From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 1 Jul 2015 14:23:11 +0000 (+0100)
Subject: house keeping
X-Git-Tag: Release_2_10_0~585^2~2^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=330763451812f4422e4027a8ee7dc81ab52b269d;p=jalview.git

house keeping
---

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 089f50b..73be79f 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -96,7 +96,6 @@ public class BioJsHTMLOutput
             { "HTML files" }, "HTML files");
     jvFileChooser.setFileView(new JalviewFileView());
 
-    // TODO uncomment when supported by MassageManager
     jvFileChooser.setDialogTitle(MessageManager
             .getString("label.save_as_biojs_html"));
     jvFileChooser.setDialogTitle("save as BioJs HTML");
@@ -201,10 +200,13 @@ public class BioJsHTMLOutput
         try
         {
           String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
-          BioJSRepositoryPojo release = new BioJSRepositoryPojo(
-                  gitRepoPkgJson);
-          syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
-          refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+          if (gitRepoPkgJson != null)
+          {
+            BioJSRepositoryPojo release = new BioJSRepositoryPojo(
+                    gitRepoPkgJson);
+            syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
+            refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+          }
         } catch (URISyntaxException e)
         {
           e.printStackTrace();
diff --git a/src/jalview/jbgui/PDBDocFieldPreferences.java b/src/jalview/jbgui/PDBDocFieldPreferences.java
index 96e27e6..4ec649a 100644
--- a/src/jalview/jbgui/PDBDocFieldPreferences.java
+++ b/src/jalview/jbgui/PDBDocFieldPreferences.java
@@ -51,15 +51,15 @@ public class PDBDocFieldPreferences extends JScrollPane
     {
     case SEARCH_SUMMARY:
       columnNames = new String[]
-      { "PDB Feild", "Show in search summary" };
+      { "PDB Field", "Show in search summary" };
       break;
     case STRUCTURE_CHOOSER:
       columnNames = new String[]
-      { "PDB Feild", "Show in structure summary" };
+      { "PDB Field", "Show in structure summary" };
       break;
     case PREFERENCES:
       columnNames = new String[]
-      { "PDB Feild", "Show in search summary", "Show in structure summary" };
+      { "PDB Field", "Show in search summary", "Show in structure summary" };
       break;
     default:
       break;
diff --git a/src/jalview/json/binding/v1/BioJSRepositoryPojo.java b/src/jalview/json/binding/v1/BioJSRepositoryPojo.java
index 4028a9d..1e6ef7e 100644
--- a/src/jalview/json/binding/v1/BioJSRepositoryPojo.java
+++ b/src/jalview/json/binding/v1/BioJSRepositoryPojo.java
@@ -3,6 +3,7 @@ package jalview.json.binding.v1;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Iterator;
+import java.util.Objects;
 
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
@@ -36,6 +37,8 @@ public class BioJSRepositoryPojo
   @SuppressWarnings("unchecked")
   private void parse(String jsonString) throws ParseException
   {
+    Objects.requireNonNull(jsonString,
+            "Supplied jsonString must not be null");
     JSONParser jsonParser = new JSONParser();
     JSONObject JsonObj = (JSONObject) jsonParser.parse(jsonString);
     this.description = (String) JsonObj.get("description");
diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index 67ab3f2..09c10ef 100644
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -269,27 +269,27 @@ public class PDBRestClient
    * table. The PDB Id serves as a unique identifier for a given row in the
    * summary table
    * 
-   * @param wantedFeilds
+   * @param wantedFields
    *          the available table columns in no particular order
    * @return the pdb id field column index
    */
   public static int getPDBIdColumIndex(
-          Collection<PDBDocField> wantedFeilds, boolean hasRefSeq)
+          Collection<PDBDocField> wantedFields, boolean hasRefSeq)
   {
 
     // If a reference sequence is attached then start counting from 1 else
     // start from zero
-    int pdbFeildIndexCounter = hasRefSeq ? 1 : 0;
+    int pdbFieldIndexCounter = hasRefSeq ? 1 : 0;
 
-    for (PDBDocField feild : wantedFeilds)
+    for (PDBDocField field : wantedFields)
     {
-      if (feild.equals(PDBDocField.PDB_ID))
+      if (field.equals(PDBDocField.PDB_ID))
       {
         break; // Once PDB Id index is determined exit iteration
       }
-      ++pdbFeildIndexCounter;
+      ++pdbFieldIndexCounter;
     }
-    return pdbFeildIndexCounter;
+    return pdbFieldIndexCounter;
   }
 
   /**