X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=32aad84a7a2aad655b385849eb38ed3245f1b6b2;hb=f24dacb1da56fccf05d684e2f4899facec2aecf7;hp=bf26c0d5e8350ea7f9b2d25ca6a0d8f532c6f028;hpb=1402060fb2ca7b2639ef98da3e22766d01149b16;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index bf26c0d..32aad84 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -18,8 +18,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.*;
-
 import jalview.io.*;
 
 import jalview.jbgui.*;
@@ -45,8 +43,26 @@ import jalview.bin.Cache;
 public class Preferences extends GPreferences
 {
     /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
-    public static Vector sequenceURLLinks = new Vector();
-    static { sequenceURLLinks.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");}
+    public static Vector sequenceURLLinks;
+    static
+    {
+      String string = Cache.getDefault("SEQUENCE_LINKS",
+                                       "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
+      sequenceURLLinks = new Vector();
+
+      try
+      {
+        StringTokenizer st = new StringTokenizer(string, "|");
+        while (st.hasMoreElements())
+        {
+          sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
+        }
+      }
+      catch (Exception ex)
+      {
+        System.out.println(ex + "\nError parsing sequence links");
+      }
+    }
     Vector nameLinks, urlLinks;
 
     JInternalFrame frame;
@@ -65,9 +81,9 @@ public class Preferences extends GPreferences
 
         fullID.setSelected(      Cache.getDefault("SHOW_FULL_ID", true));
         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));
-        annotations.setSelected( Cache.getDefault("SHOW_FULL_ID", true));
-        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
+        annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
 
+        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
@@ -75,21 +91,14 @@ public class Preferences extends GPreferences
         quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
         identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 
-        for (int i = 0; i < 12; i++)
+        for (int i = 0; i < 13; i++)
         {
             colour.addItem(ColourSchemeProperty.getColourName(i));
         }
 
-        String string = Cache.getProperty("DEFAULT_COLOUR");
+        String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 
-        if (string != null)
-        {
-            colour.setSelectedItem(string);
-        }
-        else
-        {
-            colour.setSelectedIndex(11);
-        }
+        colour.setSelectedItem(string);
 
         String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
                                                      .getAvailableFontFamilyNames();
@@ -121,23 +130,19 @@ public class Preferences extends GPreferences
         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
          "http://www.jalview.org/examples/exampleFile.jar"));
 
+        sortby.addItem("No sort");
+        sortby.addItem("Id");
+        sortby.addItem("Pairwise Identity");
+        sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
+
+        epsRendering.addItem("Prompt each time");
+        epsRendering.addItem("Lineart");
+        epsRendering.addItem("Text");
+        epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));
+
   /****************************************************
    * Set up Connections
    */
-
-      string = Cache.getDefault("SEQUENCE_LINKS",
-                            "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
-      sequenceURLLinks = new Vector();
-
-        try{
-          StringTokenizer st = new StringTokenizer(string, "|");
-          while (st.hasMoreElements())
-          {
-            sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
-          }
-        }catch(Exception ex)
-        {System.out.println(ex+"\nError parsing sequence links");}
-
         nameLinks = new Vector();
         urlLinks = new Vector();
         for(int i=0; i<sequenceURLLinks.size(); i++)
@@ -194,6 +199,13 @@ public class Preferences extends GPreferences
       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));
 
+      Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
+
+      if(epsRendering.getSelectedItem().equals("Prompt each time"))
+        Cache.applicationProperties.remove("EPS_RENDERING");
+      else
+        Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());
+
       if(defaultBrowser.getText().trim().length()<1)
         Cache.applicationProperties.remove("DEFAULT_BROWSER");
       else