Allow for frame insets

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

diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index f2592ff..b4833b1 100644 (file)
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -6,14 +6,12 @@ import javax.swing.*;
 \r
 import vamsas.objects.simple.JpredResult;\r
 \r
-import ext.vamsas.*;\r
 import jalview.analysis.*;\r
 import jalview.bin.*;\r
 import jalview.datamodel.*;\r
 import jalview.gui.*;\r
 import jalview.io.*;\r
 import jalview.util.*;\r
-import jalview.ws.WSThread.*;\r
 \r
 class JPredThread\r
 extends WSThread\r
@@ -95,8 +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
@@ -139,7 +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