3253 reconciled with develop

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

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 3f0fea0..d9ed516 100755 (executable)
--- 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());