X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Furls%2FIdentifiersUrlProvider.java;h=c298639253029a0df96f3b6278f95a2634f7c9f8;hb=baca3e1d25692175ab0d6e392427c0ff97534c37;hp=0dab7198e2fff8c617d09be7c63bb60d7bdf7a3c;hpb=8e7cf85a7f61f425e808cac53ead7bc27e402242;p=jalview.git

diff --git a/src/jalview/urls/IdentifiersUrlProvider.java b/src/jalview/urls/IdentifiersUrlProvider.java
index 0dab719..c298639 100644
--- a/src/jalview/urls/IdentifiersUrlProvider.java
+++ b/src/jalview/urls/IdentifiersUrlProvider.java
@@ -63,7 +63,7 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
   public IdentifiersUrlProvider(String cachedUrlList)
   {
     urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
-    selectedUrls = new ArrayList<String>();
+    selectedUrls = new ArrayList<>();
     checkSelectionMatchesUrls(cachedUrlList);
   }
 
@@ -75,19 +75,20 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
    * @return hashmap of identifiers.org data, keyed by MIRIAM id
    */
   @SuppressWarnings("unchecked")
-private HashMap<String, UrlLink> readIdentifiers(String idFileName)
+  private HashMap<String, UrlLink> readIdentifiers(String idFileName)
   {
     // identifiers.org data
-    HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
+    HashMap<String, UrlLink> idData = new HashMap<>();
 
     String errorMessage = null;
     try
     {
-    	// NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER
-    
+      // NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER
+
       FileReader reader = new FileReader(idFileName);
       String key = "";
-      Map<String, Object> obj = (Map<String, Object>) JSONUtils.parse(reader);
+      Map<String, Object> obj = (Map<String, Object>) JSONUtils
+              .parse(reader);
       if (obj.containsKey(ID_ORG_KEY))
       {
         key = ID_ORG_KEY;
@@ -98,7 +99,7 @@ private HashMap<String, UrlLink> readIdentifiers(String idFileName)
       }
       else
       {
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "Unexpected key returned from identifiers jalview service");
         return idData;
       }
@@ -119,16 +120,21 @@ private HashMap<String, UrlLink> readIdentifiers(String idFileName)
     } catch (IOException | ParseException e)
     {
       // unnecessary e.printStackTrace();
-      // Note how in JavaScript we can grab the first bytes from any file reader. 
+      // Note how in JavaScript we can grab the first bytes from any file
+      // reader.
       // Typical report here is "NetworkError" because the file does not exist.
-      // "https://." is coming from System.getProperty("user.home"), but this could
+      // "https://." is coming from System.getProperty("user.home"), but this
+      // could
       // be set by the page developer to anything, of course.
-      errorMessage = (/** @j2sNative String.fromCharCode.apply(null, reader.$in.is.buf.slice(0,12)) || */e.toString());
+      errorMessage = e.toString();
       idData.clear();
     }
     // BH 2018 -- added more valuable report
     if (errorMessage != null)
-      System.err.println("IdentifiersUrlProvider: cannot read " + idFileName + ": " + errorMessage);
+    {
+      jalview.bin.Console.errPrintln("IdentifiersUrlProvider: cannot read " + idFileName
+              + ": " + errorMessage);
+    }
     return idData;
   }
 
@@ -193,7 +199,7 @@ private HashMap<String, UrlLink> readIdentifiers(String idFileName)
   @Override
   public List<String> getLinksForMenu()
   {
-    List<String> links = new ArrayList<String>();
+    List<String> links = new ArrayList<>();
     for (String key : selectedUrls)
     {
       links.add(urls.get(key).toStringWithTarget());
@@ -210,7 +216,7 @@ private HashMap<String, UrlLink> readIdentifiers(String idFileName)
   @Override
   public void setUrlData(List<UrlLinkDisplay> links)
   {
-    selectedUrls = new ArrayList<String>();
+    selectedUrls = new ArrayList<>();
 
     Iterator<UrlLinkDisplay> it = links.iterator();
     while (it.hasNext())