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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 636a8d6..b2226db 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -18,6 +18,23 @@ 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;
+  public void setQuerySeqPosition(int QuerySeqPosition)
+  {
+    this.QuerySeqPosition = QuerySeqPosition;
+  }
+
+  public int getQuerySeqPosition()
+  {
+    return QuerySeqPosition;
+  }
+  public Hashtable getScores() {
+    return Scores;
+  }
+  public Hashtable getSymscores() {
+    return Symscores;
+  }
+
   public JPredFile(String inStr)
   {
     super(inStr);
@@ -30,7 +47,6 @@ public class JPredFile
     Scores = new Hashtable();
     ids = null;
     conf = null;
-    QuerySeqPosition = -1;
   }
 
   public JPredFile(String inFile, String type)
@@ -43,11 +59,10 @@ public class JPredFile
   /**
    * parse a JPred concise file into a sequence-alignment like object.
    */
-  int QuerySeqPosition;
   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;
@@ -121,7 +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++)
@@ -226,7 +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();
       }
     }