public class Preferences extends GPreferences\r
{\r
/** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */\r
- public static Vector sequenceURLLinks = new Vector();\r
- static { sequenceURLLinks.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");}\r
+ public static Vector sequenceURLLinks;\r
+ static\r
+ {\r
+ String string = Cache.getDefault("SEQUENCE_LINKS",\r
+ "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");\r
+ sequenceURLLinks = new Vector();\r
+\r
+ try\r
+ {\r
+ StringTokenizer st = new StringTokenizer(string, "|");\r
+ while (st.hasMoreElements())\r
+ {\r
+ sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println(ex + "\nError parsing sequence links");\r
+ }\r
+ }\r
Vector nameLinks, urlLinks;\r
\r
JInternalFrame frame;\r
quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
\r
- for (int i = 0; i < 12; i++)\r
+ for (int i = 0; i < 13; i++)\r
{\r
colour.addItem(ColourSchemeProperty.getColourName(i));\r
}\r
\r
- String string = Cache.getProperty("DEFAULT_COLOUR");\r
+ String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
\r
- if (string != null)\r
- {\r
- colour.setSelectedItem(string);\r
- }\r
- else\r
- {\r
- colour.setSelectedIndex(11);\r
- }\r
+ colour.setSelectedItem(string);\r
\r
String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
.getAvailableFontFamilyNames();\r
startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
"http://www.jalview.org/examples/exampleFile.jar"));\r
\r
+ sortby.addItem("No sort");\r
+ sortby.addItem("Id");\r
+ sortby.addItem("Pairwise Identity");\r
+ sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
+\r
/****************************************************\r
* Set up Connections\r
*/\r
-\r
- string = Cache.getDefault("SEQUENCE_LINKS",\r
- "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");\r
- sequenceURLLinks = new Vector();\r
-\r
- try{\r
- StringTokenizer st = new StringTokenizer(string, "|");\r
- while (st.hasMoreElements())\r
- {\r
- sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());\r
- }\r
- }catch(Exception ex)\r
- {System.out.println(ex+"\nError parsing sequence links");}\r
-\r
nameLinks = new Vector();\r
urlLinks = new Vector();\r
for(int i=0; i<sequenceURLLinks.size(); i++)\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(defaultBrowser.getText().trim().length()<1)\r
Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
else\r