X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=32aad84a7a2aad655b385849eb38ed3245f1b6b2;hb=f24dacb1da56fccf05d684e2f4899facec2aecf7;hp=8a2650b5d6d1a99f41adb4872094052abb1a6d0e;hpb=97c00be1121a6758439b73ded035c4edbacfa2bc;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8a2650b..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.*;
@@ -45,7 +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();
+    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;
@@ -64,9 +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));
 
@@ -74,21 +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();
@@ -120,23 +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++)
@@ -193,7 +199,20 @@ 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("DEFAULT_BROWSER", defaultBrowser.getText());
+      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
+        Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
+                                                defaultBrowser.getText());
+
+        jalview.util.BrowserLauncher.resetBrowser();
 
         if(nameLinks.size()>0)
         {
@@ -209,16 +228,33 @@ public class Preferences extends GPreferences
           links.setLength( links.length()-1 );
           Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
         }
+        else
+          Cache.applicationProperties.remove("SEQUENCE_LINKS");
+
 
         Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
-        Cache.applicationProperties.setProperty("PROXY_SERVER",proxyServerTB.getText());
-        Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+
+        if (proxyServerTB.getText().trim().length() < 1)
+          Cache.applicationProperties.remove("PROXY_SERVER");
+        else
+          Cache.applicationProperties.setProperty("PROXY_SERVER",
+                                                  proxyServerTB.getText());
+
+        if (proxyPortTB.getText().trim().length() < 1)
+          Cache.applicationProperties.remove("PROXY_PORT");
+        else
+          Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
 
         if(useProxy.isSelected())
         {
           System.setProperty("http.proxyHost", proxyServerTB.getText());
           System.setProperty("http.proxyPort", proxyPortTB.getText());
         }
+        else
+        {
+          System.setProperty("http.proxyHost","");
+          System.setProperty("http.proxyPort","");
+        }