+ Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",\r
+ Boolean.toString(seqLimit.\r
+ isSelected()));\r
+ Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",\r
+ Boolean.toString(rightAlign.\r
+ isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",\r
+ Boolean.toString(fullScreen.\r
+ isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",\r
+ Boolean.\r
+ toString(annotations.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",\r
+ Boolean.\r
+ toString(conservation.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_QUALITY",\r
+ Boolean.toString(quality.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",\r
+ Boolean.toString(identity.\r
+ isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR",\r
+ colour.getSelectedItem().toString());\r
+ Cache.applicationProperties.setProperty("GAP_SYMBOL",\r
+ gapSymbolCB.getSelectedItem().\r
+ toString());\r
+\r
+ Cache.applicationProperties.setProperty("FONT_NAME",\r
+ fontNameCB.getSelectedItem().\r
+ toString());\r
+ Cache.applicationProperties.setProperty("FONT_STYLE",\r
+ fontStyleCB.getSelectedItem().\r
+ toString());\r
+ Cache.applicationProperties.setProperty("FONT_SIZE",\r
+ fontSizeCB.getSelectedItem().\r
+ toString());\r
+\r
+ Cache.applicationProperties.setProperty("ID_ITALICS",\r
+ Boolean.toString(idItalics.\r
+ isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("ANTI_ALIAS",\r
+ Boolean.toString(smoothFont.\r
+ isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",\r
+ Boolean.toString(wrap.isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("STARTUP_FILE",\r
+ startupFileTextfield.getText());\r
+ Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",\r
+ Boolean.\r
+ toString(startupCheckbox.isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT",\r
+ sortby.getSelectedItem().toString());\r
+\r
+ if (epsRendering.getSelectedItem().equals("Prompt each time"))\r
+ {\r
+ Cache.applicationProperties.remove("EPS_RENDERING");\r
+ }\r
+ else\r
+ {\r
+ Cache.applicationProperties.setProperty("EPS_RENDERING",\r
+ epsRendering.getSelectedItem().\r
+ toString());\r
+ }\r
+\r
+ if (defaultBrowser.getText().trim().length() < 1)\r
+ {\r
+ Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
+ }\r
+ else\r
+ {\r
+ Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
+ defaultBrowser.getText());\r
+ }\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) + "|" +\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