X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=2243a3d10738674be7d8b1c0b1741080cba3d6f2;hb=c24071f7b9e6b70c94743214677871ae2dc88499;hp=ff44fe4e8c5f4811d69ff911f4a47d231d2d9739;hpb=65310fba3ddf0942d5f868130bca9e093888ce7a;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index ff44fe4..2243a3d 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.*;
@@ -81,11 +79,11 @@ public class Preferences extends GPreferences
         Desktop.addInternalFrame(frame, "Preferences", 480, 390);
         frame.setMinimumSize(new Dimension(480,390));
 
-        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));
 
@@ -137,6 +135,19 @@ public class Preferences extends GPreferences
         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"));
+
+        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
    */
@@ -178,7 +189,7 @@ 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()));
@@ -198,6 +209,11 @@ public class Preferences extends GPreferences
 
       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
@@ -249,6 +265,14 @@ 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