vamsasDemo new branch

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index be1455b..078eff1 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -18,8 +18,6 @@
  */\r
 package jalview.gui;\r
 \r
-import jalview.bin.*;\r
-\r
 import jalview.io.*;\r
 \r
 import jalview.jbgui.*;\r
@@ -83,9 +81,9 @@ public class Preferences extends GPreferences
 \r
         fullID.setSelected(      Cache.getDefault("SHOW_FULL_ID", true));\r
         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
-        annotations.setSelected( Cache.getDefault("SHOW_FULL_ID", true));\r
-        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
+        annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 \r
+        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 \r
@@ -132,6 +130,31 @@ public class Preferences extends GPreferences
         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
          "http://www.jalview.org/examples/exampleFile.jar"));\r
 \r
+        sortby.addItem("No sort");\r
+        sortby.addItem("Id");\r
+        sortby.addItem("Pairwise Identity");\r
+        sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
+\r
+        epsRendering.addItem("Prompt each time");\r
+        epsRendering.addItem("Lineart");\r
+        epsRendering.addItem("Text");\r
+        epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
+\r
+        blcdb.setSelected( Cache.getDefault("BLC_DBPREFIX", false) );\r
+        blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
+        clustaldb.setSelected( Cache.getDefault("CLUSTAL_DBPREFIX", false) );\r
+        clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
+        fastadb.setSelected( Cache.getDefault("FASTA_DBPREFIX", false) );\r
+        fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
+        msfdb.setSelected( Cache.getDefault("MSF_DBPREFIX", false) );\r
+        msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
+        pfamdb.setSelected( Cache.getDefault("PFAM_DBPREFIX", false) );\r
+        pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
+        pileupdb.setSelected( Cache.getDefault("PILEUP_DBPREFIX", false) );\r
+        pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
+        pirdb.setSelected( Cache.getDefault("PIR_DBPREFIX", false) );\r
+        pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
+\r
   /****************************************************\r
    * Set up Connections\r
    */\r
@@ -191,6 +214,13 @@ public class Preferences extends GPreferences
       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 \r
+      Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
+\r
+      if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
+        Cache.applicationProperties.remove("EPS_RENDERING");\r
+      else\r
+        Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
+\r
       if(defaultBrowser.getText().trim().length()<1)\r
         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
       else\r
@@ -242,6 +272,21 @@ public class Preferences extends GPreferences
         }\r
 \r
 \r
+        Cache.applicationProperties.setProperty("BLC_DBPREFIX", Boolean.toString(blcdb.isSelected()) );\r
+        Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
+        Cache.applicationProperties.setProperty("CLUSTAL_DBPREFIX", Boolean.toString(clustaldb.isSelected()) );\r
+        Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
+        Cache.applicationProperties.setProperty("FASTA_DBPREFIX", Boolean.toString(fastadb.isSelected()) );\r
+        Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
+        Cache.applicationProperties.setProperty("MSF_DBPREFIX", Boolean.toString(msfdb.isSelected()) );\r
+        Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
+        Cache.applicationProperties.setProperty("PFAM_DBPREFIX", Boolean.toString(pfamdb.isSelected()) );\r
+        Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
+        Cache.applicationProperties.setProperty("PILEUP_DBPREFIX", Boolean.toString(pileupdb.isSelected()) );\r
+        Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
+        Cache.applicationProperties.setProperty("PIR_DBPREFIX", Boolean.toString(pirdb.isSelected()) );\r
+        Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
+\r
 \r
         Cache.saveProperties();\r
         try\r