X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=078eff11e1e90fe68abd708c501a32b4c37e706e;hb=783520af519c958e10a2af29f1d4242e1ab890a3;hp=be1455b995eb931f2f90eea103bb1e99f2643359;hpb=d19f6b27ef8ee7350763cfaa511270bf128e76a9;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index be1455b..078eff1 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.*;
@@ -83,9 +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));
 
@@ -132,6 +130,31 @@ 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"));
+
+        blcdb.setSelected( Cache.getDefault("BLC_DBPREFIX", false) );
+        blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );
+        clustaldb.setSelected( Cache.getDefault("CLUSTAL_DBPREFIX", false) );
+        clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );
+        fastadb.setSelected( Cache.getDefault("FASTA_DBPREFIX", false) );
+        fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );
+        msfdb.setSelected( Cache.getDefault("MSF_DBPREFIX", false) );
+        msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );
+        pfamdb.setSelected( Cache.getDefault("PFAM_DBPREFIX", false) );
+        pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );
+        pileupdb.setSelected( Cache.getDefault("PILEUP_DBPREFIX", false) );
+        pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
+        pirdb.setSelected( Cache.getDefault("PIR_DBPREFIX", false) );
+        pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
+
   /****************************************************
    * Set up Connections
    */
@@ -191,6 +214,13 @@ 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
@@ -242,6 +272,21 @@ public class Preferences extends GPreferences
         }
 
 
+        Cache.applicationProperties.setProperty("BLC_DBPREFIX", Boolean.toString(blcdb.isSelected()) );
+        Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );
+        Cache.applicationProperties.setProperty("CLUSTAL_DBPREFIX", Boolean.toString(clustaldb.isSelected()) );
+        Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );
+        Cache.applicationProperties.setProperty("FASTA_DBPREFIX", Boolean.toString(fastadb.isSelected()) );
+        Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );
+        Cache.applicationProperties.setProperty("MSF_DBPREFIX", Boolean.toString(msfdb.isSelected()) );
+        Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PFAM_DBPREFIX", Boolean.toString(pfamdb.isSelected()) );
+        Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PILEUP_DBPREFIX", Boolean.toString(pileupdb.isSelected()) );
+        Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PIR_DBPREFIX", Boolean.toString(pirdb.isSelected()) );
+        Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
+
 
         Cache.saveProperties();
         try