X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Funiprot%2FUniProtFTSRestClient.java;h=df48c0dada875119da08d5a7c547cbe3bc4e6cae;hb=c932f0e85a8852824cdd8ce790af68682732c85c;hp=88397f5c740e92ad9c286370fd9a132ea7aaae35;hpb=3c3ec5343b9e441517c817c22d1b7ff36f4a78be;p=jalview.git

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 88397f5..df48c0d 100644
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -19,32 +19,6 @@
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 
-/*
- * 2022-07-20 bsoares
- * See https://issues.jalview.org/browse/JAL-4036
- * The new Uniprot API is not dissimilar to the old one, but has some important changes.
- * Some group names have changed slightly, some old groups have gone and there are quite a few new groups.
- * 
- * Most changes are mappings of old column ids to new field ids. There are a handful of old
- * columns not mapped to new fields, and new fields without an old column.
- * [aside: not all possible columns were listed in the resources/fts/uniprot_data_columns.txt file.
- * These were presumably additions after the file was created]
- * For existing/mapped fields, the same preferences found in the resource file have been migrated to
- * the new file with the new field name, id and group.
- * 
- * The new mapped groups and files are stored and read from resources/fts/uniprot_data_columns-2022.txt.
- * 
- * There is now no "sort" query string parameter.
- * 
- * See https://www.uniprot.org/help/api_queries
- * 
- * SIGNIFICANT CHANGE: Pagination is no longer performed using a record offset, but with a "cursor"
- * query string parameter that is not really a cursor.  The value is an opaque string that is passed (or
- * rather a whole URL is passed) in the "Link" header of the HTTP response of the previous page.
- * Where such a link is passed it is put into the cursors ArrayList.
- * There are @Overridden methods in UniprotFTSPanel.
- */
-
 package jalview.fts.service.uniprot;
 
 import java.lang.invoke.MethodHandles;
@@ -73,6 +47,32 @@ import jalview.util.ChannelProperties;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
+/*
+ * 2022-07-20 bsoares
+ * See https://issues.jalview.org/browse/JAL-4036
+ * The new Uniprot API is not dissimilar to the old one, but has some important changes.
+ * Some group names have changed slightly, some old groups have gone and there are quite a few new groups.
+ * 
+ * Most changes are mappings of old column ids to new field ids. There are a handful of old
+ * columns not mapped to new fields, and new fields without an old column.
+ * [aside: not all possible columns were listed in the resources/fts/uniprot_data_columns.txt file.
+ * These were presumably additions after the file was created]
+ * For existing/mapped fields, the same preferences found in the resource file have been migrated to
+ * the new file with the new field name, id and group.
+ * 
+ * The new mapped groups and files are stored and read from resources/fts/uniprot_data_columns-2022.txt.
+ * 
+ * There is now no "sort" query string parameter.
+ * 
+ * See https://www.uniprot.org/help/api_queries
+ * 
+ * SIGNIFICANT CHANGE: Pagination is no longer performed using a record offset, but with a "cursor"
+ * query string parameter that is not really a cursor.  The value is an opaque string that is passed (or
+ * rather a whole URL is passed) in the "Link" header of the HTTP response of the previous page.
+ * Where such a link is passed it is put into the cursors ArrayList.
+ * There are @Overridden methods in UniprotFTSPanel.
+ */
+
 public class UniProtFTSRestClient extends FTSRestClient
 {
   private static final String DEFAULT_UNIPROT_DOMAIN = "https://rest.uniprot.org";
@@ -219,7 +219,7 @@ public class UniProtFTSRestClient extends FTSRestClient
               .getEntity(String.class);
       // Make redundant objects eligible for garbage collection to conserve
       // memory
-      // System.out.println(">>>>> response : "
+      // jalview.bin.Console.outPrintln(">>>>> response : "
       // + uniProtTabDelimittedResponseString);
       if (clientResponse.getStatus() != 200)
       {
@@ -307,7 +307,7 @@ public class UniProtFTSRestClient extends FTSRestClient
           firstRow = false;
           continue;
         }
-        // System.out.println(dataRow);
+        // jalview.bin.Console.outPrintln(dataRow);
         result.add(getFTSData(dataRow, uniprotRestRequest));
       }
       searchResult.setNumberOfItemsFound(xTotalResults);
@@ -389,7 +389,7 @@ public class UniProtFTSRestClient extends FTSRestClient
           } catch (Exception e)
           {
             e.printStackTrace();
-            System.out.println("offending value:" + fieldData);
+            jalview.bin.Console.outPrintln("offending value:" + fieldData);
           }
         }
       } catch (Exception e)