X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=f322daa78a49e2a44204ce9d06f3db4814fec2c7;hb=49057b644ae4dc904a3245b695ba86678ac01ede;hp=bf26c0d5e8350ea7f9b2d25ca6a0d8f532c6f028;hpb=1402060fb2ca7b2639ef98da3e22766d01149b16;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index bf26c0d..f322daa 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;
@@ -60,14 +76,14 @@ public class Preferences extends GPreferences
 
         frame = new JInternalFrame();
         frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, "Preferences", 480, 390);
-        frame.setMinimumSize(new Dimension(480,390));
+        Desktop.addInternalFrame(frame, "Preferences", 480, 395);
+        frame.setMinimumSize(new Dimension(480,395));
 
-        fullID.setSelected(      Cache.getDefault("SHOW_FULL_ID", true));
+        seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", 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();
@@ -112,6 +121,8 @@ public class Preferences extends GPreferences
         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
 
+        smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+
         gapSymbolCB.addItem("-");
         gapSymbolCB.addItem(".");
 
@@ -121,23 +132,27 @@ public class Preferences extends GPreferences
         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
          "http://www.jalview.org/examples/exampleFile.jar"));
 
-  /****************************************************
-   * Set up Connections
-   */
+        sortby.addItem("No sort");
+        sortby.addItem("Id");
+        sortby.addItem("Pairwise Identity");
+        sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
 
-      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();
+        epsRendering.addItem("Prompt each time");
+        epsRendering.addItem("Lineart");
+        epsRendering.addItem("Text");
+        epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));
 
-        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");}
+        blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );
+        clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );
+        fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );
+        msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );
+        pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );
+        pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
+        pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
 
+  /****************************************************
+   * Set up Connections
+   */
         nameLinks = new Vector();
         urlLinks = new Vector();
         for(int i=0; i<sequenceURLLinks.size(); i++)
@@ -176,7 +191,7 @@ public class Preferences extends GPreferences
     public void ok_actionPerformed(ActionEvent e)
     {
 
-      Cache.applicationProperties.setProperty("SHOW_FULL_ID", Boolean.toString(fullID.isSelected()));
+      Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));
       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
 
       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));
@@ -191,9 +206,18 @@ public class Preferences extends GPreferences
       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
 
+      Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
+
       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
@@ -245,6 +269,14 @@ public class Preferences extends GPreferences
         }
 
 
+        Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );
+        Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );
+        Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );
+        Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
+
 
         Cache.saveProperties();
         try