+ 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) + "|" +\r
+ 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
+ {\r
+ Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
+ }\r
+\r
+ Cache.applicationProperties.setProperty("USE_PROXY",\r
+ Boolean.toString(useProxy.\r
+ isSelected()));\r
+\r
+ if (proxyServerTB.getText().trim().length() < 1)\r
+ {\r
+ Cache.applicationProperties.remove("PROXY_SERVER");\r
+ }\r
+ else\r
+ {\r
+ Cache.applicationProperties.setProperty("PROXY_SERVER",\r
+ proxyServerTB.getText());\r
+ }\r
+\r
+ if (proxyPortTB.getText().trim().length() < 1)\r
+ {\r
+ Cache.applicationProperties.remove("PROXY_PORT");\r
+ }\r
+ else\r
+ {\r
+ Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
+ }\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
+ Cache.applicationProperties.setProperty("BLC_JVSUFFIX",\r
+ Boolean.toString(blcjv.isSelected()));\r
+ Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",\r
+ Boolean.\r
+ toString(clustaljv.isSelected()));\r
+ Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",\r
+ Boolean.toString(fastajv.isSelected()));\r
+ Cache.applicationProperties.setProperty("MSF_JVSUFFIX",\r
+ Boolean.toString(msfjv.isSelected()));\r
+ Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",\r
+ Boolean.toString(pfamjv.isSelected()));\r
+ Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",\r
+ Boolean.toString(pileupjv.\r
+ isSelected()));\r
+ Cache.applicationProperties.setProperty("PIR_JVSUFFIX",\r
+ Boolean.toString(pirjv.isSelected()));\r
+ Cache.applicationProperties.setProperty("PIR_MODELLER",\r
+ Boolean.toString(modellerOutput.\r
+ isSelected()));\r
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
+\r
+ Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
+ Boolean.toString(\r
+ 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