Correct Preferences to check for SEQUENCE_NAME as well as SEQUENCE_ID on

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 84baa1c..b57b951 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -20,6 +20,12 @@
  */
 package jalview.gui;
 
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.OLD_EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+import static jalview.util.UrlConstants.SEQUENCE_NAME;
+import static jalview.util.UrlConstants.SRS_STRING;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
@@ -110,10 +116,7 @@ public class Preferences extends GPreferences
   public static List<String> groupURLLinks;
   static
   {
-    String string = Cache
-            .getDefault(
-                    "SEQUENCE_LINKS",
-                    "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+    String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
     sequenceURLLinks = new Vector<String>();
 
     try
@@ -124,7 +127,11 @@ public class Preferences extends GPreferences
         String name = st.nextToken();
         String url = st.nextToken();
         // check for '|' within a regex
-        int rxstart = url.indexOf("$SEQUENCE_ID$");
+        int rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+        if (rxstart == -1)
+        {
+          rxstart = url.indexOf("$" + SEQUENCE_NAME + "$");
+        }
         while (rxstart == -1 && url.indexOf("/=$") == -1)
         {
           url = url + "|" + st.nextToken();
@@ -137,14 +144,16 @@ public class Preferences extends GPreferences
     }
     {
       // upgrade old SRS link
-      int srsPos = sequenceURLLinks
-              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
       if (srsPos > -1)
       {
-        sequenceURLLinks
-                .setElementAt(
-                        "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                        srsPos);
+        sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
+      }
+      // upgrade old EMBL-EBI link
+      int emblPos = sequenceURLLinks.indexOf(OLD_EMBLEBI_STRING);
+      if (emblPos > -1)
+      {
+        sequenceURLLinks.setElementAt(EMBLEBI_STRING, emblPos);
       }
     }
 
@@ -164,6 +173,16 @@ public class Preferences extends GPreferences
 
   private WsPreferences wsPrefs;
 
+  private OptionsParam promptEachTimeOpt = new OptionsParam(
+          MessageManager.getString("label.prompt_each_time"),
+          "Prompt each time");
+
+  private OptionsParam lineArtOpt = new OptionsParam(
+          MessageManager.getString("label.lineart"), "Lineart");
+
+  private OptionsParam textOpt = new OptionsParam(
+          MessageManager.getString("action.text"), "Text");
+
   /**
    * Creates a new Preferences object.
    */
@@ -359,28 +378,22 @@ public class Preferences extends GPreferences
     /*
      * Set Output tab defaults
      */
-    epsRendering.addItem(new OptionsParam(MessageManager
-            .getString("label.prompt_each_time"), "Prompt each time"));
-    epsRendering.addItem(new OptionsParam(MessageManager
-            .getString("label.lineart"), "Lineart"));
-    epsRendering.addItem(new OptionsParam(MessageManager
-            .getString("action.text"), "Text"));
+    epsRendering.addItem(promptEachTimeOpt);
+    epsRendering.addItem(lineArtOpt);
+    epsRendering.addItem(textOpt);
     String defaultEPS = Cache.getDefault("EPS_RENDERING",
             "Prompt each time");
     if (defaultEPS.equalsIgnoreCase("Text"))
     {
-      epsRendering.setSelectedItem(new OptionsParam(MessageManager
-              .getString("action.text"), "Text"));
+      epsRendering.setSelectedItem(textOpt);
     }
     else if (defaultEPS.equalsIgnoreCase("Lineart"))
     {
-      epsRendering.setSelectedItem(new OptionsParam(MessageManager
-              .getString("label.lineart"), "Lineart"));
+      epsRendering.setSelectedItem(lineArtOpt);
     }
     else
     {
-      epsRendering.setSelectedItem(new OptionsParam(MessageManager
-              .getString("label.prompt_each_time"), "Prompt each time"));
+      epsRendering.setSelectedItem(promptEachTimeOpt);
     }
     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
     userIdWidth.setEnabled(!autoIdWidth.isSelected());
@@ -532,15 +545,8 @@ public class Preferences extends GPreferences
     /*
      * Save Output settings
      */
-    if (epsRendering.getSelectedItem().equals("Prompt each time"))
-    {
-      Cache.applicationProperties.remove("EPS_RENDERING");
-    }
-    else
-    {
-      Cache.applicationProperties.setProperty("EPS_RENDERING",
-              ((OptionsParam) epsRendering.getSelectedItem()).getCode());
-    }
+    Cache.applicationProperties.setProperty("EPS_RENDERING",
+            ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 
     /*
      * Save Connections settings
@@ -1049,7 +1055,8 @@ public class Preferences extends GPreferences
     }
 
     @Override
-    public int hashCode(){
+    public int hashCode()
+    {
       return name.hashCode() + code.hashCode();
     }
   }