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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index ac181ec..b2226db 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -18,7 +18,7 @@ public class JPredFile
   Vector conf;
   Hashtable Scores; // Hash of names and score vectors
   Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
-  private int QuerySeqPosition = -1;
+  private int QuerySeqPosition;
   public void setQuerySeqPosition(int QuerySeqPosition)
   {
     this.QuerySeqPosition = QuerySeqPosition;
@@ -47,7 +47,6 @@ public class JPredFile
     Scores = new Hashtable();
     ids = null;
     conf = null;
-    QuerySeqPosition = -1;
   }
 
   public JPredFile(String inFile, String type)
@@ -63,7 +62,7 @@ public class JPredFile
   public void parse()
       throws IOException
   {
-System.out.println("all read in ");
+    // JBPNote log.System.out.println("all read in ");
     String line;
     QuerySeqPosition = -1;
     noSeqs = 0;
@@ -137,7 +136,7 @@ System.out.println("all read in ");
       }
       else if (id.equals("jnetconf"))
       {
-        System.out.println("here");
+        // log.debug System.out.println("here");
         id = "Prediction Confidence";
         this.conf = new Vector(numSymbols);
         for (int i = 0; i < numSymbols; i++)
@@ -242,7 +241,7 @@ System.out.println("all read in ");
       }
       catch (java.io.IOException e)
       {
-        System.out.println("Exception " + e);
+        System.err.println("Exception " + e);
         e.printStackTrace();
       }
     }