Merge branch 'develop' into bug/JAL-2510amendFeatures

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

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index 7fbae89..27f5271 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -259,7 +259,8 @@ public class RestClient extends WSClient implements WSClientI,
         {
           // intersect groups with selected region
           _input = new AlignmentView(av.getAlignment(),
-                  av.getColumnSelection(), av.getSelectionGroup(),
+ av.getAlignment()
+                  .getHiddenColumns(), av.getSelectionGroup(),
                   av.hasHiddenColumns(), true, true);
           viewTitle = MessageManager.formatMessage(
                   "label.select_visible_region_of",
@@ -272,7 +273,8 @@ public class RestClient extends WSClient implements WSClientI,
         {
           // use selected region to partition alignment
           _input = new AlignmentView(av.getAlignment(),
-                  av.getColumnSelection(), av.getSelectionGroup(),
+ av.getAlignment()
+                  .getHiddenColumns(), av.getSelectionGroup(),
                   av.hasHiddenColumns(), false, true);
         }
         viewTitle = MessageManager.formatMessage(
@@ -286,7 +288,8 @@ public class RestClient extends WSClient implements WSClientI,
       {
         // just take selected region intersection
         _input = new AlignmentView(av.getAlignment(),
-                av.getColumnSelection(), av.getSelectionGroup(),
+ av.getAlignment()
+                .getHiddenColumns(), av.getSelectionGroup(),
                 av.hasHiddenColumns(), true, true);
         viewTitle = MessageManager.formatMessage(
                 "label.select_visible_region_of",
@@ -300,7 +303,8 @@ public class RestClient extends WSClient implements WSClientI,
     {
       // standard alignment view without selection present
       _input = new AlignmentView(av.getAlignment(),
-              av.getColumnSelection(), null, av.hasHiddenColumns(), false,
+ av.getAlignment()
+              .getHiddenColumns(), null, av.hasHiddenColumns(), false,
               true);
       viewTitle = ""
               + (av.hasHiddenColumns() ? (new StringBuffer(" ")