ignore jnetconf

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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 9ecb54a..92d9819 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -44,7 +44,7 @@ public class JPredFile
   public void parse()
       throws IOException
   {
-
+System.out.println("all read in ");
     String line;
 
     noSeqs = 0;
@@ -56,7 +56,6 @@ public class JPredFile
       // Concise format allows no comments or non comma-formatted data
       StringTokenizer str = new StringTokenizer(line, ":");
       String id = "";
-      String seq = "";
       if (!str.hasMoreTokens())
       {
         continue;
@@ -96,6 +95,7 @@ public class JPredFile
             Float score = new Float(ascore);
             scores.addElement( (Object) score);
           }
+          Scores.put(id, scores);
         }
         catch (Exception e)
         {
@@ -115,9 +115,10 @@ public class JPredFile
           }
           Scores.put(id, scores);
         }
-      } else
-      if (id.equals("jnetconf"))
+      }
+      else if (id.equals("jnetconf"))
       {
+        System.out.println("here");
         id = "Prediction Confidence";
         this.conf = new Vector(numSymbols);
         for (int i = 0; i < numSymbols; i++)
@@ -128,13 +129,13 @@ public class JPredFile
       else
         {
           // Sequence or a prediction string (rendered as sequence)
-          
+
           StringBuffer newseq = new StringBuffer();
-          
+
           for (int i = 0; i < numSymbols; i++) {
             newseq.append(symbols.nextToken());
           }
-          
+
           if (id.indexOf(";") > -1) {
             seq_entries.addElement(newseq);
             int i=1;