X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredClient.java;h=c463c5173a67cbbca66d757e5ff8fa312dc2dbe4;hb=06fef82a8d6fcdcfadc58d747f9f774297cd639d;hp=3ebc1f0bef33745d234f71dd99f1237d749b8905;hpb=aafe9bfd2c035d1683c42d767ff0a6b9071fa081;p=jalview.git

diff --git a/src/jalview/io/JPredClient.java b/src/jalview/io/JPredClient.java
index 3ebc1f0..c463c51 100755
--- a/src/jalview/io/JPredClient.java
+++ b/src/jalview/io/JPredClient.java
@@ -198,9 +198,9 @@ public class JPredClient
         if (this.msa!=null && result.getAligfile()!=null) {
           // we ignore the returned alignment if we only predicted on a single sequence
           String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), "Paste");
-          if (jalview.io.FormatProperties.contains(format))
+          if (jalview.io.FormatAdapter.formats.contains(format))
           {
-            al = new Alignment(jalview.io.FormatAdapter.read(result.getAligfile(),"Paste",format));
+            al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format));
             noMsa = false;
             FirstSeq = 0;
           }
@@ -278,15 +278,15 @@ public class JPredClient
         }
 
         Hashtable scores = prediction.Scores;
-        addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
+      /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
                             "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
 
         addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
-                            "JnetpropB", "Jnet Beta Sheed Propensity", 0f,1f,1);
+                            "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
 
         addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
                             "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
-
+       */
         AlignFrame af = new AlignFrame(al);