Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / src / jalview / ws / rest / RestJobThread.java

diff --git a/src/jalview/ws/rest/RestJobThread.java b/src/jalview/ws/rest/RestJobThread.java
index e397c79..cff127b 100644 (file)
--- a/src/jalview/ws/rest/RestJobThread.java
+++ b/src/jalview/ws/rest/RestJobThread.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws.rest;
 
+import java.util.Locale;
+
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -435,7 +437,7 @@ public class RestJobThread extends AWSThread
      */
     String f;
     StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
-    f = f.toLowerCase();
+    f = f.toLowerCase(Locale.ROOT);
     int body = f.indexOf("<body");
     if (body > -1)
     {
@@ -609,12 +611,12 @@ public class RestJobThread extends AWSThread
     /**
      * alignment panels derived from each alignment set returned by service.
      */
-    ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<jalview.gui.AlignmentPanel>();
+    ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<>();
     /**
      * list of instructions for how to process each distinct alignment set
      * returned by the job set
      */
-    ArrayList<AddDataTo> resultDest = new ArrayList<AddDataTo>();
+    ArrayList<AddDataTo> resultDest = new ArrayList<>();
     /**
      * when false, zeroth pane is panel derived from input deta.
      */
@@ -633,9 +635,9 @@ public class RestJobThread extends AWSThread
     boolean vsepjobs = restClient.service.isVseparable();
     // total number of distinct alignment sets generated by job set.
     int numAlSets = 0, als = 0;
-    List<AlignmentI> destAls = new ArrayList<AlignmentI>();
-    List<jalview.datamodel.HiddenColumns> destColsel = new ArrayList<jalview.datamodel.HiddenColumns>();
-    List<List<NewickFile>> trees = new ArrayList<List<NewickFile>>();
+    List<AlignmentI> destAls = new ArrayList<>();
+    List<jalview.datamodel.HiddenColumns> destColsel = new ArrayList<>();
+    List<List<NewickFile>> trees = new ArrayList<>();
 
     do
     {
@@ -694,7 +696,7 @@ public class RestJobThread extends AWSThread
 
               if (alset.trees != null)
               {
-                trees.add(new ArrayList<NewickFile>(alset.trees));
+                trees.add(new ArrayList<>(alset.trees));
               }
               else
               {
@@ -722,8 +724,8 @@ public class RestJobThread extends AWSThread
        */
       int vrestjob = 0;
       // Destination alignments for all result data.
-      ArrayList<SequenceGroup> visgrps = new ArrayList<SequenceGroup>();
-      Hashtable<String, SequenceGroup> groupNames = new Hashtable<String, SequenceGroup>();
+      ArrayList<SequenceGroup> visgrps = new ArrayList<>();
+      Hashtable<String, SequenceGroup> groupNames = new Hashtable<>();
       ArrayList<AlignmentAnnotation> visAlAn = null;
       for (nvertsep = 0; nvertsep < nvertseps; nvertsep++)
       {
@@ -987,7 +989,7 @@ public class RestJobThread extends AWSThread
                 }
                 if (visAlAn == null)
                 {
-                  visAlAn = new ArrayList<AlignmentAnnotation>();
+                  visAlAn = new ArrayList<>();
                 }
                 AlignmentAnnotation visan = null;
                 for (AlignmentAnnotation v : visAlAn)
@@ -1071,8 +1073,9 @@ public class RestJobThread extends AWSThread
       HiddenColumns destcs;
       String alTitle = MessageManager
               .formatMessage("label.webservice_job_title_on", new String[]
-              { restClient.service.details.Action,
-                  restClient.service.details.Name, restClient.viewTitle });
+              { restClient.service.details.getAction(),
+                  restClient.service.details.getName(),
+                  restClient.viewTitle });
       switch (action)
       {
       case newAlignment:
@@ -1282,7 +1285,7 @@ public class RestJobThread extends AWSThread
    */
   public boolean isValid()
   {
-    ArrayList<String> _warnings = new ArrayList<String>();
+    ArrayList<String> _warnings = new ArrayList<>();
     boolean validt = true;
     if (jobs != null)
     {