X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=d9ed5166d9f88d04d0818007dc6114cd8f297b7f;hb=92d66803db3319c4db605177d502de91302ef684;hp=3f0fea0034f6b38c241a38ac4e8519b295d4a4ce;hpb=208f2c3de82e3327c4f930ab7d04f5b812ccd277;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 3f0fea0..d9ed516 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -20,16 +20,18 @@
  */
 package jalview.io;
 
-import jalview.bin.Cache;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
 import java.io.IOException;
+import java.util.Vector;
 
 public class PIRFile extends AlignFile
 {
-  // Vector words = new Vector(); // Stores the words in a line after splitting
+  public static boolean useModellerOutput = false;
+
+  Vector words = new Vector(); // Stores the words in a line after splitting
 
   public PIRFile()
   {
@@ -109,7 +111,7 @@ public class PIRFile extends AlignFile
     StringBuffer out = new StringBuffer();
     int i = 0;
     ModellerDescription md;
-    boolean useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+
     while ((i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
@@ -145,6 +147,7 @@ public class PIRFile extends AlignFile
       }
       else
       {
+
         if (useModellerOutput)
         {
           out.append(">P1;" + s[i].getName());