Remove redundancy in Eclipse

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

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 8f94e97..fdf0cec 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -137,7 +137,7 @@ public class JPredClient
                              " Service location failed\nfor URL :" + WsURL +\r
                              "\n" +\r
                              ex.getMessage());\r
-      wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
 \r
       return false;\r
     }\r
@@ -172,9 +172,8 @@ public class JPredClient
       this.sequence.setSeq(AlignSeq.extractGaps("-. ",\r
                                                 msf[0].getSequence()));\r
 \r
-      jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
       this.msa = new vamsas.objects.simple.Msfalignment();\r
-      msa.setMsf(mwrite.print(msf));\r
+      msa.setMsf(jalview.io.PileUpfile.print(msf));\r
     }\r
 \r
     public void run()\r
@@ -334,7 +333,7 @@ public class JPredClient
 \r
 \r
 \r
-    private void addFloatAnnotations(Alignment al, int[] gapmap,\r
+  /*  private void addFloatAnnotations(Alignment al, int[] gapmap,\r
                                      Vector values, String Symname,\r
                                      String Visname, float min,\r
                                      float max, int winLength)\r
@@ -350,7 +349,7 @@ public class JPredClient
 \r
       al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
                                                annotations, min, max, winLength));\r
-    }\r
+    }*/\r
 \r
     void parseResult()\r
     {\r
@@ -518,7 +517,7 @@ public class JPredClient
           i++;\r
         }\r
 \r
-        Hashtable scores = prediction.getScores();\r
+        //Hashtable scores = prediction.getScores();\r
 \r
         /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),\r
                               "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r