+ 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
+\r
+ dasSource.saveProperties(Cache.applicationProperties);\r
+\r
+ Cache.saveProperties();\r
+ try\r
+ {\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r