send rotCanvas sequence and viewport

[jalview.git] / src / jalview / io / JPredClient.java

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