Remove redundancy in Eclipse

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index bf26c0d..32aad84 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -18,8 +18,6 @@
  */\r
 package jalview.gui;\r
 \r
-import jalview.bin.*;\r
-\r
 import jalview.io.*;\r
 \r
 import jalview.jbgui.*;\r
@@ -45,8 +43,26 @@ import jalview.bin.Cache;
 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
@@ -65,9 +81,9 @@ public class Preferences extends GPreferences
 \r
         fullID.setSelected(      Cache.getDefault("SHOW_FULL_ID", true));\r
         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
-        annotations.setSelected( Cache.getDefault("SHOW_FULL_ID", true));\r
-        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
+        annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 \r
+        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 \r
@@ -75,21 +91,14 @@ public class Preferences extends GPreferences
         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
@@ -121,23 +130,19 @@ public class Preferences extends GPreferences
         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
+        epsRendering.addItem("Prompt each time");\r
+        epsRendering.addItem("Lineart");\r
+        epsRendering.addItem("Text");\r
+        epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\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
@@ -194,6 +199,13 @@ public class Preferences extends GPreferences
       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