JAL-2446 merged to spike branch

[jalview.git] / src / jalview / ws / jws1 / SeqSearchWSThread.java

diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index 70056a6..edc9ae8 100644 (file)
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -209,7 +209,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           if (inFile != null && inFile.length() > 0)
           {
             new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
-                    jalview.io.AppletFormatAdapter.PASTE);
+                    jalview.io.DataSourceType.PASTE);
           }
         } catch (Exception e)
         {
@@ -225,7 +225,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           if (inFile != null && inFile.length() > 0)
           {
             jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
-                    inFile, jalview.io.AppletFormatAdapter.PASTE);
+                    inFile, jalview.io.DataSourceType.PASTE);
             ff.parse(al, featureColours, false);
           }
         } catch (Exception e)
@@ -242,7 +242,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           if (inFile != null && inFile.length() > 0)
           {
             nf = new jalview.io.NewickFile(inFile,
-                    jalview.io.AppletFormatAdapter.PASTE);
+                    jalview.io.DataSourceType.PASTE);
             if (!nf.isValid())
             {
               nf.close();
@@ -666,7 +666,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       if (nf != null)
       {
-        af.ShowNewickTree(nf, MessageManager.formatMessage(
+        af.showNewickTree(nf, MessageManager.formatMessage(
                 "label.tree_from", new String[] { this.alTitle }));
       }
       // initialise with same renderer settings as in parent alignframe.