X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=9ac8acf3645ce9e8db160af7f574a1992b5f5ba6;hb=b437b816507d2acc59e34f70a9cf8c7f81921681;hp=be1455b995eb931f2f90eea103bb1e99f2643359;hpb=d19f6b27ef8ee7350763cfaa511270bf128e76a9;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index be1455b..9ac8acf 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.*;
@@ -78,14 +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));
 
@@ -123,6 +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(".");
 
@@ -132,6 +132,29 @@ 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"));
+
+        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) );
+
+        modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
+
+        autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+        padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
+
   /****************************************************
    * Set up Connections
    */
@@ -173,7 +196,7 @@ 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()));
@@ -188,9 +211,18 @@ 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
@@ -242,7 +274,20 @@ 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.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );
+        jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+
+        Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+                                                Boolean.toString(autoCalculateConsCheck.isSelected()));
+        Cache.applicationProperties.setProperty("PAD_GAPS",
+                                                Boolean.toString(padGaps.isSelected()));
         Cache.saveProperties();
         try
         {