitle("Select default web browser");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JFileChooser.APPROVE_OPTION)\r
+ {\r
+ defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
+ }\r