New view copies annotations across

[jalview.git] / src / jalview / ws / JPredThread.java

diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 0e4e396..b4833b1 100644 (file)
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -93,8 +93,8 @@ implements WSClientI
             al = new Alignment(sqs);\r
             alcsel=(ColumnSelection) alandcolsel[1];\r
           } else {\r
-            al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),\r
-                "Paste", format));\r
+            al = new FormatAdapter().readFile(result.getAligfile(),\r
+                "Paste", format);\r
             sqs = new SequenceI[al.getHeight()];\r
 \r
             for (int i = 0, j = al.getHeight(); i < j; i++)\r
@@ -137,7 +137,7 @@ implements WSClientI
           /////\r
           new jalview.commands.RemoveGapsCommand("Remove Gaps",\r
                                                  new SequenceI[] {sqs[msaIndex]},\r
-                                                 gc);\r
+                                                 alignFrame.getCurrentView().getAlignment());\r
 \r
           SequenceI profileseq=al.getSequenceAt(FirstSeq);\r
           profileseq.setSequence(sqs[msaIndex].getSequenceAsString());\r